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  1. Parsing ERK Activation Reveals Quantitatively Equivalent Contributions From Epidermal Growth Factor Receptor and HER2 In Human Mammary Epithelial Cells

    Energy Technology Data Exchange (ETDEWEB)

    Hendriks, Bart S.; Orr, Galya; Wells, Alan H.; Wiley, H. S.; Lauffenburger, Douglas A.

    2005-02-18

    HER2, a member of the EGFR tyrosine kinase family, functions as an accessory EGFR signaling component and alters EGFR trafficking by heterodimerization. HER2 overexpression leads to aberrant cell behavior including enhanced proliferation and motility. Here we apply a combination of computational modeling and quantitative experimental studies of the dynamic interactions between EGFR and HER2, and their downstream activation of extracellular signal-related kinase (ERK) to understand this complex signaling system. Using cells expressing different levels of HER2 relative to the EGFR, we can separate relative contributions of EGFR and HER2 to signaling amplitude and duration. Based on our model calculations, we demonstrate that, in contrast with previous suggestions in the literature, the intrinsic capabilities of EGFR and HER2 to activated ERK are quantitatively equivalent . We find that HER2-mediated effects on EGFR dimerization and trafficking are sufficient to explain the detected HER2-mediated amplification of EGF-induced ERK signaling. Our model suggests that transient amplification of ERK activity by HER2 arises predominantly from the 2-to-1 stoichiometry of receptor kinase to bound ligand in EGFR/HER2 heterodimers compared to the 1-to-1 stoichiometry of the EGFR homodimer, but alterations in receptor trafficking, with resultant EGFR sparing, cause the sustained HER2-mediated enhancement of ERK signaling.

  2. A semi-quantitative equivalence for abstracting from fast reactions

    CERN Document Server

    Galpin, Vashti; Ciocchetta, Federica; 10.4204/EPTCS.67.5

    2011-01-01

    Semantic equivalences are used in process algebra to capture the notion of similar behaviour, and this paper proposes a semi-quantitative equivalence for a stochastic process algebra developed for biological modelling. We consider abstracting away from fast reactions as suggested by the Quasi-Steady-State Assumption. We define a fast-slow bisimilarity based on this idea. We also show congruence under an appropriate condition for the cooperation operator of Bio-PEPA. The condition requires that there is no synchronisation over fast actions, and this distinguishes fast-slow bisimilarity from weak bisimilarity. We also show congruence for an operator which extends the reactions available for a species. We characterise models for which it is only necessary to consider the matching of slow transitions and we illustrate the equivalence on two models of competitive inhibition.

  3. Quantitative proteomics reveals cellular targets of celastrol.

    Directory of Open Access Journals (Sweden)

    Jakob Hansen

    Full Text Available Celastrol, a natural substance isolated from plant extracts used in traditional Chinese medicine, has been extensively investigated as a possible drug for treatment of cancer, autoimmune diseases, and protein misfolding disorders. Although studies focusing on celastrol's effects in specific cellular pathways have revealed a considerable number of targets in a diverse array of in vitro models there is an essential need for investigations that can provide a global view of its effects. To assess cellular effects of celastrol and to identify target proteins as biomarkers for monitoring treatment regimes, we performed large-scale quantitative proteomics in cultured human lymphoblastoid cells, a cell type that can be readily prepared from human blood samples. Celastrol substantially modified the proteome composition and 158 of the close to 1800 proteins with robust quantitation showed at least a 1.5 fold change in protein levels. Up-regulated proteins play key roles in cytoprotection with a prominent group involved in quality control and processing of proteins traversing the endoplasmic reticulum. Increased levels of proteins essential for the cellular protection against oxidative stress including heme oxygenase 1, several peroxiredoxins and thioredoxins as well as proteins involved in the control of iron homeostasis were also observed. Specific analysis of the mitochondrial proteome strongly indicated that the mitochondrial association of certain antioxidant defense and apoptosis-regulating proteins increased in cells exposed to celastrol. Analysis of selected mRNA transcripts showed that celastrol activated several different stress response pathways and dose response studies furthermore showed that continuous exposure to sub-micromolar concentrations of celastrol is associated with reduced cellular viability and proliferation. The extensive catalog of regulated proteins presented here identifies numerous cellular effects of celastrol and constitutes

  4. An equivalent magnetic dipoles model for quantitative damage recognition of broken wire

    Institute of Scientific and Technical Information of China (English)

    TAN Ji-wen; ZHAN Wei-xia; LI Chun-jing; WEN Yan; SHU Jie

    2005-01-01

    By simplifying saturatedly magnetized wire-rope to magnetic dipoles of the same magnetic field strength, an equivalent magnetic dipoles model is developed and the measuring principle for recognising damage of broken wire was presented. The relevant calculation formulas were also deduced. A composite solution method about nonlinear optimization was given. An example was given to illustrate the use of the equivalent magnetic dipoles method for quantitative damage recognition, and demonstrates that the result of this method is consistent with the real situation, so the method is valid and practical.

  5. The application of drug dose equivalence in the quantitative analysis of receptor occupation and drug combinations

    OpenAIRE

    Tallarida, Ronald J.; Raffa, Robert B.

    2010-01-01

    In this review we show that the concept of dose equivalence for two drugs, the theoretical basis of the isobologram, has a wider use in the analysis of pharmacological data derived from single and combination drug use. In both its application to drug combination analysis with isoboles and certain other actions, listed below, the determination of doses, or receptor occupancies, that yield equal effects provide useful metrics that can be used to obtain quantitative information on drug actions w...

  6. Research on Quantitative Models of Electric Vehicle Charging Stations Based on Principle of Energy Equivalence

    Directory of Open Access Journals (Sweden)

    Zhenpo Wang

    2013-01-01

    Full Text Available In order to adapt the matching and planning requirements of charging station in the electric vehicle (EV marketization application, with related layout theories of the gas stations, a location model of charging stations is established based on electricity consumption along the roads among cities. And a quantitative model of charging stations is presented based on the conversion of oil sales in a certain area. Both are combining the principle based on energy consuming equivalence substitution in process of replacing traditional vehicles with EVs. Defined data are adopted in the example analysis of two numerical case models and analyze the influence on charging station layout and quantity from the factors like the proportion of vehicle types and the EV energy consumption at the same time. The results show that the quantitative model of charging stations is reasonable and feasible. The number of EVs and the energy consumption of EVs bring more significant impact on the number of charging stations than that of vehicle type proportion, which provides a basis for decision making for charging stations construction layout in reality.

  7. The application of drug dose equivalence in the quantitative analysis of receptor occupation and drug combinations.

    Science.gov (United States)

    Tallarida, Ronald J; Raffa, Robert B

    2010-08-01

    In this review we show that the concept of dose equivalence for two drugs, the theoretical basis of the isobologram, has a wider use in the analysis of pharmacological data derived from single and combination drug use. In both its application to drug combination analysis with isoboles and certain other actions, listed below, the determination of doses, or receptor occupancies, that yield equal effects provide useful metrics that can be used to obtain quantitative information on drug actions without postulating any intimate mechanism of action. These other drug actions discussed here include (1) combinations of agonists that produce opposite effects, (2) analysis of inverted U-shaped dose-effect curves of single agents, (3) analysis on the effect scale as an alternative to isoboles and (4) the use of occupation isoboles to examine competitive antagonism in the dual receptor case. New formulas derived to assess the statistical variance for additive combinations are included, and the more detailed mathematical topics are included in the Appendix.

  8. China's new problems of food security revealed by the Food Equivalent Unit

    Directory of Open Access Journals (Sweden)

    Huilong LIN,Ruichao LI,Cangyu JIN,Chong WANG,Maohong WEI,Jizhou REN

    2014-02-01

    Full Text Available China's food security has a great influence on the world, and has always been the top priority in China. In recent years, as the concept of food security is evolving into one of nutrition security and the importance of food diversity is increasing, research based on nutrition security and broad food systems are increasingly needed in today's China. Thus, not only grain for human consumption, but also animal foods have been integrated into the Food Equivalent, which is used to analyze China's current agriculture system and reveal the water resource distribution. The results indicated that the average animal food consumption has risen by 78.6%, and now China's daily supply of animal food per capita has reached about 50% of that in the USA and 80% of that in the South Korea. So there exist an obvious disparity in animal food supply between China and these two countries. It is impossible for the China's current agricultural system to achieve the level in the USA. Under China's current agricultural system, the consumption proportion of feed grain had surpassed the consumption of food grain, increased sharply from 33% in 1992 to 67% in 2011. However, the growth potential of total grain output is approaching an upper limit, so the continued growth of feed grain demand exerts great pressure on the China's food supply. The discordance of the spatial distribution of water resource and virtual water revealed that China's current agriculture system had a low efficiency in being able to achieve food and nutrition security. China's current "grain farming" cannot meet the demand of increasing nutrition and appropriate resource utilization. The implementation of grassland agriculture appears feasible and necessary for saving feed grain, providing a large number of high-quality animal foods and appropriate water resource utilization.

  9. Statistical equivalent of the classical TDT for quantitative traits and multivariate phenotypes

    Indian Academy of Sciences (India)

    Tanushree Haldar; Saurabh Ghosh

    2015-12-01

    Clinical end-point traits are usually governed by quantitative precursors. Hence, there is active research interest in developing statistical methods for association mapping of quantitative traits. Unlike population-based tests for association, family-based tests for transmission disequilibrium are protected against population stratification. In this study, we propose a logistic regression model to test the association for quantitative traits based on a trio design. We show that the method can be viewed as a direct extension of the classical transmission diequilibrium test for binary traits to quantitative traits. We evaluate the performance of our method using extensive simulations and compare it with an existing method, family-based association test. We found that the two methods yield comparable powers if all families are considered. However, unlike FBAT, which yields an inflated rate of false positives when noninformative trios with all three individuals’ heterozygous are removed, our method maintains the correct size without compromising too much on power. We show that our method can be easily modified to incorporate multivariate phenotypes. Here, we applied this method to analyse a quantitative endophenotype associated with alcoholism.

  10. Long-lived states of magnetically equivalent spins populated by dissolution-DNP and revealed by enzymatic reactions.

    Science.gov (United States)

    Bornet, Aurélien; Ji, Xiao; Mammoli, Daniele; Vuichoud, Basile; Milani, Jonas; Bodenhausen, Geoffrey; Jannin, Sami

    2014-12-15

    Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) offers a way of enhancing NMR signals by up to five orders of magnitude in metabolites and other small molecules. Nevertheless, the lifetime of hyperpolarization is inexorably limited, as it decays toward thermal equilibrium with the nuclear spin-lattice relaxation time. This lifetime can be extended by storing the hyperpolarization in the form of long-lived states (LLS) that are immune to most dominant relaxation mechanisms. Levitt and co-workers have shown how LLS can be prepared for a pair of inequivalent spins by D-DNP. Here, we demonstrate that this approach can also be applied to magnetically equivalent pairs of spins such as the two protons of fumarate, which can have very long LLS lifetimes. As in the case of para-hydrogen, these hyperpolarized equivalent LLS (HELLS) are not magnetically active. However, a chemical reaction such as the enzymatic conversion of fumarate into malate can break the magnetic equivalence and reveal intense NMR signals.

  11. Long-Lived States of Magnetically Equivalent Spins Populated by Dissolution-DNP and Revealed by Enzymatic Reactions**

    Science.gov (United States)

    Bornet, Aurélien; Ji, Xiao; Mammoli, Daniele; Vuichoud, Basile; Milani, Jonas; Bodenhausen, Geoffrey; Jannin, Sami

    2014-01-01

    Hyperpolarization by dissolution dynamic nuclear polarization (d-DNP) offers a way of enhancing NMR signals by up to five orders of magnitude in metabolites and other small molecules. Nevertheless, the lifetime of hyperpolarization is inexorably limited, as it decays toward thermal equilibrium with the nuclear spin-lattice relaxation time. This lifetime can be extended by storing the hyperpolarization in the form of long-lived states (LLS) that are immune to most dominant relaxation mechanisms. Levitt and co-workers have shown how LLS can be prepared for a pair of inequivalent spins by d-DNP. Here, we demonstrate that this approach can also be applied to magnetically equivalent pairs of spins such as the two protons of fumarate, which can have very long LLS lifetimes. As in the case of para-hydrogen, these hyperpolarized equivalent LLS (HELLS) are not magnetically active. However, a chemical reaction such as the enzymatic conversion of fumarate into malate can break the magnetic equivalence and reveal intense NMR signals. PMID:25346515

  12. Quantitative Genetic Interactions Reveal Layers of Biological Modularity

    Science.gov (United States)

    Beltrao, Pedro; Cagney, Gerard; Krogan, Nevan J.

    2010-01-01

    In the past, biomedical research has embraced a reductionist approach, primarily focused on characterizing the individual components that comprise a system of interest. Recent technical developments have significantly increased the size and scope of data describing biological systems. At the same time, advances in the field of systems biology have evoked a broader view of how the underlying components are interconnected. In this essay, we discuss how quantitative genetic interaction mapping has enhanced our view of biological systems, allowing a deeper functional interrogation at different biological scales. PMID:20510918

  13. Quantitative Proteomics of Intracellular Campylobacter jejuni Reveals Metabolic Reprogramming.

    Directory of Open Access Journals (Sweden)

    Xiaoyun Liu

    Full Text Available Campylobacter jejuni is the major cause of bacterial food-borne illness in the USA and Europe. An important virulence attribute of this bacterial pathogen is its ability to enter and survive within host cells. Here we show through a quantitative proteomic analysis that upon entry into host cells, C. jejuni undergoes a significant metabolic downshift. Furthermore, our results indicate that intracellular C. jejuni reprograms its respiration, favoring the respiration of fumarate. These results explain the poor ability of C. jejuni obtained from infected cells to grow under standard laboratory conditions and provide the bases for the development of novel anti microbial strategies that would target relevant metabolic pathways.

  14. Quantitative analyses of the plant cytoskeleton reveal underlying organizational principles

    CERN Document Server

    Breuer, David; Sampathkumar, Arun; Hollandt, Florian; Persson, Staffan; Nikoloski, Zoran

    2015-01-01

    The actin and microtubule cytoskeletons are vital structures for cell growth and development across all species. While individual molecular mechanisms underpinning actin and microtubule dynamics have been intensively studied, principles that govern the cytoskeleton organization remain largely unexplored. Here, we captured biologically relevant characteristics of the plant cytoskeleton through a network-driven imaging-based approach allowing to quantitatively assess dynamic features of the cytoskeleton. By introducing suitable null models, we demonstrate that the plant cytoskeletal networks exhibit properties required for efficient transport, namely, short average path lengths and high robustness. We further show that these advantageous features are maintained during temporal cytoskeletal re-arrangements. Interestingly, man-made transportation networks exhibit similar properties, suggesting general laws of network organization supporting diverse transport processes. The proposed network-driven analysis can be ...

  15. Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis.

    Science.gov (United States)

    Wen, Chengping; Zheng, Zhijun; Shao, Tiejuan; Liu, Lin; Xie, Zhijun; Le Chatelier, Emmanuelle; He, Zhixing; Zhong, Wendi; Fan, Yongsheng; Zhang, Linshuang; Li, Haichang; Wu, Chunyan; Hu, Changfeng; Xu, Qian; Zhou, Jia; Cai, Shunfeng; Wang, Dawei; Huang, Yun; Breban, Maxime; Qin, Nan; Ehrlich, Stanislav Dusko

    2017-07-27

    The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers. Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.

  16. Quantitative flux analysis reveals folate-dependent NADPH production

    Science.gov (United States)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  17. Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia

    KAUST Repository

    Mojib, Nazia

    2014-06-01

    The tropical oligotrophic oceanic areas are characterized by high water transparency and annual solar radiation. Under these conditions, a large number of phylogenetically diverse mesozooplankton species living in the surface waters (neuston) are found to be blue pigmented. In the present study, we focused on understanding the metabolic and genetic basis of the observed blue phenotype functional equivalence between the blue-pigmented organisms from the phylum Arthropoda, subclass Copepoda (Acartia fossae) and the phylum Chordata, class Appendicularia (Oikopleura dioica) in the Red Sea. Previous studies have shown that carotenoid–protein complexes are responsible for blue coloration in crustaceans. Therefore, we performed carotenoid metabolic profiling using both targeted and nontargeted (high-resolution mass spectrometry) approaches in four different blue-pigmented genera of copepods and one blue-pigmented species of appendicularia. Astaxanthin was found to be the principal carotenoid in all the species. The pathway analysis showed that all the species can synthesize astaxanthin from β-carotene, ingested from dietary sources, via 3-hydroxyechinenone, canthaxanthin, zeaxanthin, adonirubin or adonixanthin. Further, using de novo assembled transcriptome of blue A. fossae (subclass Copepoda), we identified highly expressed homologous β-carotene hydroxylase enzymes and putative carotenoid-binding proteins responsible for astaxanthin formation and the blue phenotype. In blue O. dioica (class Appendicularia), corresponding putative genes were identified from the reference genome. Collectively, our data provide molecular evidences for the bioconversion and accumulation of blue astaxanthin–protein complexes underpinning the observed ecological functional equivalence and adaptive convergence among neustonic mesozooplankton.

  18. Comparative study of matrix-assisted laser desorption/ionization and gas chromatography for quantitative determination of cocoa butter and cocoa butter equivalent triacylglycerol composition.

    Science.gov (United States)

    Guyon, F; Absalon, Ch; Eloy, A; Salagoity, M H; Esclapez, M; Medina, B

    2003-01-01

    The triacylglycerol (TAG) composition study of cocoa butter (CB) and cocoa butter equivalents (CBEs) has been performed by gas chromatography (GC) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). These two techniques provided comparable results. The advantage of the MALDI technique was the detection of each compound comprising the triacylglycerol classes (Cn). Moreover, comparison of the data obtained by these two techniques indicated that TAG relative percentages could be obtained quantitatively with the MALDI technique. These techniques have been applied for the composition determination of CB + CBE mixtures. Encouraging results showed that it is possible to quantify an admixture containing as little as 4% of CBE.

  19. Quantitative mass spectrometry measurements reveal stoichiometry of principal postsynaptic density proteins.

    Science.gov (United States)

    Lowenthal, Mark S; Markey, Sanford P; Dosemeci, Ayse

    2015-06-05

    Quantitative studies are presented of postsynaptic density (PSD) fractions from rat cerebral cortex with the ultimate goal of defining the average copy numbers of proteins in the PSD complex. Highly specific and selective isotope dilution mass spectrometry assays were developed using isotopically labeled polypeptide concatemer internal standards. Interpretation of PSD protein stoichiometry was achieved as a molar ratio with respect to PSD-95 (SAP-90, DLG4), and subsequently, copy numbers were estimated using a consensus literature value for PSD-95. Average copy numbers for several proteins at the PSD were estimated for the first time, including those for AIDA-1, BRAGs, and densin. Major findings include evidence for the high copy number of AIDA-1 in the PSD (144 ± 30)-equivalent to that of the total GKAP family of proteins (150 ± 27)-suggesting that AIDA-1 is an element of the PSD scaffold. The average copy numbers for NMDA receptor sub-units were estimated to be 66 ± 18, 27 ± 9, and 45 ± 15, respectively, for GluN1, GluN2A, and GluN2B, yielding a total of 34 ± 10 NMDA channels. Estimated average copy numbers for AMPA channels and their auxiliary sub-units TARPs were 68 ± 36 and 144 ± 38, respectively, with a stoichiometry of ∼1:2, supporting the assertion that most AMPA receptors anchor to the PSD via TARP sub-units. This robust, quantitative analysis of PSD proteins improves upon and extends the list of major PSD components with assigned average copy numbers in the ongoing effort to unravel the complex molecular architecture of the PSD.

  20. Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations.

    Science.gov (United States)

    Fu, Glenn K; Xu, Weihong; Wilhelmy, Julie; Mindrinos, Michael N; Davis, Ronald W; Xiao, Wenzhong; Fodor, Stephen P A

    2014-02-01

    We present a simple molecular indexing method for quantitative targeted RNA sequencing, in which mRNAs of interest are selectively captured from complex cDNA libraries and sequenced to determine their absolute concentrations. cDNA fragments are individually labeled so that each molecule can be tracked from the original sample through the library preparation and sequencing process. Multiple copies of cDNA fragments of identical sequence become distinct through labeling, and replicate clones created during PCR amplification steps can be identified and assigned to their distinct parent molecules. Selective capture enables efficient use of sequencing for deep sampling and for the absolute quantitation of rare or transient transcripts that would otherwise escape detection by standard sequencing methods. We have also constructed a set of synthetic barcoded RNA molecules, which can be introduced as controls into the sample preparation mix and used to monitor the efficiency of library construction. The quantitative targeted sequencing revealed extremely low efficiency in standard library preparations, which were further confirmed by using synthetic barcoded RNA molecules. This finding shows that standard library preparation methods result in the loss of rare transcripts and highlights the need for monitoring library efficiency and for developing more efficient sample preparation methods.

  1. Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

    Science.gov (United States)

    Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

    2014-03-01

    Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein

  2. Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

    Directory of Open Access Journals (Sweden)

    Lit-Hsin Loo

    2014-03-01

    Full Text Available Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST, an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to

  3. Quantitative immunohistochemical analysis reveals association between sodium iodide symporter and estrogen receptor expression in breast cancer.

    Directory of Open Access Journals (Sweden)

    Sushmita Chatterjee

    Full Text Available BACKGROUND: Human sodium iodide symporter (hNIS gene over-expression is under active consideration worldwide as an alternative target molecule for breast cancer (BC diagnosis and targeted radio-iodine treatment. However, the field demands better stratified analysis of endogenous hNIS expression across major BC subtypes. Therefore, we have analyzed subtype-specific variation of hNIS overexpression in breast tumor tissue samples by immunohistochemistry (IHC and also report the development of a homogeneous, quantitative analysis method of digital IHC images. METHODS: hNIS expression was analyzed from 108 BC tissue samples by IHC. Sub-cellular localization of hNIS protein was analyzed by dual immunofluorescence (IF staining method using hNIS and HER2 antibodies. An ImageJ based two-step digital analysis method was developed and applied for the bias-free analysis of the images. RESULTS: Staining of the tumor samples show 70% cases are hNIS positive indicating high incidence of hNIS positive cases in BC. More importantly, a subtype specific analysis done for the first time shows that hNIS expression is overly dominated in estrogen receptor (ER positive cases than the receptor negative cases. Further, 56% of the ER+ve, PgR+ve, HER2-ve and 36% of ER+ve, PgR+ve, HER2+ve cases show highest intensity staining equivalent to the thyroid tissue. A significant positive correlation is also observed between hNIS and estrogen receptor expression (p = 0.0033, CI = 95% suggesting hNIS mediated targeted radio-iodine therapy procedures may benefit both ER+ve, PgR+ve, HER2-ve as well as HER2+ve cases. Further, in a few cases, hNIS and HER2 protein localization is demonstrated by overlapping membrane co-expression. ImageJ based image analysis method shows over 70% match with manual pathological scoring method. CONCLUSION: The study indicates a positive link between hNIS and ER expression in BC. The quantitative IHC image analysis method reported here will

  4. Quantitative proteomics reveal proteins enriched in tubular endoplasmic reticulum of Saccharomyces cerevisiae

    Science.gov (United States)

    Wang, Xinbo; Li, Shanshan; Wang, Haicheng; Shui, Wenqing; Hu, Junjie

    2017-01-01

    The tubular network is a critical part of the endoplasmic reticulum (ER). The network is shaped by the reticulons and REEPs/Yop1p that generate tubules by inducing high membrane curvature, and the dynamin-like GTPases atlastin and Sey1p/RHD3 that connect tubules via membrane fusion. However, the specific functions of this ER domain are not clear. Here, we isolated tubule-based microsomes from Saccharomyces cerevisiae via classical cell fractionation and detergent-free immunoprecipitation of Flag-tagged Yop1p, which specifically localizes to ER tubules. In quantitative comparisons of tubule-derived and total microsomes, we identified a total of 79 proteins that were enriched in the ER tubules, including known proteins that organize the tubular ER network. Functional categorization of the list of proteins revealed that the tubular ER network may be involved in membrane trafficking, lipid metabolism, organelle contact, and stress sensing. We propose that affinity isolation coupled with quantitative proteomics is a useful tool for investigating ER functions. DOI: http://dx.doi.org/10.7554/eLife.23816.001 PMID:28287394

  5. Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response

    Science.gov (United States)

    Gao, Xing-Huang; Krokowski, Dawid; Guan, Bo-Jhih; Bederman, Ilya; Majumder, Mithu; Parisien, Marc; Diatchenko, Luda; Kabil, Omer; Willard, Belinda; Banerjee, Ruma; Wang, Benlian; Bebek, Gurkan; Evans, Charles R.; Fox, Paul L.; Gerson, Stanton L.; Hoppel, Charles L.; Liu, Ming; Arvan, Peter; Hatzoglou, Maria

    2015-01-01

    The sulfhydration of cysteine residues in proteins is an important mechanism involved in diverse biological processes. We have developed a proteomics approach to quantitatively profile the changes of sulfhydrated cysteines in biological systems. Bioinformatics analysis revealed that sulfhydrated cysteines are part of a wide range of biological functions. In pancreatic β cells exposed to endoplasmic reticulum (ER) stress, elevated H2S promotes the sulfhydration of enzymes in energy metabolism and stimulates glycolytic flux. We propose that transcriptional and translational reprogramming by the integrated stress response (ISR) in pancreatic β cells is coupled to metabolic alternations triggered by sulfhydration of key enzymes in intermediary metabolism. DOI: http://dx.doi.org/10.7554/eLife.10067.001 PMID:26595448

  6. A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis.

    Science.gov (United States)

    Grimsrud, Paul A; Carson, Joshua J; Hebert, Alex S; Hubler, Shane L; Niemi, Natalie M; Bailey, Derek J; Jochem, Adam; Stapleton, Donald S; Keller, Mark P; Westphall, Michael S; Yandell, Brian S; Attie, Alan D; Coon, Joshua J; Pagliarini, David J

    2012-11-07

    Mitochondria are dynamic organelles that play a central role in a diverse array of metabolic processes. Elucidating mitochondrial adaptations to changing metabolic demands and the pathogenic alterations that underlie metabolic disorders represent principal challenges in cell biology. Here, we performed multiplexed quantitative mass spectrometry-based proteomics to chart the remodeling of the mouse liver mitochondrial proteome and phosphoproteome during both acute and chronic physiological transformations in more than 50 mice. Our analyses reveal that reversible phosphorylation is widespread in mitochondria, and is a key mechanism for regulating ketogenesis during the onset of obesity and type 2 diabetes. Specifically, we have demonstrated that phosphorylation of a conserved serine on Hmgcs2 (S456) significantly enhances its catalytic activity in response to increased ketogenic demand. Collectively, our work describes the plasticity of this organelle at high resolution and provides a framework for investigating the roles of proteome restructuring and reversible phosphorylation in mitochondrial adaptation.

  7. Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome

    DEFF Research Database (Denmark)

    Grassl, Niklas; Kulak, Nils Alexander; Pichler, Garwin

    2016-01-01

    , disruptions in saliva secretion and changes in the oral microbiome contribute to conditions such as tooth decay and respiratory tract infections. Here we set out to quantitatively map the saliva proteome in great depth with a rapid and in-depth mass spectrometry-based proteomics workflow. METHODS: We used...... with next-generation sequencing data from the Human Microbiome Project as well as a comparison to MALDI-TOF mass spectrometry on microbial cultures revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing. CONCLUSION: Rapid shotgun...... and robust technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid and is therefore a valuable complement to genomic studies. This opens new frontiers for the study of host-pathogen interactions and clinical saliva diagnostics....

  8. Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici.

    Science.gov (United States)

    Stewart, Ethan L; Croll, Daniel; Lendenmann, Mark H; Sanchez-Vallet, Andrea; Hartmann, Fanny E; Palma-Guerrero, Javier; Ma, Xin; McDonald, Bruce A

    2016-11-21

    We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.

  9. Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol.

    Science.gov (United States)

    Tian, Xiaoxu; Chen, Lei; Wang, Jiangxin; Qiao, Jianjun; Zhang, Weiwen

    2013-01-14

    Butanol is a promising biofuel, and recent metabolic engineering efforts have demonstrated the use of photosynthetic cyanobacterial hosts for its production. However, cyanobacteria have very low tolerance to butanol, limiting the economic viability of butanol production from these renewable producing systems. The existing knowledge of molecular mechanism involved in butanol tolerance in cyanobacteria is very limited. To build a foundation necessary to engineer robust butanol-producing cyanobacterial hosts, in this study, the responses of Synechocystis PCC 6803 to butanol were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. The resulting high-quality dataset consisted of 25,347 peptides corresponding to 1452 unique proteins, a coverage of approximately 40% of the predicted proteins in Synechocystis. Comparative quantification of protein abundances led to the identification of 303 differentially regulated proteins by butanol. Annotation and GO term enrichment analysis showed that multiple biological processes were regulated, suggesting that Synechocystis probably employed multiple and synergistic resistance mechanisms in dealing with butanol stress. Notably, the analysis revealed the induction of heat-shock protein and transporters, along with modification of cell membrane and envelope were the major protection mechanisms against butanol. A conceptual cellular model of Synechocystis PCC 6803 responses to butanol stress was constructed to illustrate the putative molecular mechanisms employed to defend against butanol stress. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Rotating Snakes Illusion—Quantitative Analysis Reveals a Region in Luminance Space With Opposite Illusory Rotation

    Science.gov (United States)

    Atala-Gérard, Lea

    2017-01-01

    The Rotating Snakes Illusion employs patterns with repetitive asymmetric luminance steps forming a “snake wheel.” In the underlying luminance sequence {black, dark grey, white, light grey}, coded as {0, g1, 100, g2}, we varied g1 and g2 and measured illusion strength via nulling: Saccades were performed next to a “snake wheel” that rotated physically; observers adjusted rotation until a stationary percept obtained. Observers performed the perceptual nulling of the seeming rotation reliably. Typical settings for (g1, g2), measured from images by Kitaoka, are around (20%, 60%). Indeed, we found a marked illusion in the region (g1≈{0%–25%}, g2≈{20%–75%}) with a rotation speed of ≈1°/s. Surprisingly, we detected a second “island” around (70%, 95%) with opposite direction of the illusory rotation and weaker illusion. Our quantitative measurements of illusion strength confirmed the optimal luminance choices of the standard snake wheel and, unexpectedly, revealed an opposite rotation illusion. PMID:28228928

  11. Rotating Snakes Illusion-Quantitative Analysis Reveals a Region in Luminance Space With Opposite Illusory Rotation.

    Science.gov (United States)

    Atala-Gérard, Lea; Bach, Michael

    2017-01-01

    The Rotating Snakes Illusion employs patterns with repetitive asymmetric luminance steps forming a "snake wheel." In the underlying luminance sequence {black, dark grey, white, light grey}, coded as {0, g1, 100, g2}, we varied g1 and g2 and measured illusion strength via nulling: Saccades were performed next to a "snake wheel" that rotated physically; observers adjusted rotation until a stationary percept obtained. Observers performed the perceptual nulling of the seeming rotation reliably. Typical settings for (g1, g2), measured from images by Kitaoka, are around (20%, 60%). Indeed, we found a marked illusion in the region (g1≈{0%-25%}, g2≈{20%-75%}) with a rotation speed of ≈1°/s. Surprisingly, we detected a second "island" around (70%, 95%) with opposite direction of the illusory rotation and weaker illusion. Our quantitative measurements of illusion strength confirmed the optimal luminance choices of the standard snake wheel and, unexpectedly, revealed an opposite rotation illusion.

  12. Quantitative proteomics analysis reveals the tolerance of Mirabilis jalapa L. to petroleum contamination.

    Science.gov (United States)

    Chen, Shuisen; Ma, Hui; Guo, Zhifu; Feng, Yaping; Lin, Jingwei; Zhang, Menghua; Zhong, Ming

    2017-03-01

    Petroleum is not only an important energy resource but is also a major soil pollutant. To gain better insight into the adaptability mechanism of Mirabilis jalapa to petroleum-contaminated soil, the protein profiles of M. jalapa root were investigated using label-free quantitative proteomics technique. After exposing to petroleum-contaminated soil for 24 h, 34 proteins significantly changed their protein abundance and most of the proteins increased in protein abundance (91.18%). Combined with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as data from previous studies, our results revealed that M. jalapa enhanced tolerance to petroleum by changing antioxidation and detoxification, cell wall organization, amino acid and carbohydrate metabolism, transportation and protein process, and so on. These metabolism alterations could result in the production and secretion of low molecular carbohydrate, amino acid, and functional protein, which enhanced the bioavailability of petroleum and reducing the toxicity of the petroleum. Taken together, these results provided novel information for better understanding of the tolerance of M. jalapa to petroleum stress.

  13. Dynamics of Natural Killer Cell Receptor Revealed by Quantitative Analysis of Photoswitchable Protein

    Science.gov (United States)

    Pageon, Sophie V.; Aquino, Gerardo; Lagrue, Kathryn; Köhler, Karsten; Endres, Robert G.; Davis, Daniel M.

    2013-11-01

    Natural Killer (NK) cell activation is dynamically regulated by numerous activating and inhibitory surface receptors that accumulate at the immune synapse. Quantitative analysis of receptor dynamics has been limited by methodologies which rely on indirect measurements such as fluorescence recovery after photobleaching. Here, we report a novel approach to study how proteins traffic to and from the immune synapse using NK cell receptors tagged with the photoswitchable fluorescent protein tdEosFP, which can be irreversibly photoswitched from a green to red fluorescent state by ultraviolet light. Thus, following a localized switching event, the movement of the photoswitched molecules can be temporally and spatially resolved by monitoring fluorescence in two regions of interest. By comparing images with mathematical models, we evaluated the diffusion coefficient of the receptor KIR2DL1 (0.23 +- 0.06 micron^2/s) and assessed how synapse formation affects receptor dynamics. Our data conclude that the inhibitory NK cell receptor KIR2DL1 is continually trafficked into the synapse and remains surprisingly stable there. Unexpectedly however, in NK cells forming synapses with multiple target cells simultaneously, KIR2DL1 at one synapse can relocate to another synapse. Thus, our results reveal a previously undetected inter-synaptic exchange of protein.

  14. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape.

    Science.gov (United States)

    Baker, Robert L; Leong, Wen Fung; Brock, Marcus T; Markelz, R J Cody; Covington, Michael F; Devisetty, Upendra K; Edwards, Christine E; Maloof, Julin; Welch, Stephen; Weinig, Cynthia

    2015-10-01

    Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange.

  15. Quantitative proteomics reveals distinct differences in the protein content of outer membrane vesicle vaccines.

    Science.gov (United States)

    van de Waterbeemd, Bas; Mommen, Geert P M; Pennings, Jeroen L A; Eppink, Michel H; Wijffels, René H; van der Pol, Leo A; de Jong, Ad P J M

    2013-04-05

    At present, only vaccines containing outer membrane vesicles (OMV) have successfully stopped Neisseria meningitidis serogroup B epidemics. These vaccines however require detergent-extraction to remove endotoxin, which changes immunogenicity and causes production difficulties. To investigate this in more detail, the protein content of detergent-extracted OMV is compared with two detergent-free alternatives. A novel proteomics strategy has been developed that allows quantitative analysis of many biological replicates despite inherent multiplex restrictions of dimethyl labeling. This enables robust statistical analysis of relative protein abundance. The comparison with detergent-extracted OMV reveales that detergent-free OMV are enriched with membrane (lipo)proteins and contain less cytoplasmic proteins due to a milder purification process. These distinct protein profiles are substantiated with serum blot proteomics, confirming enrichment with immunogenic proteins in both detergent-free alternatives. Therefore, the immunogenic protein content of OMV vaccines depends at least partially on the purification process. This study demonstrates that detergent-free OMV have a preferred composition.

  16. Optomechanical properties of cancer cells revealed by light-induced deformation and quantitative phase microscopy

    Science.gov (United States)

    Kastl, Lena; Budde, Björn; Isbach, Michael; Rommel, Christina; Kemper, Björn; Schnekenburger, Jürgen

    2015-05-01

    There is a growing interest in cell biology and clinical diagnostics in label-free, optical techniques as the interaction with the sample is minimized and substances like dyes or fixatives do not affect the investigated cells. Such techniques include digital holographic microscopy (DHM) and the optical stretching by fiber optical two beam traps. DHM enables quantitative phase contrast imaging and thereby the determination of the cellular refractive index, dry mass and the volume, whereas optical cell stretching reveals the deformability of cells. Since optical stretching strongly depends on the optical properties and the shape of the investigated material we combined the usage of fiber optical stretching and DHM for the characterization of pancreatic tumor cells. The risk of tumors is their potential to metastasize, spread through the bloodstream and build distal tumors/metastases. The grade of dedifferentiation in which the cells lose their cell type specific properties is a measure for this metastatic potential. The less differentiated the cells are, the higher is their risk to metastasize. Our results demonstrate that pancreatic tumor cells, which are from the same tumor but vary in their grade of differentiation, show significant differences in their deformability. The retrieved data show that differentiated cells have a higher stiffness than less differentiated cells of the same tumor. Even cells that differ only in the expression of a single tumor suppressor gene which is responsible for cell-cell adhesions can be distinguished by their mechanical properties. Additionally, results from DHM measurements yield that the refractive index shows only few variations, indicating that it does not significantly influence optical cell stretching. The obtained results show a promising new approach for the phenotyping of different cell types, especially in tumor cell characterization and cancer diagnostics.

  17. Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis.

    Science.gov (United States)

    Chopra, Tarun; Hamelin, Romain; Armand, Florence; Chiappe, Diego; Moniatte, Marc; McKinney, John D

    2014-11-01

    Mycobacterium tuberculosis has a remarkable ability to persist within the human host as a clinically inapparent or chronically active infection. Fatty acids are thought to be an important carbon source used by the bacteria during long term infection. Catabolism of fatty acids requires reprogramming of metabolic networks, and enzymes central to this reprogramming have been targeted for drug discovery. Mycobacterium smegmatis, a nonpathogenic relative of M. tuberculosis, is often used as a model system because of the similarity of basic cellular processes in these two species. Here, we take a quantitative proteomics-based approach to achieve a global view of how the M. smegmatis metabolic network adjusts to utilization of fatty acids as a carbon source. Two-dimensional liquid chromatography and mass spectrometry of isotopically labeled proteins identified a total of 3,067 proteins with high confidence. This number corresponds to 44% of the predicted M. smegmatis proteome and includes most of the predicted metabolic enzymes. Compared with glucose-grown cells, 162 proteins showed differential abundance in acetate- or propionate-grown cells. Among these, acetate-grown cells showed a higher abundance of proteins that could constitute a functional glycerate pathway. Gene inactivation experiments confirmed that both the glyoxylate shunt and the glycerate pathway are operational in M. smegmatis. In addition to proteins with annotated functions, we demonstrate carbon source-dependent differential abundance of proteins that have not been functionally characterized. These proteins might play as-yet-unidentified roles in mycobacterial carbon metabolism. This study reveals several novel features of carbon assimilation in M. smegmatis, which suggests significant functional plasticity of metabolic networks in this organism.

  18. Quantitative X-ray Diffraction (QXRD) analysis for revealing thermal transformations of red mud.

    Science.gov (United States)

    Liao, Chang-Zhong; Zeng, Lingmin; Shih, Kaimin

    2015-07-01

    Red mud is a worldwide environmental problem, and many authorities are trying to find an economic solution for its beneficial application or/and safe disposal. Ceramic production is one of the potential waste-to-resource strategies for using red mud as a raw material. Before implementing such a strategy, an unambiguous understanding of the reaction behavior of red mud under thermal conditions is essential. In this study, the phase compositions and transformation processes were revealed for the Pingguo red mud (PRM) heat-treated at different sintering temperatures. Hematite, perovskite, andradite, cancrinite, kaolinite, diaspore, gibbsite and calcite phases were observed in the samples. However, unlike those red mud samples from the other regions, no TiO2 (rutile or anatase) or quartz were observed. Titanium was found to exist mainly in perovskite and andradite while the iron mainly existed in hematite and andradite. A new silico-ferrite of calcium and aluminum (SFCA) phase was found in samples treated at temperatures above 1100°C, and two possible formation pathways for SFCA were suggested. This is the first SFCA phase to be reported in thermally treated red mud, and this finding may turn PRM waste into a material resource for the iron-making industry. Titanium was found to be enriched in the perovskite phase after 1200°C thermal treatment, and this observation indicated a potential strategy for the recovery of titanium from PRM. In addition to noting these various resource recovery opportunities, this is also the first study to quantitatively summarize the reaction details of PRM phase transformations at various temperatures.

  19. Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Siwo Geoffrey

    2010-10-01

    Full Text Available Abstract Background Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth and development of Plasmodium falciparum through its erythrocytic cycle are not well understood. We previously showed that strains HB3 and Dd2 diverge in their proliferation rates, and here use quantitative trait loci mapping in 34 progeny from a cross between these parent clones along with integrative bioinformatics to identify genetic loci and candidate genes that control divergences in cell cycle duration. Results Genetic mapping of cell cycle duration revealed a four-locus genetic model, including a major genetic effect on chromosome 12, which accounts for 75% of the inherited phenotype variation. These QTL span 165 genes, the majority of which have no predicted function based on homology. We present a method to systematically prioritize candidate genes using the extensive sequence and transcriptional information available for the parent lines. Putative functions were assigned to the prioritized genes based on protein interaction networks and expression eQTL from our earlier study. DNA metabolism or antigenic variation functional categories were enriched among our prioritized candidate genes. Genes were then analyzed to determine if they interact with cyclins or other proteins known to be involved in the regulation of cell cycle. Conclusions We show that the divergent proliferation rate between a drug resistant and drug sensitive parent clone is under genetic regulation and is segregating as a complex trait in 34 progeny. We map a major locus along with additional secondary effects, and use the wealth of genome data to identify key candidate genes. Of particular interest are a nucleosome assembly protein (PFL0185c, a Zinc finger transcription factor (PFL0465c both on chromosome 12 and a ribosomal protein L7Ae-related on chromosome 4 (PFD0960c.

  20. What Is "Good" Research? Revealing the Paradigmatic Tensions in Quantitative Criticalist Work

    Science.gov (United States)

    Hernández, Ebelia

    2014-01-01

    If quantitative criticalism is thought to be a bridge between positivist epistemologies prevalent in quantitative work and social constructionism often found in critical qualitative work, then this bridge is fraught with challenges and tensions. This chapter examines the methodological issues, questions, and tensions that emerged from a research…

  1. What Is "Good" Research? Revealing the Paradigmatic Tensions in Quantitative Criticalist Work

    Science.gov (United States)

    Hernández, Ebelia

    2014-01-01

    If quantitative criticalism is thought to be a bridge between positivist epistemologies prevalent in quantitative work and social constructionism often found in critical qualitative work, then this bridge is fraught with challenges and tensions. This chapter examines the methodological issues, questions, and tensions that emerged from a research…

  2. Fiber architecture in remodeled myocardium revealed with a quantitative diffusion CMR tractography framework and histological validation

    National Research Council Canada - National Science Library

    Choukri Mekkaoui; Shuning Huang; Howard H Chen; Guangping Dai; Timothy G Reese; William J Kostis; Aravinda Thiagalingam; Pal Maurovich-Horvat; Jeremy N Ruskin; Udo Hoffmann; Marcel P Jackowski; David E Sosnovik

    2012-01-01

    .... The aim of this study was therefore to develop a technique for quantitative 3D diffusion CMR tractography of the heart, and to apply this method to quantify fiber architecture in the remote zone of remodeled hearts. Methods...

  3. Image processing techniques revealing the relationship between the field-measured ambient gamma dose equivalent rate and geological conditions at a granitic area, Velence Mountains, Hungary

    Science.gov (United States)

    Beltran Torres, Silvana; Petrik, Attila; Zsuzsanna Szabó, Katalin; Jordan, Gyozo; Szabó, Csaba

    2017-04-01

    In order to estimate the annual dose that the public receive from natural radioactivity, the identification of the potential risk areas is required which, in turn, necessitates understanding the relationship between the spatial distribution of natural radioactivity and the geogenic risk factors (e.g., rock types, dykes, faults, soil conditions, etc.). A detailed spatial analysis of ambient gamma dose equivalent rate was performed in the western side of Velence Mountains, the largest outcropped granitic area in Hungary. In order to assess the role of local geology in the spatial distribution of ambient gamma dose rates, field measurements were carried out at ground level at 300 sites along a 250 m x 250 m regular grid in a total surface of 14.7 km2. Digital image processing methods were applied to identify anomalies, heterogeneities and spatial patterns in the measured gamma dose rates, including local maxima and minima determination, digital cross sections, gradient magnitude and gradient direction, second derivative profile curvature, local variability, lineament density, 2D autocorrelation and directional variogram analyses. Statistical inference showed that different gamma dose rate levels are associated with the rock types (i.e., Carboniferous granite, Pleistocene colluvial, proluvial, deluvial sediments and talus, and Pannonian sand and pebble), with the highest level on the Carboniferous granite including outlying values. Moreover, digital image processing revealed that linear gamma dose rate spatial features are parallel to the SW-NE dyke system and possibly to the NW-SE main fractures. The results of this study underline the importance of understanding the role of geogenic risk factors influencing the ambient gamma dose rate received by public. The study also demonstrates the power of the image processing techniques for the identification of spatial pattern in field-measured geogenic radiation.

  4. Quantitative comparisons of genotoxic effects of atomic energy and fossil-fuelled energy. Rad-equivalences for ethylene, ethylene oxide and formaldehyde - consequences for decisions at Government level

    Energy Technology Data Exchange (ETDEWEB)

    Latarjet, R.; Averbeck, D.; Levy, S.; Poirier, V. (Section de Biologie, Institut Curie, Paris, France)

    1982-01-01

    Rad-equivalences have been determined on the basis of data on the genotoxic effects of low linear energy transfer ionizing radiation and of three chemical pollutants - ethylene, ethylene oxide and formaldehyde - emitted from energy-producing power plants. In the case of ethylene and its metabolite, ethylene oxide, the conditions were particularly favourable because the equivalences could be based on the induction of total mutations in the mouse, which is the same genetic end-point used for the assessment of radiation risks. Once established, the rad-equivalences were used (a) to extrapolate the rules adopted for radiation to each of these two compounds and (b) to make recommendations for exposed workers at 'hot spots' and for the general population. Measurements of ethylene in power plants and in the atmosphere of Paris have indicated that in most cases the measured values fall within the recommended values. However, pollution by ethylene oxide in cold sterilization units should be reduced. Rad-equivalences obtained for lethal effects, and for the induction of chromosome aberrations by formaldehyde in human cells in vitro, suggest that the maximum admissible concentrations are far too high in most countries and must be reconsidered. In France, the Ministry of Health is taking the rad-equivalences into consideration for the preparation of a law regulating pollution by ethylene and ethylene oxide - as a first step. These results show that rad-equivalences can be used for risk assessments of genotoxic effects from power plants and that decisions can be made by extrapolating the rules adopted for radiation protection to some chemical mutagens, when certain strict conditions are fulfilled.

  5. A Methodological Self-Study of Quantitizing: Negotiating Meaning and Revealing Multiplicity

    Science.gov (United States)

    Seltzer-Kelly, Deborah; Westwood, Sean J.; Pena-Guzman, David M.

    2012-01-01

    This inquiry developed during the process of "quantitizing" qualitative data the authors had gathered for a mixed methods curriculum efficacy study. Rather than providing the intended rigor to their data coding process, their use of an intercoder reliability metric prompted their investigation of the multiplicity and messiness that, as they…

  6. Quantitative PCR analysis of house dust can reveal abnormal mold conditions†

    OpenAIRE

    Meklin, Teija; Haugland, Richard A.; Reponen, Tiina; Varma, Manju; Lummus, Zana; Bernstein, David; Wymer, Larry J; Vesper, Stephen J.

    2004-01-01

    Indoor mold concentrations were measured in the dust of moldy homes (MH) and reference homes (RH) by quantitative PCR (QPCR) assays for 82 species or related groups of species (assay groups). About 70% of the species and groups were never or only rarely detected. The ratios (MH geometric mean : RH geometric mean) for 6 commonly detected species (Aspergillus ochraceus, A. penicillioides, A. unguis, A. versicolor, Eurotium group, and Cladosporium sphaerospermum) were > 1 (Group I). Logistic reg...

  7. Infrared spectroscopy reveals both qualitative and quantitative differences in equine subchondral bone during maturation

    Science.gov (United States)

    Kobrina, Yevgeniya; Isaksson, Hanna; Sinisaari, Miikka; Rieppo, Lassi; Brama, Pieter A.; van Weeren, René; Helminen, Heikki J.; Jurvelin, Jukka S.; Saarakkala, Simo

    2010-11-01

    The collagen phase in bone is known to undergo major changes during growth and maturation. The objective of this study is to clarify whether Fourier transform infrared (FTIR) microspectroscopy, coupled with cluster analysis, can detect quantitative and qualitative changes in the collagen matrix of subchondral bone in horses during maturation and growth. Equine subchondral bone samples (n = 29) from the proximal joint surface of the first phalanx are prepared from two sites subjected to different loading conditions. Three age groups are studied: newborn (0 days old), immature (5 to 11 months old), and adult (6 to 10 years old) horses. Spatial collagen content and collagen cross-link ratio are quantified from the spectra. Additionally, normalized second derivative spectra of samples are clustered using the k-means clustering algorithm. In quantitative analysis, collagen content in the subchondral bone increases rapidly between the newborn and immature horses. The collagen cross-link ratio increases significantly with age. In qualitative analysis, clustering is able to separate newborn and adult samples into two different groups. The immature samples display some nonhomogeneity. In conclusion, this is the first study showing that FTIR spectral imaging combined with clustering techniques can detect quantitative and qualitative changes in the collagen matrix of subchondral bone during growth and maturation.

  8. Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics.

    Science.gov (United States)

    Muller, Leslie; Fornecker, Luc; Van Dorsselaer, Alain; Cianférani, Sarah; Carapito, Christine

    2016-12-01

    Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD). A series of UPS1 standard mixtures (at 0.5, 1, 2.5, 5, 10, and 25 fmol) were spiked in a complex yeast lysate background. TG preparation allowed more yeast proteins to be identified than did the SG and LD approaches, with mean numbers of 1979, 1788, and 1323 proteins identified, respectively. Furthermore, the TG method proved equivalent to SG and superior to LD in terms of the repeatability of the subsequent experiments, with mean CV for yeast protein label-free quantifications of 7, 9, and 10%. Finally, known variant UPS1 proteins were successfully detected in the TG-prepared sample within a complex background with high sensitivity. All the data from this study are accessible on ProteomeXchange (PXD003841).

  9. Gyrokinetic equivalence

    Energy Technology Data Exchange (ETDEWEB)

    Parra, Felix I; Catto, Peter J [Plasma Science and Fusion Center, MIT, Cambridge, MA 02139 (United States)], E-mail: fparra@mit.edu, E-mail: catto@psfc.mit.edu

    2009-06-15

    We compare two different derivations of the gyrokinetic equation: the Hamiltonian approach in Dubin D H E et al (1983 Phys. Fluids 26 3524) and the recursive methodology in Parra F I and Catto P J (2008 Plasma Phys. Control. Fusion 50 065014). We prove that both approaches yield the same result at least to second order in a Larmor radius over macroscopic length expansion. There are subtle differences in the definitions of some of the functions that need to be taken into account to prove the equivalence.

  10. Gyrokinetic equivalence

    Science.gov (United States)

    Parra, Felix I.; Catto, Peter J.

    2009-06-01

    We compare two different derivations of the gyrokinetic equation: the Hamiltonian approach in Dubin D H E et al (1983 Phys. Fluids 26 3524) and the recursive methodology in Parra F I and Catto P J (2008 Plasma Phys. Control. Fusion 50 065014). We prove that both approaches yield the same result at least to second order in a Larmor radius over macroscopic length expansion. There are subtle differences in the definitions of some of the functions that need to be taken into account to prove the equivalence.

  11. Quantitative trait variation is revealed in a novel hypomethylated population of woodland strawberry (Fragaria vesca).

    Science.gov (United States)

    Xu, Jihua; Tanino, Karen K; Horner, Kyla N; Robinson, Stephen J

    2016-11-04

    Phenotypic variation is determined by a combination of genotype, environment and their interactions. The realization that allelic diversity can be both genetic and epigenetic allows the environmental component to be further separated. Partitioning phenotypic variation observed among inbred lines with an altered epigenome can allow the epigenetic component controlling quantitative traits to be estimated. To assess the contribution of epialleles on phenotypic variation and determine the fidelity with which epialleles are inherited, we have developed a novel hypomethylated population of strawberry (2n = 2x = 14) using 5-azacytidine from which individuals with altered phenotypes can be identified, selected and characterized. The hypomethylated population was generated using an inbred strawberry population in the F. vesca ssp. vesca accession Hawaii 4. Analysis of whole genome sequence data from control and hypomethylated lines indicate that 5-azacytidine exposure does not increase SNP above background levels. The populations contained only Hawaii 4 alleles, removing introgression of alternate F. vesca alleles as a potential source of variation. Although genome sequencing and genetic marker data are unable to rule out 5-azacytidine induced chromosomal rearrangements as a potential source of the trait variation observed, none were detected in our survey. Quantitative trait variation focusing on flowering time and rosette diameter was scored in control and treated populations where expanded levels of variation were observed among the hypomethylated lines. Methylation sensitive molecular markers indicated that 5-azacytidine induced alterations in DNA methylation patterns and inheritance of methylation patterns were confirmed by bisulfite sequencing of targeted regions. It is possible that methylation polymorphisms might underlie or have induced genetic changes underlying the observable differences in quantitative phenotypes. This population developed in a uniform

  12. Quantitative iTRAQ Proteomics Revealed Possible Roles for Antioxidant Proteins in Sorghum Aluminum Tolerance

    Science.gov (United States)

    Zhou, Dangwei; Yang, Yong; Zhang, Jinbiao; Jiang, Fei; Craft, Eric; Thannhauser, Theodore W.; Kochian, Leon V.; Liu, Jiping

    2017-01-01

    Aluminum (Al) toxicity inhibits root growth and limits crop yields on acid soils worldwide. However, quantitative information is scarce on protein expression profiles under Al stress in crops. In this study, we report on the identification of potential Al responsive proteins from root tips of Al sensitive BR007 and Al tolerant SC566 sorghum lines using a strategy employing iTRAQ and 2D-liquid chromatography (LC) coupled to MS/MS (2D-LC-MS/MS). A total of 771 and 329 unique proteins with abundance changes of >1.5 or sorghum. PMID:28119720

  13. Quantitative Proteomics of Sleep-Deprived Mouse Brains Reveals Global Changes in Mitochondrial Proteins

    Science.gov (United States)

    Li, Tie-Mei; Zhang, Ju-en; Lin, Rui; Chen, She; Luo, Minmin; Dong, Meng-Qiu

    2016-01-01

    Sleep is a ubiquitous, tightly regulated, and evolutionarily conserved behavior observed in almost all animals. Prolonged sleep deprivation can be fatal, indicating that sleep is a physiological necessity. However, little is known about its core function. To gain insight into this mystery, we used advanced quantitative proteomics technology to survey the global changes in brain protein abundance. Aiming to gain a comprehensive profile, our proteomics workflow included filter-aided sample preparation (FASP), which increased the coverage of membrane proteins; tandem mass tag (TMT) labeling, for relative quantitation; and high resolution, high mass accuracy, high throughput mass spectrometry (MS). In total, we obtained the relative abundance ratios of 9888 proteins encoded by 6070 genes. Interestingly, we observed significant enrichment for mitochondrial proteins among the differentially expressed proteins. This finding suggests that sleep deprivation strongly affects signaling pathways that govern either energy metabolism or responses to mitochondrial stress. Additionally, the differentially-expressed proteins are enriched in pathways implicated in age-dependent neurodegenerative diseases, including Parkinson’s, Huntington’s, and Alzheimer’s, hinting at possible connections between sleep loss, mitochondrial stress, and neurodegeneration. PMID:27684481

  14. Quantitative metabolomics reveals an epigenetic blueprint for iron acquisition in uropathogenic Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Jeffrey P Henderson

    2009-02-01

    Full Text Available Bacterial pathogens are frequently distinguished by the presence of acquired genes associated with iron acquisition. The presence of specific siderophore receptor genes, however, does not reliably predict activity of the complex protein assemblies involved in synthesis and transport of these secondary metabolites. Here, we have developed a novel quantitative metabolomic approach based on stable isotope dilution to compare the complement of siderophores produced by Escherichia coli strains associated with intestinal colonization or urinary tract disease. Because uropathogenic E. coli are believed to reside in the gut microbiome prior to infection, we compared siderophore production between urinary and rectal isolates within individual patients with recurrent UTI. While all strains produced enterobactin, strong preferential expression of the siderophores yersiniabactin and salmochelin was observed among urinary strains. Conventional PCR genotyping of siderophore receptors was often insensitive to these differences. A linearized enterobactin siderophore was also identified as a product of strains with an active salmochelin gene cluster. These findings argue that qualitative and quantitative epi-genetic optimization occurs in the E. coli secondary metabolome among human uropathogens. Because the virulence-associated biosynthetic pathways are distinct from those associated with rectal colonization, these results suggest strategies for virulence-targeted therapies.

  15. Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch

    Directory of Open Access Journals (Sweden)

    Cristian Araneda

    2012-01-01

    Full Text Available Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss, various quantitative trait loci (QTL that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch. The four loci were identified in females from two populations (early and late spawners produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC that were strongly associated with spawning time in coho salmon (p < 0.0002 were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10 with a suggestive association (p = 0.00035 mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map.

  16. Quantitative fluorescence imaging reveals point of release for lipoproteins during LDLR-dependent uptake[S

    Science.gov (United States)

    Pompey, Shanica; Zhao, Zhenze; Luby-Phelps, Kate; Michaely, Peter

    2013-01-01

    The LDL receptor (LDLR) supports efficient uptake of both LDL and VLDL remnants by binding lipoprotein at the cell surface, internalizing lipoprotein through coated pits, and releasing lipoprotein in endocytic compartments before returning to the surface for further rounds of uptake. While many aspects of lipoprotein binding and receptor entry are well understood, it is less clear where, when, and how the LDLR releases lipoprotein. To address these questions, the current study employed quantitative fluorescence imaging to visualize the uptake and endosomal processing of LDL and the VLDL remnant β-VLDL. We find that lipoprotein release is rapid, with most release occurring prior to entry of lipoprotein into early endosomes. Published biochemical studies have identified two mechanisms of lipoprotein release: one that involves the β-propeller module of the LDLR and a second that is independent of this module. Quantitative imaging comparing uptake supported by the normal LDLR or by an LDLR variant incapable of β-propeller-dependent release shows that the β-propeller-independent process is sufficient for release for both lipoproteins but that the β-propeller process accelerates both LDL and β-VLDL release. Together these findings define where, when, and how lipoprotein release occurs and provide a generalizable methodology for visualizing endocytic handling in situ. PMID:23296879

  17. Quantitative fluorescence imaging reveals point of release for lipoproteins during LDLR-dependent uptake.

    Science.gov (United States)

    Pompey, Shanica; Zhao, Zhenze; Luby-Phelps, Kate; Michaely, Peter

    2013-03-01

    The LDL receptor (LDLR) supports efficient uptake of both LDL and VLDL remnants by binding lipoprotein at the cell surface, internalizing lipoprotein through coated pits, and releasing lipoprotein in endocytic compartments before returning to the surface for further rounds of uptake. While many aspects of lipoprotein binding and receptor entry are well understood, it is less clear where, when, and how the LDLR releases lipoprotein. To address these questions, the current study employed quantitative fluorescence imaging to visualize the uptake and endosomal processing of LDL and the VLDL remnant β-VLDL. We find that lipoprotein release is rapid, with most release occurring prior to entry of lipoprotein into early endosomes. Published biochemical studies have identified two mechanisms of lipoprotein release: one that involves the β-propeller module of the LDLR and a second that is independent of this module. Quantitative imaging comparing uptake supported by the normal LDLR or by an LDLR variant incapable of β-propeller-dependent release shows that the β-propeller-independent process is sufficient for release for both lipoproteins but that the β-propeller process accelerates both LDL and β-VLDL release. Together these findings define where, when, and how lipoprotein release occurs and provide a generalizable methodology for visualizing endocytic handling in situ.

  18. Quantitative proteomic analysis of mice corneal tissues reveals angiogenesis-related proteins involved in corneal neovascularization.

    Science.gov (United States)

    Shen, Minqian; Tao, Yimin; Feng, Yifan; Liu, Xing; Yuan, Fei; Zhou, Hu

    2016-07-01

    Corneal neovascularization (CNV) was induced in Balb/c mice by alkali burns in the central area of the cornea with a diameter of 2.5mm. After fourteen days, the cornea from one eye was collected for histological staining for CNV examination, while the cornea from the other eye of the same mouse was harvested for proteomic analysis. The label-free quantitative proteomic approach was applied to analyze five normal corneal tissues (normal group mice n=5) and five corresponding neovascularized corneal tissues (model group mice n=5). A total of 2124 proteins were identified, and 1682 proteins were quantified from these corneal tissues. Among these quantified proteins, 290 proteins were significantly changed between normal and alkali burned corneal tissues. Of these significantly changed proteins, 35 were reported or predicted as angiogenesis-related proteins. Then, these 35 proteins were analyzed using Ingenuity Pathway Analysis Software, resulting in 26 proteins enriched and connected to each other in the protein-protein interaction network, such as Lcn-2, αB-crystallin and Serpinf1 (PEDF). These three significantly changed proteins were selected for further Western blotting validation. Consistent with the quantitative proteomic results, Western blotting showed that Lcn-2 and αB-crystallin were significantly up-regulated in CNV model, while PEDF was down-regulated. This study provided increased understanding of angiogenesis-related proteins involved in corneal vascular development, which will be useful in the ophthalmic clinic of specifically target angiogenesis.

  19. Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics

    DEFF Research Database (Denmark)

    Pan, Cuiping; Olsen, Jesper V; Daub, Henrik;

    2009-01-01

    to identify the direct targets of kinase inhibitors upon affinity purification from cellular extracts. Here we introduce a complementary approach to evaluate the effects of kinase inhibitors on the entire cell signaling network. We used triple labeling SILAC (stable isotope labeling by amino acids in cell...... culture) to compare cellular phosphorylation levels for control, epidermal growth factor stimulus, and growth factor combined with kinase inhibitors. Of thousands of phosphopeptides, less than 10% had a response pattern indicative of targets of U0126 and SB202190, two widely used MAPK inhibitors....... Interestingly, 83% of the growth factor-induced phosphorylation events were affected by either or both inhibitors, showing quantitatively that early signaling processes are predominantly transmitted through the MAPK cascades. In contrast to MAPK inhibitors, dasatinib, a clinical drug directed against BCR...

  20. Quantitative Lipoproteomics in Clostridium difficile Reveals a Role for Lipoproteins in Sporulation.

    Science.gov (United States)

    Charlton, Thomas M; Kovacs-Simon, Andrea; Michell, Stephen L; Fairweather, Neil F; Tate, Edward W

    2015-11-19

    Bacterial lipoproteins are surface exposed, anchored to the membrane by S-diacylglyceryl modification of the N-terminal cysteine thiol. They play important roles in many essential cellular processes and in bacterial pathogenesis. For example, Clostridium difficile is a Gram-positive anaerobe that causes severe gastrointestinal disease; however, its lipoproteome remains poorly characterized. Here we describe the application of metabolic tagging with alkyne-tagged lipid analogs, in combination with quantitative proteomics, to profile protein lipidation across diverse C. difficile strains and on inactivation of specific components of the lipoprotein biogenesis pathway. These studies provide the first comprehensive map of the C. difficile lipoproteome, demonstrate the existence of two active lipoprotein signal peptidases, and provide insights into lipoprotein function, implicating the lipoproteome in transmission of this pathogen.

  1. Strigolactone-Regulated Proteins Revealed by iTRAQ-Based Quantitative Proteomics in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhou [ORNL; Czarnecki, Olaf [ORNL; Chourey, Karuna [ORNL; Yang, Jun [ORNL; Tuskan, Gerald A [ORNL; Hurst, Gregory {Greg} B [ORNL; Pan, Chongle [ORNL; Chen, Jay [ORNL

    2014-01-01

    Strigolactones (SLs) are a new class of plant hormones. In addition to acting as a key inhibitor of shoot branching, SLs stimulate seed germination of root parasitic plants and promote hyphal branching and root colonization of symbiotic arbuscular mycorrhizal fungi. They also regulate many other aspects of plant growth and development. At the transcription level, SL-regulated genes have been reported. However, nothing is known about the proteome regulated by this new class of plant hormones. Here, a quantitative proteomics approach using an isobaric chemical labeling reagent, iTRAQ, to identify the proteome regulated by SLs in Arabidopsis seedlings is presented. It was found SLs regulate the expression of about three dozens of proteins that have not been previously assigned to SL pathways. These findings provide a new tool to investigate the molecular mechanism of action of SLs.

  2. iTRAQ quantitative proteomic analysis reveals the pathways for methanation of propionate facilitated by magnetite

    DEFF Research Database (Denmark)

    Jing, Yuhang; Wan, Jingjing; Angelidaki, Irini

    2017-01-01

    by around 44% in batch experiments, and both direct interspecies electron transfer and interspecies H2 transfer were thermodynamically feasible with the addition of magnetite. The methanation of propionate facilitated by magnetite was also demonstrated in a long-term operated continuous reactor. The methane...... enriched with the addition of magnetite. iTRAQ quantitative proteomic analysis, which was used in mixed culture for the first time, showed that magnetite induced the changes of protein expression levels involved in various pathways during the methanation of propionate. The up-regulation of proteins...... electron transfer considering its up-regulation with the addition of magnetite and origination from Thauera. Most of the up-regulated proteins in methane metabolism were originated from Methanosaeta, while most of the enzymes with down-regulated proteins were originated from Methanosarcina. However, the up-regulated...

  3. Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis.

    Science.gov (United States)

    Beisser, Daniela; Kaschani, Farnusch; Graupner, Nadine; Grossmann, Lars; Jensen, Manfred; Ninck, Sabrina; Schulz, Florian; Rahmann, Sven; Boenigk, Jens; Kaiser, Markus

    2017-01-01

    Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to a direct

  4. Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles.

    Science.gov (United States)

    Julien, Olivier; Zhuang, Min; Wiita, Arun P; O'Donoghue, Anthony J; Knudsen, Giselle M; Craik, Charles S; Wells, James A

    2016-04-05

    Proteases constitute the largest enzyme family, yet their biological roles are obscured by our rudimentary understanding of their cellular substrates. There are 12 human caspases that play crucial roles in inflammation and cell differentiation and drive the terminal stages of cell death. Recent N-terminomics technologies have begun to enumerate the diverse substrates individual caspases can cleave in complex cell lysates. It is clear that many caspases have shared substrates; however, few data exist about the catalytic efficiencies (kcat/KM) of these substrates, which is critical to understanding their true substrate preferences. In this study, we use quantitative MS to determine the catalytic efficiencies for hundreds of natural protease substrates in cellular lysate for two understudied members: caspase-2 and caspase-6. Most substrates are new, and the cleavage rates vary up to 500-fold. We compare the cleavage rates for common substrates with those found for caspase-3, caspase-7, and caspase-8, involved in apoptosis. There is little correlation in catalytic efficiencies among the five caspases, suggesting each has a unique set of preferred substrates, and thus more specialized roles than previously understood. We synthesized peptide substrates on the basis of protein cleavage sites and found similar catalytic efficiencies between the protein and peptide substrates. These data suggest the rates of proteolysis are dominated more by local primary sequence, and less by the tertiary protein fold. Our studies highlight that global quantitative rate analysis for posttranslational modification enzymes in complex milieus for native substrates is critical to better define their functions and relative sequence of events.

  5. Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

    Directory of Open Access Journals (Sweden)

    Takahiro Tsujikawa

    2017-04-01

    Full Text Available Here, we describe a multiplexed immunohistochemical platform with computational image processing workflows, including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination and revealed that response to therapy correlated with degree of mono-myelocytic cell density and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification and provide digital image processing pipelines to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to improve biomarker discovery and assessment.

  6. Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism

    DEFF Research Database (Denmark)

    Casanovas, Albert; Sprenger, Richard R; Tarasov, Kirill

    2015-01-01

    architecture and processes during physiological adaptations in yeast. Our results reveal that activation of cardiolipin synthesis and remodeling supports mitochondrial biogenesis in the transition from fermentative to respiratory metabolism, that down-regulation of de novo sterol synthesis machinery prompts......Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular...

  7. Assigning Quantitative Function to Post-Translational Modifications Reveals Multiple Sites of Phosphorylation That Tune Yeast Pheromone Signaling Output

    Energy Technology Data Exchange (ETDEWEB)

    Pincus, David; Ryan, Christopher J.; Smith, Richard D.; Brent, Roger; Resnekov, Orna; Hakimi, Mohamed Ali

    2013-03-12

    Cell signaling systems transmit information by post-­translationally modifying signaling proteins, often via phosphorylation. While thousands of sites of phosphorylation have been identified in proteomic studies, the vast majority of sites have no known function. Assigning functional roles to the catalog of uncharacterized phosphorylation sites is a key research challenge. Here we present a general approach to address this challenge and apply it to a prototypical signaling pathway, the pheromone response pathway in Saccharomyces cerevisiae. The pheromone pathway includes a mitogen activated protein kinase (MAPK) cascade activated by a G-­protein coupled receptor (GPCR). We used mass spectrometry-based proteomics to identify sites whose phosphorylation changed when the system was active, and evolutionary conservation to assign priority to a list of candidate MAPK regulatory sites. We made targeted alterations in those sites, and measured the effects of the mutations on pheromone pathway output in single cells. Our work identified six new sites that quantitatively tuned system output. We developed simple computational models to find system architectures that recapitulated the quantitative phenotypes of the mutants. Our results identify a number of regulated phosphorylation events that contribute to adjust the input-­output relationship of this model eukaryotic signaling system. We believe this combined approach constitutes a general means not only to reveal modification sites required to turn a pathway on and off, but also those required for more subtle quantitative effects that tune pathway output. Our results further suggest that relatively small quantitative influences from individual regulatory phosphorylation events endow signaling systems with plasticity that evolution may exploit to quantitatively tailor signaling outcomes.

  8. Quantitative transcription dynamic analysis reveals candidate genes and key regulators for ethanol tolerance in Saccharomyces cerevisiae.

    Science.gov (United States)

    Ma, Menggen; Liu, Lewis Z

    2010-06-10

    Derived from our lignocellulosic conversion inhibitor-tolerant yeast, we generated an ethanol-tolerant strain Saccharomyces cerevisiae NRRL Y-50316 by enforced evolutionary adaptation. Using a newly developed robust mRNA reference and a master equation unifying gene expression data analyses, we investigated comparative quantitative transcription dynamics of 175 genes selected from previous studies for an ethanol-tolerant yeast and its closely related parental strain. A highly fitted master equation was established and applied for quantitative gene expression analyses using pathway-based qRT-PCR array assays. The ethanol-tolerant Y-50316 displayed significantly enriched background of mRNA abundance for at least 35 genes without ethanol challenge compared with its parental strain Y-50049. Under the ethanol challenge, the tolerant Y-50316 responded in consistent expressions over time for numerous genes belonging to groups of heat shock proteins, trehalose metabolism, glycolysis, pentose phosphate pathway, fatty acid metabolism, amino acid biosynthesis, pleiotropic drug resistance gene family and transcription factors. The parental strain showed repressed expressions for many genes and was unable to withstand the ethanol stress and establish a viable culture and fermentation. The distinct expression dynamics between the two strains and their close association with cell growth, viability and ethanol fermentation profiles distinguished the tolerance-response from the stress-response in yeast under the ethanol challenge. At least 82 genes were identified as candidate and key genes for ethanol-tolerance and subsequent fermentation under the stress. Among which, 36 genes were newly recognized by the present study. Most of the ethanol-tolerance candidate genes were found to share protein binding motifs of transcription factors Msn4p/Msn2p, Yap1p, Hsf1p and Pdr1p/Pdr3p. Enriched background of transcription abundance and enhanced expressions of ethanol-tolerance genes

  9. Quantitative transcription dynamic analysis reveals candidate genes and key regulators for ethanol tolerance in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Ma Menggen

    2010-06-01

    Full Text Available Abstract Background Derived from our lignocellulosic conversion inhibitor-tolerant yeast, we generated an ethanol-tolerant strain Saccharomyces cerevisiae NRRL Y-50316 by enforced evolutionary adaptation. Using a newly developed robust mRNA reference and a master equation unifying gene expression data analyses, we investigated comparative quantitative transcription dynamics of 175 genes selected from previous studies for an ethanol-tolerant yeast and its closely related parental strain. Results A highly fitted master equation was established and applied for quantitative gene expression analyses using pathway-based qRT-PCR array assays. The ethanol-tolerant Y-50316 displayed significantly enriched background of mRNA abundance for at least 35 genes without ethanol challenge compared with its parental strain Y-50049. Under the ethanol challenge, the tolerant Y-50316 responded in consistent expressions over time for numerous genes belonging to groups of heat shock proteins, trehalose metabolism, glycolysis, pentose phosphate pathway, fatty acid metabolism, amino acid biosynthesis, pleiotropic drug resistance gene family and transcription factors. The parental strain showed repressed expressions for many genes and was unable to withstand the ethanol stress and establish a viable culture and fermentation. The distinct expression dynamics between the two strains and their close association with cell growth, viability and ethanol fermentation profiles distinguished the tolerance-response from the stress-response in yeast under the ethanol challenge. At least 82 genes were identified as candidate and key genes for ethanol-tolerance and subsequent fermentation under the stress. Among which, 36 genes were newly recognized by the present study. Most of the ethanol-tolerance candidate genes were found to share protein binding motifs of transcription factors Msn4p/Msn2p, Yap1p, Hsf1p and Pdr1p/Pdr3p. Conclusion Enriched background of transcription abundance

  10. Mass Spectrometry-Based Quantitative Metabolomics Revealed a Distinct Lipid Profile in Breast Cancer Patients

    Directory of Open Access Journals (Sweden)

    Yun Yen

    2013-04-01

    Full Text Available Breast cancer accounts for the largest number of newly diagnosed cases in female cancer patients. Although mammography is a powerful screening tool, about 20% of breast cancer cases cannot be detected by this method. New diagnostic biomarkers for breast cancer are necessary. Here, we used a mass spectrometry-based quantitative metabolomics method to analyze plasma samples from 55 breast cancer patients and 25 healthy controls. A number of 30 patients and 20 age-matched healthy controls were used as a training dataset to establish a diagnostic model and to identify potential biomarkers. The remaining samples were used as a validation dataset to evaluate the predictive accuracy for the established model. Distinct separation was obtained from an orthogonal partial least squares-discriminant analysis (OPLS-DA model with good prediction accuracy. Based on this analysis, 39 differentiating metabolites were identified, including significantly lower levels of lysophosphatidylcholines and higher levels of sphingomyelins in the plasma samples obtained from breast cancer patients compared with healthy controls. Using logical regression, a diagnostic equation based on three metabolites (lysoPC a C16:0, PC ae C42:5 and PC aa C34:2 successfully differentiated breast cancer patients from healthy controls, with a sensitivity of 98.1% and a specificity of 96.0%.

  11. iTRAQ-based quantitative proteomic analysis reveals potential virulence factors of Erysipelothrix rhusiopathiae.

    Science.gov (United States)

    Wang, Ya; Li, Jingtao; Zhang, Anding; Zhu, Weifeng; Zhang, Qiang; Xu, Zhongmin; Yan, Shuxian; Sun, Xiaomei; Chen, Huanchun; Jin, Meilin

    2017-03-08

    Erysipelothrix rhusiopathiae is a ubiquitous pathogen that has caused considerable economic losses to pig farmers. However, the mechanisms of E. rhusiopathiae pathogenesis remain unclear. To identify new virulence-associated factors, the differentially abundant cell wall-associated proteins (CWPs) between high- and low-virulence strains were investigated through isobaric Tags for Relative and Absolute Quantitation (iTRAQ) combined with liquid chromatography-quadrupole mass spectrometry (LC-MS/MS). In total, 100 CWPs showed significant differences in abundance. Selected differences were verified by western blotting to support the iTRAQ data. Among the differential proteins, the proteins with higher abundance in the high-virulence strain were mostly ABC transporter proteins and adhesion proteins, and the proteins with lower abundance in the high-virulence strain were mainly stress-response proteins. The more abundant proteins in the high-virulence strain may be related to bacterial virulence. The iTRAQ results showed that the abundance of the sugar ABC transporter substrate-binding protein Sbp (No. 5) was higher by 1.73-fold. We further constructed an sbp-deletion mutant. Experiments in animal models showed that the sbp-deletion mutant caused decreased mortality. Together, our data indicated that transporter proteins and adhesion proteins may play important roles in E. rhusiopathiae virulence and confirmed that sbp contributed to the virulence of E. rhusiopathiae.

  12. Quantitative PCR analysis of house dust can reveal abnormal mold conditions.

    Science.gov (United States)

    Meklin, Teija; Haugland, Richard A; Reponen, Tiina; Varma, Manju; Lummus, Zana; Bernstein, David; Wymer, Larry J; Vesper, Stephen J

    2004-07-01

    Indoor mold concentrations were measured in the dust of moldy homes (MH) and reference homes (RH) by quantitative PCR (QPCR) assays for 82 species or related groups of species (assay groups). About 70% of the species and groups were never or only rarely detected. The ratios (MH geometric mean : RH geometric mean) for 6 commonly detected species (Aspergillus ochraceus, A. penicillioides, A. unguis, A. versicolor, Eurotium group, and Cladosporium sphaerospermum) were >1 (Group I). Logistic regression analysis of the sum of the logs of the concentrations of Group I species resulted in a 95% probability for separating MH from RH. These results suggest that it may be possible to evaluate whether a home has an abnormal mold condition by quantifying a limited number of mold species in a dust sample. Also, four common species of Aspergillus were quantified by standard culturing procedures and their concentrations compared to QPCR results. Culturing underestimated the concentrations of these four species by 2 to 3 orders of magnitude compared to QPCR.

  13. Quantitative PCR analysis of house dust can reveal abnormal mold conditions†

    Science.gov (United States)

    Meklin, Teija; Haugland, Richard A.; Reponen, Tiina; Varma, Manju; Lummus, Zana; Bernstein, David; Wymer, Larry J.; Vesper, Stephen J.

    2007-01-01

    Indoor mold concentrations were measured in the dust of moldy homes (MH) and reference homes (RH) by quantitative PCR (QPCR) assays for 82 species or related groups of species (assay groups). About 70% of the species and groups were never or only rarely detected. The ratios (MH geometric mean : RH geometric mean) for 6 commonly detected species (Aspergillus ochraceus, A. penicillioides, A. unguis, A. versicolor, Eurotium group, and Cladosporium sphaerospermum) were > 1 (Group I). Logistic regression analysis of the sum of the logs of the concentrations of Group I species resulted in a 95% probability for separating MH from RH. These results suggest that it may be possible to evaluate whether a home has an abnormal mold condition by quantifying a limited number of mold species in a dust sample. Also, four common species of Aspergillus were quantified by standard culturing procedures and their concentrations compared to QPCR results. Culturing underestimated the concentrations of these four species by 2 to 3 orders of magnitude compared to QPCR. PMID:15237292

  14. Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

    Directory of Open Access Journals (Sweden)

    David A. Orlando

    2014-11-01

    Full Text Available Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.

  15. Quantitative proteomic profiling reveals photosynthesis responsible for inoculum size dependent variation in Chlorella sorokiniana.

    Science.gov (United States)

    Ma, Qian; Wang, Jiangxin; Lu, Shuhuan; Lv, Yajin; Yuan, Yingjin

    2013-03-01

    High density cultivation is essential to industrial production of biodiesel from microalgae, which involves in variations of micro-environment around individual cells, including light intensity, nutrition distribution, other abiotic stress and so on. To figure out the main limit factor in high inoculum cultivation, a quantitative proteomic analysis (iTRAQ-on-line 2-D nano-LC/MS) in a non-model green microalga, Chlorella sorokiniana, under different inoculum sizes was conducted. The resulting high-quality proteomic dataset consisted of 695 proteins. Using a cutoff of P photosynthesis (light reaction) and Calvin cycle (carbon reaction pathway) had highest expression levels under inoculum size of 1 × 10(6) cells mL(-1), and lowest levels under 1 × 10(7) cells mL(-1). Canonical correlation analysis of the photosynthesis related proteins and metabolites biomarkers showed that a good correlation existed between them (canonical coefficient was 0.987), suggesting photosynthesis process greatly affected microalgae biodiesel productivity and quality. Proteomic study of C. sorokiniana under different illuminations was also conducted to confirm light intensity as a potential limit factor of high inoculum size. Nearly two thirds of proteins showed up-regulation under the illumination of 70-110 µmol m(-2) s(-1), compared to those of 40 µmol m(-2) s(-1). This result suggested that by elegantly adjusting light conditions, high cell density cultivation and high biodiesel production might be achieved. Copyright © 2012 Wiley Periodicals, Inc.

  16. Quantitative proteomics reveals differential regulation of protein expression in recipient myocardium after trilineage cardiovascular cell transplantation.

    Science.gov (United States)

    Chang, Ying-Hua; Ye, Lei; Cai, Wenxuan; Lee, Yoonkyu; Guner, Huseyin; Lee, Youngsook; Kamp, Timothy J; Zhang, Jianyi; Ge, Ying

    2015-08-01

    Intramyocardial transplantation of cardiomyocytes (CMs), endothelial cells (ECs), and smooth muscle cells (SMCs) derived from human induced pluripotent stem cells (hiPSCs) has beneficial effects on the post-infarction heart. However, the mechanisms underlying the functional improvements remain undefined. We employed large-scale label-free quantitative proteomics to identify proteins that were differentially regulated following cellular transplantation in a swine model of myocardial infarction (MI). We identified 22 proteins that were significantly up-regulated after trilineage cell transplantation compared to both MI and Sham groups. Among them, 12 proteins, including adenylyl cyclase-associated protein 1 and tropomodulin-1, are associated with positive regulation of muscular contraction whereas 11 proteins, such as desmoplakin and zyxin, are involved in embryonic and muscular development and regeneration. Moreover, we identified 21 proteins up-regulated and another 21 down-regulated in MI, but reversed after trilineage cell transplantation. Proteins up-regulated after MI but reversed by transplantation are related to fibrosis and apoptosis. Conversely, proteins down-regulated in MI but restored after cell therapy are regulators of protein nitrosylation. Our results show that the functionally beneficial effects of trilineage cell therapy are accompanied by differential regulation of protein expression in the recipient myocardium, which may contribute to the improved cardiac function.

  17. Quantitative Susceptibility Mapping Reveals an Association between Brain Iron Load and Depression Severity

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    Shun Yao

    2017-08-01

    Full Text Available Previous studies have detected abnormal serum ferritin levels in patients with depression; however, the results have been inconsistent. This study used quantitative susceptibility mapping (QSM for the first time to examine brain iron concentration in depressed patients and evaluated whether it is related to severity. We included three groups of age- and gender-matched participants: 30 patients with mild-moderate depression (MD, 14 patients with major depression disorder (MDD and 20 control subjects. All participants underwent MR scans with a 3D gradient-echo sequence reconstructing for QSM and performed the 17-item Hamilton Depression Rating Scale (HDRS test. In MDD, the susceptibility value in the bilateral putamen was significantly increased compared with MD or control subjects. In addition, a significant difference was also observed in the left thalamus in MDD patients compared with controls. However, the susceptibility values did not differ between MD patients and controls. The susceptibility values positively correlated with the severity of depression as indicated by the HDRS scores. Our results provide evidence that brain iron deposition may be associated with depression and may even be a biomarker for investigating the pathophysiological mechanism of depression.

  18. Context influences on TALE-DNA binding revealed by quantitative profiling.

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    Rogers, Julia M; Barrera, Luis A; Reyon, Deepak; Sander, Jeffry D; Kellis, Manolis; Joung, J Keith; Bulyk, Martha L

    2015-06-11

    Transcription activator-like effector (TALE) proteins recognize DNA using a seemingly simple DNA-binding code, which makes them attractive for use in genome engineering technologies that require precise targeting. Although this code is used successfully to design TALEs to target specific sequences, off-target binding has been observed and is difficult to predict. Here we explore TALE-DNA interactions comprehensively by quantitatively assaying the DNA-binding specificities of 21 representative TALEs to ∼5,000-20,000 unique DNA sequences per protein using custom-designed protein-binding microarrays (PBMs). We find that protein context features exert significant influences on binding. Thus, the canonical recognition code does not fully capture the complexity of TALE-DNA binding. We used the PBM data to develop a computational model, Specificity Inference For TAL-Effector Design (SIFTED), to predict the DNA-binding specificity of any TALE. We provide SIFTED as a publicly available web tool that predicts potential genomic off-target sites for improved TALE design.

  19. Quantitative Analysis of Fundus-Image Sequences Reveals Phase of Spontaneous Venous Pulsations

    Science.gov (United States)

    Moret, Fabrice; Reiff, Charlotte M.; Lagrèze, Wolf A.; Bach, Michael

    2015-01-01

    Purpose Spontaneous venous pulsation correlates negatively with elevated intracranial pressure and papilledema, and it relates to glaucoma. Yet, its etiology remains unclear. A key element to elucidate its underlying mechanism is the time at which collapse occurs with respect to the heart cycle, but previous reports are contradictory. We assessed this question in healthy subjects using quantitative measurements of both vein diameters and artery lateral displacements; the latter being used as the marker of the ocular systole time. Methods We recorded 5-second fundus sequences with a near-infrared scanning laser ophthalmoscope in 12 young healthy subjects. The image sequences were coregistered, cleaned from microsaccades, and filtered via a principal component analysis to remove nonpulsatile dynamic features. Time courses of arterial lateral displacement and of diameter at sites of spontaneous venous pulsation or proximal to the disk were retrieved from those image sequences and compared. Results Four subjects displayed both arterial and venous pulsatile waveforms. On those, we observed venous diameter waveforms differing markedly among the subjects, ranging from a waveform matching the typical intraocular pressure waveform to a close replica of the arterial waveform. Conclusions The heterogeneity in waveforms and arteriovenous phases suggests that the mechanism governing the venous outflow resistance differs among healthy subjects. Translational relevance Further characterizations are necessary to understand the heterogeneous mechanisms governing the venous outflow resistance as this resistance is altered in glaucoma and is instrumental when monitoring intracranial hypertension based on fundus observations. PMID:26396929

  20. Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae.

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    Wei Niu

    2008-07-01

    Full Text Available Regulation of cell cycle progression is fundamental to cell health and reproduction, and failures in this process are associated with many human diseases. Much of our knowledge of cell cycle regulators derives from loss-of-function studies. To reveal new cell cycle regulatory genes that are difficult to identify in loss-of-function studies, we performed a near-genome-wide flow cytometry assay of yeast gene overexpression-induced cell cycle delay phenotypes. We identified 108 genes whose overexpression significantly delayed the progression of the yeast cell cycle at a specific stage. Many of the genes are newly implicated in cell cycle progression, for example SKO1, RFA1, and YPR015C. The overexpression of RFA1 or YPR015C delayed the cell cycle at G2/M phases by disrupting spindle attachment to chromosomes and activating the DNA damage checkpoint, respectively. In contrast, overexpression of the transcription factor SKO1 arrests cells at G1 phase by activating the pheromone response pathway, revealing new cross-talk between osmotic sensing and mating. More generally, 92%-94% of the genes exhibit distinct phenotypes when overexpressed as compared to their corresponding deletion mutants, supporting the notion that many genes may gain functions upon overexpression. This work thus implicates new genes in cell cycle progression, complements previous screens, and lays the foundation for future experiments to define more precisely roles for these genes in cell cycle progression.

  1. Quantitative proteomics analysis by iTRAQ revealed underlying changes in thermotolerance of Arthrospira platensis.

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    Chang, Rong; Lv, Bingxin; Li, Bosheng

    2017-08-08

    Growth temperature is a critical factor that affects cultivation of Arthrospira platensis which is a type of cyanobacterium widely known as Spirulina that has significant commercial value. To investigate the molecular mechanism underlying the thermotolerance of Spirulina, differential protein expression profiling was carried out using iTRAQ-based quantitative proteomic analysis. This study only analyzed changes in thylakoids. Among the 2085 proteins quantified, 43 differentially expressed proteins were selected based on the fold change cutoff scores of ≥2 or ≤0.5 for up-regulation or down-regulation, respectively. An analysis of these 43 proteins found that 23% of them are photosynthetic system proteins which include photosynthetic enzymes and pigment proteins. The dynamic change of these proteins indicates that photosynthetic system functions were profoundly affected under heat stress and the light-dependent reactions were probably the most sensitive to temperature changes. Meanwhile, to cope with the low energy production due to impaired photosynthesis there was a considerable down-shift in protein synthesis which is a very energy demanding process. The impaired photosynthesis led to low energy generation that was compensated by a down-shift in translation (the most energy-demanding process) and an up-shift of glycolysis. The reduction of many ribosome proteins may lead to a loss in translation efficiency; therefore, Spirulina may adopted a different mechanism to increase translational elongation under heat stress to compensate for this loss, such as elevate L7/L12 proteins. Changes were also found in the classical heat shock proteins, the ROS scavenging system, DNA-binding proteins, and some membrane proteins. In conclusion, this research demonstrate that heat stress induces profound changes in cellular physiology and shed light on the mechanism of the heat stress response and thermotolerance of Arthrospira platensis. Arthrospira platensis, widely known as

  2. Quantitative trait locus (QTL mapping reveals a role for unstudied genes in Aspergillus virulence.

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    Julian K Christians

    Full Text Available Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91. We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7-24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as "hypothetical". This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation.

  3. Fiber architecture in remodeled myocardium revealed with a quantitative diffusion CMR tractography framework and histological validation

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    Mekkaoui Choukri

    2012-10-01

    Full Text Available Abstract Background The study of myofiber reorganization in the remote zone after myocardial infarction has been performed in 2D. Microstructural reorganization in remodeled hearts, however, can only be fully appreciated by considering myofibers as continuous 3D entities. The aim of this study was therefore to develop a technique for quantitative 3D diffusion CMR tractography of the heart, and to apply this method to quantify fiber architecture in the remote zone of remodeled hearts. Methods Diffusion Tensor CMR of normal human, sheep, and rat hearts, as well as infarcted sheep hearts was performed ex vivo. Fiber tracts were generated with a fourth-order Runge-Kutta integration technique and classified statistically by the median, mean, maximum, or minimum helix angle (HA along the tract. An index of tract coherence was derived from the relationship between these HA statistics. Histological validation was performed using phase-contrast microscopy. Results In normal hearts, the subendocardial and subepicardial myofibers had a positive and negative HA, respectively, forming a symmetric distribution around the midmyocardium. However, in the remote zone of the infarcted hearts, a significant positive shift in HA was observed. The ratio between negative and positive HA variance was reduced from 0.96 ± 0.16 in normal hearts to 0.22 ± 0.08 in the remote zone of the remodeled hearts (p Conclusions A significant reorganization of the 3D fiber continuum is observed in the remote zone of remodeled hearts. The positive (rightward shift in HA in the remote zone is greatest in the subepicardium, but involves all layers of the myocardium. Tractography-based quantification, performed here for the first time in remodeled hearts, may provide a framework for assessing regional changes in the left ventricle following infarction.

  4. Resting-state quantitative electroencephalography reveals increased neurophysiologic connectivity in depression.

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    Andrew F Leuchter

    Full Text Available Symptoms of Major Depressive Disorder (MDD are hypothesized to arise from dysfunction in brain networks linking the limbic system and cortical regions. Alterations in brain functional cortical connectivity in resting-state networks have been detected with functional imaging techniques, but neurophysiologic connectivity measures have not been systematically examined. We used weighted network analysis to examine resting state functional connectivity as measured by quantitative electroencephalographic (qEEG coherence in 121 unmedicated subjects with MDD and 37 healthy controls. Subjects with MDD had significantly higher overall coherence as compared to controls in the delta (0.5-4 Hz, theta (4-8 Hz, alpha (8-12 Hz, and beta (12-20 Hz frequency bands. The frontopolar region contained the greatest number of "hub nodes" (surface recording locations with high connectivity. MDD subjects expressed higher theta and alpha coherence primarily in longer distance connections between frontopolar and temporal or parietooccipital regions, and higher beta coherence primarily in connections within and between electrodes overlying the dorsolateral prefrontal cortical (DLPFC or temporal regions. Nearest centroid analysis indicated that MDD subjects were best characterized by six alpha band connections primarily involving the prefrontal region. The present findings indicate a loss of selectivity in resting functional connectivity in MDD. The overall greater coherence observed in depressed subjects establishes a new context for the interpretation of previous studies showing differences in frontal alpha power and synchrony between subjects with MDD and normal controls. These results can inform the development of qEEG state and trait biomarkers for MDD.

  5. Quantitative MRI reveals decelerated fatty infiltration in muscles of active FSHD patients.

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    Janssen, Barbara; Voet, Nicoline; Geurts, Alexander; van Engelen, Baziel; Heerschap, Arend

    2016-05-03

    To investigate the effects of aerobic exercise training (AET) and cognitive-behavioral therapy (CBT), directed towards an increase in daily physical activity, on the progression of fatty infiltration and edema in skeletal muscles of patients with facioscapulohumeral muscular dystrophy (FSHD) type 1 by T2 MRI. Quantitative T2 MRI (qT2 MRI) and fat-suppressed T2 MRI of the thigh were performed at 3T on 31 patients, 13 of whom received usual care (UC), 9 AET, and 9 CBT. Muscle-specific fat fractions (%), derived from qT2 MRI, were recorded pretreatment and posttreatment. Intervention effects were analyzed by comparing fat fraction progression rates of the UC with the treated groups using Mann-Whitney tests, and intermuscle differences by a linear mixed model. Edematous hyperintense lesions were identified on the fat-suppressed T2 MRI. The intraclass correlation coefficient for reproducibility of qT2 MRI fat assessment was 0.99. In the UC group, the fat fraction increased by 6.7/year (95% confidence interval [CI] 4.3 to 9.1). This rate decreased to 2.9/year (95% CI 0.7 to 5.2) in the AET (p = 0.03) and 1.7/year (95% CI -0.2 to 3.6) in the CBT group (p = 0.00015). The treatment effect differed among individual muscles. Fewer new edematous lesions occurred after therapy. Fat fraction derived from qT2 MRI is a reproducible and sensitive biomarker to monitor the effects of increased physical activity in individual muscles. This biomarker reports a favorable effect of AET and CBT on the rate of muscular deterioration in FSHD as reflected in decelerated fat replacement. This study provides Class II evidence that for patients with FSHD type 1, both AET and CBT decrease the rate of fatty infiltration in muscles. © 2016 American Academy of Neurology.

  6. Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism.

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    Casanovas, Albert; Sprenger, Richard R; Tarasov, Kirill; Ruckerbauer, David E; Hannibal-Bach, Hans Kristian; Zanghellini, Jürgen; Jensen, Ole N; Ejsing, Christer S

    2015-03-19

    Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular architecture and processes during physiological adaptations in yeast. Our results reveal that activation of cardiolipin synthesis and remodeling supports mitochondrial biogenesis in the transition from fermentative to respiratory metabolism, that down-regulation of de novo sterol synthesis machinery prompts differential turnover of lipid droplet-associated triacylglycerols and sterol esters during respiratory growth, that sphingolipid metabolism is regulated in a previously unrecognized growth stage-specific manner, and that endogenous synthesis of unsaturated fatty acids constitutes an in vivo upstream activator of peroxisomal biogenesis, via the heterodimeric Oaf1/Pip2 transcription factor. Our work demonstrates the pivotal role of lipid metabolism in adaptive processes and provides a resource to investigate its regulation at the cellular level.

  7. Quantitative expression profiling guided by common retroviral insertion sites reveals novel and cell type–specific cancer genes in leukemia

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    Sauvageau, Martin; Miller, Michelle; Lemieux, Sébastien; Lessard, Julie; Hébert, Josée; Sauvageau, Guy

    2017-01-01

    Proviral insertional mutagenesis is a powerful tool for the discovery of cancer-associated genes. The ability of integrated proviruses to affect gene expression over long distances combined with the lack of methods to determine the expression levels of large numbers of genes in a systematic and truly quantitative manner have limited the identification of cancer genes by proviral insertional mutagenesis. Here, we have characterized a new model of proviral insertional mutagenesis-induced lymphoid tumors derived from Eed Polycomb group gene mutant mice and quantitatively determined the expression levels of all genes within 100 kb of 20 different retroviral common insertion sites (CISs) identified in these tumors. Using high-throughput quantitative reverse transcription–polymerase chain reaction (Q-RT-PCR), we document an average of 13 CIS-associated genes deregulated per tumor, half of which are leukemia subtype–specific, while the others are coordinately deregulated in the majority of tumors analyzed. Interestingly, we find that genes located distantly from common proviral integration sites are as frequently deregulated as proximal genes, with multiple genes affected per integration. Our studies reveal an unsuspected conservation in the group of genes deregulated among phenotypically similar subtypes of lymphoid leukemias, and suggest that identification of common molecular determinants of this disease is within reach. PMID:17906077

  8. Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences.

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    Stanley, Dragana; Geier, Mark S; Chen, Honglei; Hughes, Robert J; Moore, Robert J

    2015-02-27

    quantitatively different. Fecal samples can be effectively used to detect some shifts and responses of cecal microbiota.

  9. Cis-Expression Quantitative Trait Loci Mapping Reveals Replicable Associations with Heroin Addiction in OPRM1

    Science.gov (United States)

    Hancock, Dana B.; Levy, Joshua L.; Gaddis, Nathan C.; Glasheen, Cristie; Saccone, Nancy L.; Page, Grier P.; Hulse, Gary; Wildenauer, Dieter; Kelty, Erin; Schwab, Sibylle; Degenhardt, Louisa; Martin, Nicholas G.; Montgomery, Grant W.; Attia, John; Holliday, Elizabeth G.; McEvoy, Mark; Scott, Rodney J.; Bierut, Laura J.; Nelson, Elliot C.; Kral, Alex; Johnson, Eric O.

    2015-01-01

    Background No opioid receptor, mu 1 (OPRM1) gene polymorphisms, including the functional single nucleotide polymorphism (SNP) rs1799971, have been conclusively associated with heroin/other opioid addiction, despite their biological plausibility. We used evidence of polymorphisms altering OPRM1 expression in normal human brain tissue to nominate and then test associations with heroin addiction. Methods We tested 103 OPRM1 SNPs for association with OPRM1 mRNA expression in prefrontal cortex from 224 European Americans and African Americans of the BrainCloud cohort. We then tested the 16 putative cis-quantitative trait loci (cis-eQTL) SNPs for association with heroin addiction in the Urban Health Study and two replication cohorts, totaling 16,729 European Americans, African Americans, and Australians of European ancestry. Results Four putative cis-eQTL SNPs were significantly associated with heroin addiction in the Urban Health Study (smallest P=8.9×10−5): rs9478495, rs3778150, rs9384169, and rs562859. Rs3778150, located in OPRM1 intron 1, was significantly replicated (P=6.3×10−5). Meta-analysis across all case-control cohorts resulted in P=4.3×10−8: the rs3778150-C allele (frequency=16%-19%) being associated with increased heroin addiction risk. Importantly, the functional SNP allele rs1799971-A was associated with heroin addiction only in the presence of rs3778150-C (P=1.48×10−6 for rs1799971-A/rs3778150-C and P=0.79 for rs1799971-A/rs3778150-T haplotypes). Lastly, replication was observed for six other intron 1 SNPs which had prior suggestive associations with heroin addiction (smallest P=2.7×10−8 for rs3823010). Conclusions Our findings show that common OPRM1 intron 1 SNPs have replicable associations with heroin addiction. The haplotype structure of rs3778150 and nearby SNPs may underlie the inconsistent associations between rs1799971 and heroin addiction. PMID:25744370

  10. A quorum-sensing factor in vegetative Dictyostelium discoideum cells revealed by quantitative migration analysis.

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    Laurent Golé

    Full Text Available BACKGROUND: Many cells communicate through the production of diffusible signaling molecules that accumulate and once a critical concentration has been reached, can activate or repress a number of target genes in a process termed quorum sensing (QS. In the social amoeba Dictyostelium discoideum, QS plays an important role during development. However little is known about its effect on cell migration especially in the growth phase. METHODS AND FINDINGS: To investigate the role of cell density on cell migration in the growth phase, we use multisite timelapse microscopy and automated cell tracking. This analysis reveals a high heterogeneity within a given cell population, and the necessity to use large data sets to draw reliable conclusions on cell motion. In average, motion is persistent for short periods of time (t ≤ 5 min, but normal diffusive behavior is recovered over longer time periods. The persistence times are positively correlated with the migrated distances. Interestingly, the migrated distance decreases as well with cell density. The adaptation of cell migration to cell density highlights the role of a secreted quorum sensing factor (QSF on cell migration. Using a simple model describing the balance between the rate of QSF generation and the rate of QSF dilution, we were able to gather all experimental results into a single master curve, showing a sharp cell transition between high and low motile behaviors with increasing QSF. CONCLUSION: This study unambiguously demonstrates the central role played by QSF on amoeboid motion in the growth phase.

  11. Deficiencies in jasmonate-mediated plant defense reveal quantitative variation in Botrytis cinerea pathogenesis.

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    Heather C Rowe

    2010-04-01

    Full Text Available Despite the described central role of jasmonate signaling in plant defense against necrotrophic pathogens, the existence of intraspecific variation in pathogen capacity to activate or evade plant jasmonate-mediated defenses is rarely considered. Experimental infection of jasmonate-deficient and jasmonate-insensitive Arabidopsis thaliana with diverse isolates of the necrotrophic fungal pathogen Botrytis cinerea revealed pathogen variation for virulence inhibition by jasmonate-mediated plant defenses and induction of plant defense metabolites. Comparison of the transcriptional effects of infection by two distinct B. cinerea isolates showed only minor differences in transcriptional responses of wild-type plants, but notable isolate-specific transcript differences in jasmonate-insensitive plants. These transcriptional differences suggest B. cinerea activation of plant defenses that require plant jasmonate signaling for activity in response to only one of the two B. cinerea isolates tested. Thus, similar infection phenotypes observed in wild-type plants result from different signaling interactions with the plant that are likely integrated by jasmonate signaling.

  12. Isotopic Zonation Within Sulfate Evaporite Mineral Crystals Reveal Quantitative Paleoenvironment Details

    Science.gov (United States)

    Coleman, M.; Rhorssen, M.; Mielke, R. E.

    2008-12-01

    developed a new analytical method [2]. We use a modification of the standard TC/EA continuous-flow protocol to measure both hydrogen and oxygen of water of hydration from the same small sample. We have proved the concept of this new approach by analyzing zones within crystals and individual grains, growing epsomite (magnesium sulfate heptahydrate) in the laboratory and by analysis of natural gypsum evaporites. We are now exploring the effects of varying the controlling parameters. Eventual application to Martian sulfates will reveal amount of water involved in sulfate formation, its isotopic composition(s) and details of the paleo-atmospheric humidity. [1] Gat JR and Gonfiantini R, (Eds) (1981) IAEA Technical Report Series. [2] Rohrssen MK, Brunner B Mielke RE and Coleman M (2008) Analyt. Chem. (in press).

  13. Toward Revealing the Critical Role of Perovskite Coverage in Highly Efficient Electron-Transport Layer-Free Perovskite Solar Cells: An Energy Band and Equivalent Circuit Model Perspective.

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    Huang, Like; Xu, Jie; Sun, Xiaoxiang; Du, Yangyang; Cai, Hongkun; Ni, Jian; Li, Juan; Hu, Ziyang; Zhang, Jianjun

    2016-04-20

    Currently, most efficient perovskite solar cells (PVKSCs) with a p-i-n structure require simultaneously electron transport layers (ETLs) and hole transport layers (HTLs) to help collecting photogenerated electrons and holes for obtaining high performance. ETL free planar PVKSC is a relatively new and simple structured solar cell that gets rid of the complex and high temperature required ETL (such as compact and mesoporous TiO2). Here, we demonstrate the critical role of high coverage of perovskite in efficient ETL free PVKSCs from an energy band and equivalent circuit model perspective. From an electrical point of view, we confirmed that the low coverage of perovskite does cause localized short circuit of the device. With coverage optimization, a planar p-i-n(++) device with a power conversion efficiency of over 11% was achieved, implying that the ETL layer may not be necessary for an efficient device as long as the perovskite coverage is approaching 100%.

  14. Quantitative proteomics reveals the mechanism and consequence of gliotoxin-mediated dysregulation of the methionine cycle in Aspergillus niger.

    Science.gov (United States)

    Manzanares-Miralles, Lara; Sarikaya-Bayram, Özlem; Smith, Elizabeth B; Dolan, Stephen K; Bayram, Özgür; Jones, Gary W; Doyle, Sean

    2016-01-10

    Gliotoxin (GT) is a redox-active metabolite, produced by Aspergillus fumigatus, which inhibits the growth of other fungi. Here we demonstrate how Aspergillus niger responds to GT exposure. Quantitative proteomics revealed that GT dysregulated the abundance of 378 proteins including those involved in methionine metabolism and induced de novo abundance of two S-adenosylmethionine (SAM)-dependent methyltransferases. Increased abundance of enzymes S-adenosylhomocysteinase (p=0.0018) required for homocysteine generation from S-adenosylhomocysteine (SAH), and spermidine synthase (p=0.0068), involved in the recycling of Met, was observed. Analysis of Met-related metabolites revealed significant increases in the levels of Met and adenosine, in correlation with proteomic data. Methyltransferase MT-II is responsible for bisthiobis(methylthio)gliotoxin (BmGT) formation, deletion of MT-II abolished BmGT formation and led to increased GT sensitivity in A. niger. Proteomic analysis also revealed that GT exposure also significantly (pniger. Thus, it provides new opportunities to exploit the response of GT-naïve fungi to GT.

  15. A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing.

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    Kremsky, Isaac; Bellora, Nicolás; Eyras, Eduardo

    2015-01-01

    High-throughput sequencing, and genome-based datasets in general, are often represented as profiles centered at reference points to study the association of protein binding and other signals to particular regulatory mechanisms. Although these profiles often provide compelling evidence of these associations, they do not provide a quantitative assessment of the enrichment, which makes the comparison between signals and conditions difficult. In addition, a number of biases can confound profiles, but are rarely accounted for in the tools currently available. We present a novel computational method, ProfileSeq, for the quantitative assessment of biological profiles to provide an exact, nonparametric test that specific regions of the test profile have higher or lower signal densities than a control set. The method is applicable to high-throughput sequencing data (ChIP-Seq, GRO-Seq, CLIP-Seq, etc.) and to genome-based datasets (motifs, etc.). We validate ProfileSeq by recovering and providing a quantitative assessment of several results reported before in the literature using independent datasets. We show that input signal and mappability have confounding effects on the profile results, but that normalizing the signal by input reads can eliminate these biases while preserving the biological signal. Moreover, we apply ProfileSeq to ChIP-Seq data for transcription factors, as well as for motif and CLIP-Seq data for splicing factors. In all examples considered, the profiles were robust to biases in mappability of sequencing reads. Furthermore, analyses performed with ProfileSeq reveal a number of putative relationships between transcription factor binding to DNA and splicing factor binding to pre-mRNA, adding to the growing body of evidence relating chromatin and pre-mRNA processing. ProfileSeq provides a robust way to quantify genome-wide coordinate-based signal. Software and documentation are freely available for academic use at https://bitbucket.org/regulatorygenomicsupf/profileseq/.

  16. A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing.

    Directory of Open Access Journals (Sweden)

    Isaac Kremsky

    Full Text Available High-throughput sequencing, and genome-based datasets in general, are often represented as profiles centered at reference points to study the association of protein binding and other signals to particular regulatory mechanisms. Although these profiles often provide compelling evidence of these associations, they do not provide a quantitative assessment of the enrichment, which makes the comparison between signals and conditions difficult. In addition, a number of biases can confound profiles, but are rarely accounted for in the tools currently available. We present a novel computational method, ProfileSeq, for the quantitative assessment of biological profiles to provide an exact, nonparametric test that specific regions of the test profile have higher or lower signal densities than a control set. The method is applicable to high-throughput sequencing data (ChIP-Seq, GRO-Seq, CLIP-Seq, etc. and to genome-based datasets (motifs, etc.. We validate ProfileSeq by recovering and providing a quantitative assessment of several results reported before in the literature using independent datasets. We show that input signal and mappability have confounding effects on the profile results, but that normalizing the signal by input reads can eliminate these biases while preserving the biological signal. Moreover, we apply ProfileSeq to ChIP-Seq data for transcription factors, as well as for motif and CLIP-Seq data for splicing factors. In all examples considered, the profiles were robust to biases in mappability of sequencing reads. Furthermore, analyses performed with ProfileSeq reveal a number of putative relationships between transcription factor binding to DNA and splicing factor binding to pre-mRNA, adding to the growing body of evidence relating chromatin and pre-mRNA processing. ProfileSeq provides a robust way to quantify genome-wide coordinate-based signal. Software and documentation are freely available for academic use at https://bitbucket.org/regulatorygenomicsupf/profileseq/.

  17. Involvement of GABA transporters in atropine-treated myopic retina as revealed by iTRAQ quantitative proteomics.

    Science.gov (United States)

    Barathi, Veluchamy A; Chaurasia, Shyam S; Poidinger, Michael; Koh, Siew Kwan; Tian, Dechao; Ho, Candice; Iuvone, P Michael; Beuerman, Roger W; Zhou, Lei

    2014-11-07

    Atropine, a muscarinic antagonist, is known to inhibit myopia progression in several animal models and humans. However, the mode of action is not established yet. In this study, we compared quantitative iTRAQ proteomic analysis in the retinas collected from control and lens-induced myopic (LIM) mouse eyes treated with atropine. The myopic group received a (-15D) spectacle lens over the right eye on postnatal day 10 with or without atropine eye drops starting on postnatal day 24. Axial length was measured by optical low coherence interferometry (OLCI), AC-Master, and refraction was measured by automated infrared photorefractor at postnatal 24, 38, and 52 days. Retinal tissue samples were pooled from six eyes for each group. The experiments were repeated twice, and technical replicates were also performed for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. MetaCore was used to perform protein profiling for pathway analysis. We identified a total of 3882 unique proteins with retina proteome reported to date. Thirty proteins were found to be up-regulated (ratio for myopia/control > global mean ratio + 1 standard deviation), and 28 proteins were down-regulated (ratio for myopia/control retinas. Pathway analysis using MetaCore revealed regulation of γ-aminobutyric acid (GABA) levels in the myopic eyes. Detailed analysis of the quantitative proteomics data showed that the levels of GABA transporter 1 (GAT-1) were elevated in myopic retina and significantly reduced after atropine treatment. These results were further validated with immunohistochemistry and Western blot analysis. In conclusion, this study provides a comprehensive quantitative proteomic analysis of atropine-treated mouse retina and suggests the involvement of GABAergic signaling in the antimyopic effects of atropine in mouse eyes. The GABAergic transmission in the neural retina plays a pivotal role in the maintenance of axial eye growth in mammals.

  18. Quantitative proteomics reveals regulatory differences in the chondrocyte secretome from human medial and lateral femoral condyles in osteoarthritic patients.

    Science.gov (United States)

    Stenberg, Johan; Rüetschi, Ulla; Skiöldebrand, Eva; Kärrholm, Johan; Lindahl, Anders

    2013-10-04

    Osteoarthritis (OA) is a destructive joint disease and there are no known biomarkers available for an early diagnosis. To identify potential disease biomarkers and gain further insight into the disease mechanisms of OA we applied quantitative proteomics with SILAC technology on the secretomes from chondrocytes of OA knees, designated as high Mankin (HM) scored secretome. A quantitative comparison was made between the secretomes of the medial and lateral femur condyle chondrocytes in the same knee since the medial femur condyle is usually more affected in OA than the lateral condyle, which was confirmed by Mankin scoring. The medial/lateral comparison was also made on the secretomes from chondrocytes taken from one individual with no clinically apparent joint-disease, designated as low Mankin (LM) scored secretome. We identified 825 proteins in the HM secretome and 69 of these showed differential expression when comparing the medial and lateral femoral compartment. The LM scored femoral condyle showed early signs of OA in the medial compartment as assessed by Mankin score. We here report the identification and relative quantification of several proteins of interest for the OA disease mechanism e.g. CYTL1, DMD and STAB1 together with putative early disease markers e.g. TIMP1, PPP2CA and B2M. The present study reveals differences in protein abundance between medial/lateral femur condyles in OA patients. These regulatory differences expand the knowledge regarding OA disease markers and mechanisms.

  19. A Quantitative Model of Motility Reveals Low-Dimensional Variation in Exploratory Behavior Across Multiple Nematode Species

    Science.gov (United States)

    Helms, Stephen; Avery, Leon; Stephens, Greg; Shimizu, Tom

    2014-03-01

    Animal behavior emerges from many layers of biological organization--from molecular signaling pathways and neuronal networks to mechanical outputs of muscles. In principle, the large number of interconnected variables at each of these layers could imply dynamics that are complex and hard to control or even tinker with. Yet, for organisms to survive in a competitive, ever-changing environment, behavior must readily adapt. We applied quantitative modeling to identify important aspects of behavior in chromadorean nematodes ranging from the lab strain C. elegans N2 to wild strains and distant species. We revealed subtle yet important features such as speed control and heavy-tailed directional changes. We found that the parameters describing this behavioral model varied among individuals and across species in a correlated way that is consistent with a trade-off between exploratory and exploitative behavior.

  20. Quantitative proteomic analysis reveals that antioxidation mechanisms contribute to cold tolerance in plantain (Musa paradisiaca L.; ABB Group) seedlings.

    Science.gov (United States)

    Yang, Qiao-Song; Wu, Jun-Hua; Li, Chun-Yu; Wei, Yue-Rong; Sheng, Ou; Hu, Chun-Hua; Kuang, Rui-Bin; Huang, Yong-Hong; Peng, Xin-Xiang; McCardle, James A; Chen, Wei; Yang, Yong; Rose, Jocelyn K C; Zhang, Sheng; Yi, Gan-Jun

    2012-12-01

    Banana and its close relative, plantain are globally important crops and there is considerable interest in optimizing their cultivation. Plantain has superior cold tolerance compared with banana and a thorough understanding of the molecular mechanisms and responses of plantain to cold stress has great potential value for developing cold tolerant banana cultivars. In this study, we used iTRAQ-based comparative proteomic analysis to investigate the temporal responses of plantain to cold stress. Plantain seedlings were exposed for 0, 6, and 24 h of cold stress at 8 °C and subsequently allowed to recover for 24 h at 28 °C. A total of 3477 plantain proteins were identified, of which 809 showed differential expression from the three treatments. The majority of differentially expressed proteins were predicted to be involved in oxidation-reduction, including oxylipin biosynthesis, whereas others were associated with photosynthesis, photorespiration, and several primary metabolic processes, such as carbohydrate metabolic process and fatty acid beta-oxidation. Western blot analysis and enzyme activity assays were performed on seven differentially expressed, cold-response candidate plantain proteins to validate the proteomics data. Similar analyses of the seven candidate proteins were performed in cold-sensitive banana to examine possible functional conservation, and to compare the results to equivalent responses between the two species. Consistent results were achieved by Western blot and enzyme activity assays, demonstrating that the quantitative proteomics data collected in this study are reliable. Our results suggest that an increase of antioxidant capacity through adapted ROS scavenging capability, reduced production of ROS, and decreased lipid peroxidation contribute to molecular mechanisms for the increased cold tolerance in plantain. To the best of our knowledge, this is the first report of a global investigation on molecular responses of plantain to cold stress by

  1. Quantitative Proteomic Analysis Reveals that Antioxidation Mechanisms Contribute to Cold Tolerance in Plantain (Musa paradisiaca L.;ABB Group) Seedlings

    Institute of Scientific and Technical Information of China (English)

    Qiaosong Yang; Junhua Wu; Chunyu Li; Yuerong Wei; Ou Sheng; Chunhua Hu; Ruibin Kuang

    2012-01-01

    Banana and its close relative,plantain are globally important crops and there is of considerable interest in optimizing their cultivation.Plantain has superior cold tolerance compared to banana and a thorough understanding of the molecular mechanisms and responses of plantain to cold stress has great potential value for developing cold tolerant banana cultivars.In this study,we used iTRAQ-based comparative proteomic analysis to investigate the temporal responses of plantain to cold stress.Plantain seedlings were exposed for 0,6 and 24 h of cold stress at 8℃ and subsequently allowed to recover for 24 h at 28℃.A total of 3,477 plantain proteins were identified,of which 809 showed differential expression from the three treatments.The majority of differentially expressed proteins were predicted to be involved in oxidation-reduction,including oxylipin biosynthesis,while others were associated with photosynthesis,photorespiration and several primary metabolic processes,such as carbohydrate metabolic process and fatty acid beta-oxidation.Western blot analysis and enzyme activity assays were performed on 7 differentially expressed,cold-response candidate plantain proteins in order to validate the proteomics data.Similar analyses of the 7 candidate proteins were performed in cold-sensitive banana to examine possible functional conservation and to compare the results to equivalent responses between the two species.Consistent results were achieved by Western blot and enzyme activity assays,demonstrating that the quantitative proteomics data collected in this study are reliable.Our results suggest that an increase of antioxidant capacity through adapted ROS scavenging capability,reduced production of ROS and decreased lipid peroxidation contribute to molecular mechanisms for the higher cold tolerance in plantain.To the best of our knowledge,this is the first report of a global investigation on molecular responses of plantain to cold stress by proteomic analysis.

  2. Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution

    Science.gov (United States)

    Jain, Niyati; Lin, Hsuan-Chun; Morgan, Christopher E.; Harris, Michael E.; Tolbert, Blanton S.

    2017-01-01

    Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5′-YAG-3′ and shows how its copy number, position in the loop, and loop structure modulate affinity. For a subset of ESS3 variants, we show that specificity is determined by association rate constants and that variants lacking the minimal sequence motif bind competitively with consensus RNA. Thus, the results reveal general rules of specificity of hnRNP A1 and provide a quantitative framework for understanding how it discriminates between alternative competing RNA ligands in vivo. PMID:28193894

  3. Quantitative Proteomic Analysis Reveals Populus cathayana Females Are More Sensitive and Respond More Sophisticatedly to Iron Deficiency than Males.

    Science.gov (United States)

    Zhang, Sheng; Zhang, Yunxiang; Cao, Yanchun; Lei, Yanbao; Jiang, Hao

    2016-03-04

    Previous studies have shown that there are significant sexual differences in the morphological and physiological responses of Populus cathayana Rehder to nitrogen and phosphorus deficiencies, but little is known about the sex-specific differences in responses to iron deficiency. In this study, the effects of iron deficiency on the morphology, physiology, and proteome of P. cathayana males and females were investigated. The results showed that iron deficiency (25 days) significantly decreased height growth, photosynthetic rate, chlorophyll content, and tissue iron concentration in both sexes. A comparison between the sexes indicated that iron-deficient males had less height inhibition and photosynthesis system II or chloroplast ultrastructural damage than iron-deficient females. iTRAQ-based quantitative proteomic analysis revealed that 144 and 68 proteins were decreased in abundance (e.g., proteins involved in photosynthesis, carbohydrate and energy metabolism, and gene expression regulation) and 78 and 39 proteins were increased in abundance (e.g., proteins involved in amino acid metabolism and stress response) according to the criterion of ratio ≥1.5 in females and males, respectively. A comparison between the sexes indicated that iron-deficient females exhibited a greater change in the proteins involved in photosynthesis, carbon and energy metabolism, the redox system, and stress responsive proteins. This study reveals females are more sensitive and have a more sophisticated response to iron deficiency compared with males and provides new insights into differential sexual responses to nutrient deficiency.

  4. Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem.

    Science.gov (United States)

    Mahadevan, Chidambareswaren; Krishnan, Anu; Saraswathy, Gayathri G; Surendran, Arun; Jaleel, Abdul; Sakuntala, Manjula

    2016-01-01

    Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset

  5. Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum—Phytophthora capsici Phytopathosystem

    Science.gov (United States)

    Mahadevan, Chidambareswaren; Krishnan, Anu; Saraswathy, Gayathri G.; Surendran, Arun; Jaleel, Abdul; Sakuntala, Manjula

    2016-01-01

    Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset

  6. On Equivalence And Evaluation

    Institute of Scientific and Technical Information of China (English)

    孙贝

    2013-01-01

      Equivalence, a central and controversial issue in translation, has been studied, discussed and disputed by many scholars. For this reason, they employed various approaches and have yielded fruitful and remarkable theories. Three representative equivalence theories are selected in the thesis to elaborate equivalence:Nida’s reader-response based dynamic equivalence, Catford’s textual equivalence, Qiu Maoru’s empirical formula on equivalence. Equivalence is an applicable tool to analyze and evaluate translation.

  7. Quantitative Analysis of MicroRNAs in Vaccinia virus Infection Reveals Diversity in Their Susceptibility to Modification and Suppression.

    Directory of Open Access Journals (Sweden)

    Amy H Buck

    Full Text Available Vaccinia virus (VACV is a large cytoplasmic DNA virus that causes dramatic alterations to many cellular pathways including microRNA biogenesis. The virus encodes a poly(A polymerase which was previously shown to add poly(A tails to the 3' end of cellular miRNAs, resulting in their degradation by 24 hours post infection (hpi. Here we used small RNA sequencing to quantify the impact of VACV infection on cellular miRNAs in human cells at both early (6 h and late (24 h times post infection. A detailed quantitative analysis of individual miRNAs revealed marked diversity in the extent of their modification and relative change in abundance during infection. Some miRNAs became highly modified (e.g. miR-29a-3p, miR-27b-3p whereas others appeared resistant (e.g. miR-16-5p. Furthermore, miRNAs that were highly tailed at 6 hpi were not necessarily among the most reduced at 24 hpi. These results suggest that intrinsic features of human cellular miRNAs cause them to be differentially polyadenylated and altered in abundance during VACV infection. We also demonstrate that intermediate and late VACV gene expression are required for optimal repression of some miRNAs including miR-27-3p. Overall this work reveals complex and varied consequences of VACV infection on host miRNAs and identifies miRNAs which are largely resistant to VACV-induced polyadenylation and are therefore present at functional levels during the initial stages of infection and replication.

  8. SWATH-MS Quantitative Proteomic Investigation Reveals a Role of Jasmonic Acid during Lead Response in Arabidopsis.

    Science.gov (United States)

    Zhu, Fu-Yuan; Chan, Wai-Lung; Chen, Mo-Xian; Kong, Ricky P W; Cai, Congxi; Wang, Qiaomei; Zhang, Jian-Hua; Lo, Clive

    2016-10-07

    Lead (Pb) pollution is a growing environment problem that continuously threatens the productivity of crops. To understand the molecular mechanisms of plant adaptation to Pb toxicity, we examined proteome changes in Arabidopsis seedlings following Pb treatment by SWATH-MS, a label-free quantitative proteomic platform. We identified and quantified the expression of 1719 proteins in water- and Pb-treated plants. Among them, 231 proteins showed significant abundance changes (151 elevated and 80 reduced) upon Pb exposure. Functional categorization revealed that most of the Pb-responsive proteins are involved in different metabolic processes. For example, down-regulation of photosynthesis and biosynthesis of isoprenoids and tetrapyrroles in chloroplasts were observed. On the contrary, pathways leading to glutathione, jasmonic acid (JA), glucosinolate (GSL), and phenylpropanoid production are up-regulated. Experimental characterizations demonstrated a rapid elevation of endogenic JA production in Pb-treated Arabidopsis seedlings, while a JA-deficient mutant and a JA-insensitive mutant showed hypersensitivity to root inhibition by Pb, implicating an essential role of JA during Pb responses. Consistently, methyl jasmonate supplementation alleviated Pb toxicity in the wild-type and JA-deficient mutant. Furthermore, GSL levels were substantially enhanced following Pb treatment, while such induction was not detected in the JA mutant, suggesting that the Pb-induced GSL accumulation is JA-dependent. Overall, our work represents the first SWATH-MS analysis in Arabidopsis and highlights a potential mediating role of JA during Pb stress.

  9. Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants.

    Science.gov (United States)

    Rodrigues, Silas P; Ventura, José A; Aguilar, Clemente; Nakayasu, Ernesto S; Choi, HyungWon; Sobreira, Tiago J P; Nohara, Lilian L; Wermelinger, Luciana S; Almeida, Igor C; Zingali, Russolina B; Fernandes, Patricia M B

    2012-06-18

    Papaya meleira virus (PMeV) is so far the only described laticifer-infecting virus, the causal agent of papaya (Carica papaya L.) sticky disease. The effects of PMeV on the laticifers' regulatory network were addressed here through the proteomic analysis of papaya latex. Using both 1-DE- and 1D-LC-ESI-MS/MS, 160 unique papaya latex proteins were identified, representing 122 new proteins in the latex of this plant. Quantitative analysis by normalized spectral counting revealed 10 down-regulated proteins in the latex of diseased plants, 9 cysteine proteases (chymopapain) and 1 latex serine proteinase inhibitor. A repression of papaya latex proteolytic activity during PMeV infection was hypothesized. This was further confirmed by enzymatic assays that showed a reduction of cysteine-protease-associated proteolytic activity in the diseased papaya latex. These findings are discussed in the context of plant responses against pathogens and may greatly contribute to understand the roles of laticifers in plant stress responses.

  10. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2014-02-01

    Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

  11. Quantitative proteome analysis of an antibiotic resistant Escherichia coli exposed to tetracycline reveals multiple affected metabolic and peptidoglycan processes.

    Science.gov (United States)

    Jones-Dias, Daniela; Carvalho, Ana Sofia; Moura, Inês Barata; Manageiro, Vera; Igrejas, Gilberto; Caniça, Manuela; Matthiesen, Rune

    2017-03-06

    Tetracyclines are among the most commonly used antibiotics administrated to farm animals for disease treatment and prevention, contributing to the worldwide increase in antibiotic resistance in animal and human pathogens. Although tetracycline mechanisms of resistance are well known, the role of metabolism in bacterial reaction to antibiotic stress is still an important assignment and could contribute to the understanding of tetracycline related stress response. In this study, spectral counts-based label free quantitative proteomics has been applied to study the response to tetracycline of the environmental-borne Escherichia coli EcAmb278 isolate soluble proteome. A total of 1484 proteins were identified by high resolution mass spectrometry at a false discovery rate threshold of 1%, of which 108 were uniquely identified under absence of tetracycline whereas 126 were uniquely identified in presence of tetracycline. These proteins revealed interesting difference in e.g. proteins involved in peptidoglycan-based cell wall proteins and energy metabolism. Upon treatment, 12 proteins were differentially regulated showing more than 2-fold change and presistant E. coli provides novel insight into tetracycline related stress. The lack of new antibiotics to fight infections caused by multidrug resistant microorganisms has motivated the use of old antibiotics, and the search for new drug targets. The evolution of antibiotic resistance is complex, but it is known that agroecosystems play an important part in the selection of antibiotic resistance bacteria. Tetracyclines are still used as phytopharmaceutical agents in crops, selecting resistant bacteria and changing the ecology of farm soil. Little is known about the metabolic response of genetically resistant populations to antibiotic exposure. Indeed, to date there are no quantitative tetracycline resistance studies performed with the latest generation of high resolution mass spectrometers allowing high mass accuracy in both

  12. Plasma proteome response to severe burn injury revealed by 18O-labeled "universal" reference-based quantitative proteomics.

    Science.gov (United States)

    Qian, Wei-Jun; Petritis, Brianne O; Kaushal, Amit; Finnerty, Celeste C; Jeschke, Marc G; Monroe, Matthew E; Moore, Ronald J; Schepmoes, Athena A; Xiao, Wenzhong; Moldawer, Lyle L; Davis, Ronald W; Tompkins, Ronald G; Herndon, David N; Camp, David G; Smith, Richard D

    2010-09-01

    A burn injury represents one of the most severe forms of human trauma and is responsible for significant mortality worldwide. Here, we present the first quantitative proteomics investigation of the blood plasma proteome response to severe burn injury by comparing the plasma protein concentrations of 10 healthy control subjects with those of 15 severe burn patients at two time-points following the injury. The overall analytical strategy for this work integrated immunoaffinity depletion of the 12 most abundant plasma proteins with cysteinyl-peptide enrichment-based fractionation prior to LC-MS analyses of individual patient samples. Incorporation of an 18O-labeled "universal" reference among the sample sets enabled precise relative quantification across samples. In total, 313 plasma proteins confidently identified with two or more unique peptides were quantified. Following statistical analysis, 110 proteins exhibited significant abundance changes in response to the burn injury. The observed changes in protein concentrations suggest significant inflammatory and hypermetabolic response to the injury, which is supported by the fact that many of the identified proteins are associated with acute phase response signaling, the complement system, and coagulation system pathways. The regulation of approximately 35 proteins observed in this study is in agreement with previous results reported for inflammatory or burn response, but approximately 50 potentially novel proteins previously not known to be associated with burn response or inflammation are also found. Elucidating proteins involved in the response to severe burn injury may reveal novel targets for therapeutic interventions as well as potential predictive biomarkers for patient outcomes such as multiple organ failure.

  13. A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila.

    Science.gov (United States)

    Hoermann, Astrid; Cicin-Sain, Damjan; Jaeger, Johannes

    2016-03-15

    Understanding eukaryotic transcriptional regulation and its role in development and pattern formation is one of the big challenges in biology today. Most attempts at tackling this problem either focus on the molecular details of transcription factor binding, or aim at genome-wide prediction of expression patterns from sequence through bioinformatics and mathematical modelling. Here we bridge the gap between these two complementary approaches by providing an integrative model of cis-regulatory elements governing the expression of the gap gene giant (gt) in the blastoderm embryo of Drosophila melanogaster. We use a reverse-engineering method, where mathematical models are fit to quantitative spatio-temporal reporter gene expression data to infer the regulatory mechanisms underlying gt expression in its anterior and posterior domains. These models are validated through prediction of gene expression in mutant backgrounds. A detailed analysis of our data and models reveals that gt is regulated by domain-specific CREs at early stages, while a late element drives expression in both the anterior and the posterior domains. Initial gt expression depends exclusively on inputs from maternal factors. Later, gap gene cross-repression and gt auto-activation become increasingly important. We show that auto-regulation creates a positive feedback, which mediates the transition from early to late stages of regulation. We confirm the existence and role of gt auto-activation through targeted mutagenesis of Gt transcription factor binding sites. In summary, our analysis provides a comprehensive picture of spatio-temporal gene regulation by different interacting enhancer elements for an important developmental regulator.

  14. Novel X-linked genes revealed by quantitative polymerase chain reaction in the green anole, Anolis carolinensis.

    Science.gov (United States)

    Rovatsos, Michail; Altmanová, Marie; Pokorná, Martina Johnson; Kratochvíl, Lukáš

    2014-08-28

    The green anole, Anolis carolinensis (ACA), is the model reptile for a vast array of biological disciplines. It was the first nonavian reptile to have its genome fully sequenced. During the genome project, the XX/XY system of sex chromosomes homologous to chicken chromosome 15 (GGA15) was revealed, and 106 X-linked genes were identified. We selected 38 genes located on eight scaffolds in ACA and having orthologs located on GGA15, then tested their linkage to ACA X chromosome by using comparative quantitative fluorescent real-time polymerase chain reaction applied to male and female genomic DNA. All tested genes appeared to be X-specific and not present on the Y chromosome. Assuming that all genes located on these scaffolds should be localized to the ACA X chromosome, we more than doubled the number of known X-linked genes in ACA, from 106 to 250. While demonstrating that the gene content of chromosome X in ACA and GGA15 is largely conserved, we nevertheless showed that numerous interchromosomal rearrangements had occurred since the splitting of the chicken and anole evolutionary lineages. The presence of many ACA X-specific genes localized to distinct contigs indicates that the ACA Y chromosome should be highly degenerated, having lost a large amount of its original gene content during evolution. The identification of novel genes linked to the X chromosome and absent on the Y chromosome in the model lizard species contributes to ongoing research as to the evolution of sex determination in reptiles and provides important information for future comparative and functional genomics.

  15. Derived equivalence of algebras

    Institute of Scientific and Technical Information of China (English)

    杜先能

    1997-01-01

    The derived equivalence and stable equivalence of algebras RmA and RmB are studied It is proved, using the tilting complex, that RmA and RmB are derived-equivalent whenever algebras A and B are derived-equivalent

  16. iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis.

    Directory of Open Access Journals (Sweden)

    Linghua Chen

    Full Text Available Black rice (Oryza sativa L., whose pericarp is rich in anthocyanins (ACNs, is considered as a healthier alternative to white rice. Molecular species of ACNs in black rice have been well documented in previous studies; however, information about the metabolic mechanisms underlying ACN biosynthesis during black rice grain development is unclear.The aim of the present study was to determine changes in the metabolic pathways that are involved in the dynamic grain proteome during the development of black rice indica cultivar, (Oryza sativa L. indica var. SSP. Isobaric tags for relative and absolute quantification (iTRAQ MS/MS were employed to identify statistically significant alterations in the grain proteome. Approximately 928 proteins were detected, of which 230 were differentially expressed throughout 5 successive developmental stages, starting from 3 to 20 days after flowering (DAF. The greatest number of differentially expressed proteins was observed on 7 and 10 DAF, including 76 proteins that were upregulated and 39 that were downregulated. The biological process analysis of gene ontology revealed that the 230 differentially expressed proteins could be sorted into 14 functional groups. Proteins in the largest group were related to metabolic process, which could be integrated into multiple biochemical pathways. Specifically, proteins with a role in ACN biosynthesis, sugar synthesis, and the regulation of gene expression were upregulated, particularly from the onset of black rice grain development and during development. In contrast, the expression of proteins related to signal transduction, redox homeostasis, photosynthesis and N-metabolism decreased during grain maturation. Finally, 8 representative genes encoding different metabolic proteins were verified via quantitative real-time polymerase chain reaction (qRT-PCR analysis, these genes had differed in transcriptional and translational expression during grain development.Expression analyses

  17. Politico-economic equivalence

    DEFF Research Database (Denmark)

    Gonzalez Eiras, Martin; Niepelt, Dirk

    2015-01-01

    Traditional "economic equivalence'' results, like the Ricardian equivalence proposition, define equivalence classes over exogenous policies. We derive "politico-economic equivalence" conditions that apply in environments where policy is endogenous and chosen sequentially. A policy regime...... and a state are equivalent to another such pair if both pairs give rise to the same allocation in politico-economic equilibrium. The equivalence conditions help to identify factors that render institutional change non-neutral and to construct politico-economic equilibria in new policy regimes. We exemplify...... their use in the context of several applications, relating to social security reform, tax-smoothing policies and measures to correct externalities....

  18. Quantitative proteomic analysis of wheat grain proteins reveals differential effects of silencing of omega-5 gliadin genes in transgenic lines

    Science.gov (United States)

    Novel wheat lines with altered flour compositions can be used to decipher the roles of specific gluten proteins in flour quality. Grain proteins from transgenic wheat lines in which genes encoding the omega-5 gliadins were silenced by RNA interference (RNAi) were analyzed in detail by quantitative 2...

  19. Equivalence principles and electromagnetism

    Science.gov (United States)

    Ni, W.-T.

    1977-01-01

    The implications of the weak equivalence principles are investigated in detail for electromagnetic systems in a general framework. In particular, it is shown that the universality of free-fall trajectories (Galileo weak equivalence principle) does not imply the validity of the Einstein equivalence principle. However, the Galileo principle plus the universality of free-fall rotation states does imply the Einstein principle.

  20. Equivalence in Translation

    Institute of Scientific and Technical Information of China (English)

    李良杰

    2013-01-01

    There are many researches about translation theories and methods in western translation history. Equivalence in transla⁃tion has always been the central issue for discussion. This paper gives a general review and comment on equivalence in translation in terms of three representative translation theorists and their views about equivalence in translation.

  1. Quantitative secretome analysis reveals the interactions between epithelia and tumor cells by in vitro modulating colon cancer microenvironment.

    Science.gov (United States)

    Zeng, Xiao; Yang, Pengbo; Chen, Bing; Jin, Xuewen; Liu, Yuling; Zhao, Xia; Liang, Shufang

    2013-08-26

    In tumor microenvironment, interactions among multiple cell types are critical for cancer progression. Secreted proteins are responsible for crosstalk among these cells within tumor microenvironment. To elucidate the interactions of tumor and epithelia, we co-cultured colon cancer cell line HT29 with normal human colon mucosal epithelial cell line NCM460 to mimic tumor microenvironment in vitro and investigated the differential expression pattern of secretome. A quantitative proteomics approach based on stable isotope labeling by amino acids in cell culture (SILAC) and LC-mass spectrometry was used for secretome analysis. Totally 45 proteins were altered over 2-fold in co-cultured cellular supernatants between equal amounts of NCM460 and HT29 cells, compared with mono-cultured conditions. These differential secreted proteins involve in multiple tumor-associated biological functions. The secretion level and acting pattern of acrogranin, IGFBP6 and vimentin were changed along with different co-cultured cell number ratios between NCM460 and HT29 cells, simulating early, middle or advanced stage of colon cancer. Therefore, a quantitative secretome profiling based on a co-culture system can track secreted protein changes and their associated biological roles between tumor and epithelia, which gives a new insight on communications between tumor and epithelia as well as cancer biotherapy by inhibiting cell interactions. Tumor microenvironment is a complex system and comprised of cancer cells and host stromal cells. The growth and progression of tumor have been recognized were affected by multidirectional interactions of secreted proteins (secretome), which were produced by the cells within tumor microenvironment. Focus on general secreted molecules of living cells via proteomic tools, is promising for investigating cell communication. Stable isotope labeling by amino acids in cell culture (SILAC) is a metabolic labeling strategy for quantitative analysis, which is gaining

  2. Quantitative immunologic analysis of the methanogenic flora of digestors reveals a considerable diversity. [Methanobacterium formicicum; Methanobrevibacter arboriphilus

    Energy Technology Data Exchange (ETDEWEB)

    Macario, A.J.L.; de Macario, E.C.

    1988-01-01

    To determine which methanogens occur in digestors, we performed a quantitative immunologic analysis of a variety of samples. A comprehensive panel of calibrated polyclonal antibody probes of predefined specificity spectra was used. This allowed precise identification of bacteria by antigenic fingerprinting. A considerable diversity of methanogens was uncovered, much larger than previously reported, encompassing at least 14 strains of 11 species. Strategies were developed to measure the load of any given methanogen in a sample and to compare samples quantitatively. Two methanogens were found to predominate which were antigenically closely related with either Methanobacterium formicicum MF or Methanobrevibacter arboriphilus AZ. Fundamental data, probes, and methods are now available to monitor methanogenic subpopulations during digestor operation and thus learn about their respective roles and predictive and predictive significance.

  3. An Equivalent Gauge and the Equivalence Theorem

    CERN Document Server

    Wulzer, Andrea

    2014-01-01

    I describe a novel covariant formulation of massive gauge theories in which the longitudinal polarization vectors do not grow with the energy. Therefore in the present formalism, differently from the ordinary one, the energy and coupling power-counting is completely transparent at the level of individual Feynman diagrams, with obvious advantages both at the conceptual and practical level. Since power-counting is transparent, the high-energy limit of the amplitudes involving longitudinal particles is immediately taken, and the Equivalence Theorem is easily demonstrated at all orders in perturbation theory. Since the formalism makes the Equivalence Theorem self-evident, and because it is based on a suitable choice of the gauge, we can call it an "Equivalent Gauge".

  4. Transcriptome and quantitative proteome analysis reveals molecular processes associated with larval metamorphosis in the polychaete pseudopolydora vexillosa

    KAUST Repository

    Chandramouli, Kondethimmanahalli

    2013-03-01

    Larval growth of the polychaete worm Pseudopolydora vexillosa involves the formation of segment-specific structures. When larvae attain competency to settle, they discard swimming chaetae and secrete mucus. The larvae build tubes around themselves and metamorphose into benthic juveniles. Understanding the molecular processes, which regulate this complex and unique transition, remains a major challenge because of the limited molecular information available. To improve this situation, we conducted high-throughput RNA sequencing and quantitative proteome analysis of the larval stages of P. vexillosa. Based on gene ontology (GO) analysis, transcripts related to cellular and metabolic processes, binding, and catalytic activities were highly represented during larval-adult transition. Mitogen-activated protein kinase (MAPK), calcium-signaling, Wnt/β-catenin, and notch signaling metabolic pathways were enriched in transcriptome data. Quantitative proteomics identified 107 differentially expressed proteins in three distinct larval stages. Fourteen and 53 proteins exhibited specific differential expression during competency and metamorphosis, respectively. Dramatic up-regulation of proteins involved in signaling, metabolism, and cytoskeleton functions were found during the larval-juvenile transition. Several proteins involved in cell signaling, cytoskeleton and metabolism were up-regulated, whereas proteins related to transcription and oxidative phosphorylation were down-regulated during competency. The integration of high-throughput RNA sequencing and quantitative proteomics allowed a global scale analysis of larval transcripts/proteins associated molecular processes in the metamorphosis of polychaete worms. Further, transcriptomic and proteomic insights provide a new direction to understand the fundamental mechanisms that regulate larval metamorphosis in polychaetes. © 2013 American Chemical Society.

  5. Correlative and quantitative 1H NMR-based metabolomics reveals specific metabolic pathway disturbances in diabetic rats.

    Science.gov (United States)

    Zhang, Shucha; Nagana Gowda, G A; Asiago, Vincent; Shanaiah, Narasimhamurthy; Barbas, Coral; Raftery, Daniel

    2008-12-01

    Type 1 diabetes was induced in Sprague-Dawley rats using streptozotocin. Rat urine samples (8 diabetic and 10 control) were analyzed by 1H nuclear magnetic resonance (NMR) spectroscopy. The derived metabolites using univariate and multivariate statistical analysis were subjected to correlative analysis. Plasma metabolites were measured by a series of bioassays. A total of 17 urinary metabolites were identified in the 1H NMR spectra and the loadings plots after principal components analysis. Diabetic rats showed significantly increased levels of glucose (P cycle and a contribution from gut microbial metabolism. Specific perturbed metabolic pathways include the glucose-alanine and Cori cycles, the acetate switch, and choline metabolism. Detection of the altered metabolic pathways and bacterial metabolites using this correlative and quantitative NMR-based metabolomics approach should help to further the understanding of diabetes-related mechanisms.

  6. Behaviour of pathogenic and indicator bacteria during urban wastewater treatment and sludge composting, as revealed by quantitative PCR.

    Science.gov (United States)

    Wéry, Nathalie; Lhoutellier, Claire; Ducray, Florence; Delgenès, Jean-Philippe; Godon, Jean-Jacques

    2008-01-01

    Two enteric pathogens, Salmonella spp. and Campylobacter jejuni, and two bacteria commonly used as indicators, Escherichia coli and Clostridium perfringens, were monitored using quantitative real-time PCR during municipal wastewater treatment and sludge composting. The results were compared with those obtained using standard culture methods. A reduction of all bacteria was observed during wastewater treatment and during the thermophilic phase of composting. However, the bacterial groups studied behaved differently during the process, and the main differences were observed during biological treatment in activated sludge basins. In particular, Salmonella spp. and C. jejuni survived better during activated sludge treatment than E. coli. C. jejuni was the most resistant to wastewater treatment among the four bacterial groups. Overall, differences in survival were observed for all bacteria studied, when submitted to the same environmental pressure. This holds both for differences between indicators and pathogenic bacteria and between pathogenic bacteria. These results show the difficulty in defining reliable indicators.

  7. Elevated host lipid metabolism revealed by iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid of tuberculous meningitis patients

    Energy Technology Data Exchange (ETDEWEB)

    Mu, Jun [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Yang, Yongtao [Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing (China); Chen, Jin; Cheng, Ke; Li, Qi; Wei, Yongdong; Zhu, Dan; Shao, Weihua; Zheng, Peng [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Xie, Peng, E-mail: xiepeng@cqmu.edu.cn [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing (China)

    2015-10-30

    Purpose: Tuberculous meningitis (TBM) remains to be one of the most deadly infectious diseases. The pathogen interacts with the host immune system, the process of which is largely unknown. Various cellular processes of Mycobacterium tuberculosis (MTB) centers around lipid metabolism. To determine the lipid metabolism related proteins, a quantitative proteomic study was performed here to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n = 12) and healthy controls (n = 12). Methods: CSF samples were desalted, concentrated, labelled with isobaric tags for relative and absolute quantitation (iTRAQ™), and analyzed by multi-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene ontology and proteomic phenotyping analysis of the differential proteins were conducted using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. ApoE and ApoB were selected for validation by ELISA. Results: Proteomic phenotyping of the 4 differential proteins was invloved in the lipid metabolism. ELISA showed significantly increased ApoB levels in TBM subjects compared to healthy controls. Area under the receiver operating characteristic curve analysis demonstrated ApoB levels could distinguish TBM subjects from healthy controls and viral meningitis subjects with 89.3% sensitivity and 92% specificity. Conclusions: CSF lipid metabolism disregulation, especially elevated expression of ApoB, gives insights into the pathogenesis of TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other center nervous system infectious diseases is required for successful clinical translation. - Highlights: • The first proteomic study on the cerebrospinal fluid of tuberculous meningitis patients using iTRAQ. • Identify 4 differential proteins invloved in the lipid metabolism. • Elevated expression of ApoB gives

  8. Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development.

    Directory of Open Access Journals (Sweden)

    Omer Ziv

    2015-10-01

    Full Text Available Neural stem cells (NSCs are progenitor cells for brain development, where cellular spatial composition (cytoarchitecture and dynamics are hypothesized to be linked to critical NSC capabilities. However, understanding cytoarchitectural dynamics of this process has been limited by the difficulty to quantitatively image brain development in vivo. Here, we study NSC dynamics within Neural Rosettes--highly organized multicellular structures derived from human pluripotent stem cells. Neural rosettes contain NSCs with strong epithelial polarity and are expected to perform apical-basal interkinetic nuclear migration (INM--a hallmark of cortical radial glial cell development. We developed a quantitative live imaging framework to characterize INM dynamics within rosettes. We first show that the tendency of cells to follow the INM orientation--a phenomenon we referred to as radial organization, is associated with rosette size, presumably via mechanical constraints of the confining structure. Second, early forming rosettes, which are abundant with founder NSCs and correspond to the early proliferative developing cortex, show fast motions and enhanced radial organization. In contrast, later derived rosettes, which are characterized by reduced NSC capacity and elevated numbers of differentiated neurons, and thus correspond to neurogenesis mode in the developing cortex, exhibit slower motions and decreased radial organization. Third, later derived rosettes are characterized by temporal instability in INM measures, in agreement with progressive loss in rosette integrity at later developmental stages. Finally, molecular perturbations of INM by inhibition of actin or non-muscle myosin-II (NMII reduced INM measures. Our framework enables quantification of cytoarchitecture NSC dynamics and may have implications in functional molecular studies, drug screening, and iPS cell-based platforms for disease modeling.

  9. Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development.

    Science.gov (United States)

    Ziv, Omer; Zaritsky, Assaf; Yaffe, Yakey; Mutukula, Naresh; Edri, Reuven; Elkabetz, Yechiel

    2015-10-01

    Neural stem cells (NSCs) are progenitor cells for brain development, where cellular spatial composition (cytoarchitecture) and dynamics are hypothesized to be linked to critical NSC capabilities. However, understanding cytoarchitectural dynamics of this process has been limited by the difficulty to quantitatively image brain development in vivo. Here, we study NSC dynamics within Neural Rosettes--highly organized multicellular structures derived from human pluripotent stem cells. Neural rosettes contain NSCs with strong epithelial polarity and are expected to perform apical-basal interkinetic nuclear migration (INM)--a hallmark of cortical radial glial cell development. We developed a quantitative live imaging framework to characterize INM dynamics within rosettes. We first show that the tendency of cells to follow the INM orientation--a phenomenon we referred to as radial organization, is associated with rosette size, presumably via mechanical constraints of the confining structure. Second, early forming rosettes, which are abundant with founder NSCs and correspond to the early proliferative developing cortex, show fast motions and enhanced radial organization. In contrast, later derived rosettes, which are characterized by reduced NSC capacity and elevated numbers of differentiated neurons, and thus correspond to neurogenesis mode in the developing cortex, exhibit slower motions and decreased radial organization. Third, later derived rosettes are characterized by temporal instability in INM measures, in agreement with progressive loss in rosette integrity at later developmental stages. Finally, molecular perturbations of INM by inhibition of actin or non-muscle myosin-II (NMII) reduced INM measures. Our framework enables quantification of cytoarchitecture NSC dynamics and may have implications in functional molecular studies, drug screening, and iPS cell-based platforms for disease modeling.

  10. Quantitative Proteomic and Transcriptomic Study on Autotetraploid Paulownia and Its Diploid Parent Reveal Key Metabolic Processes Associated with Paulownia Autotetraploidization.

    Science.gov (United States)

    Dong, Yanpeng; Deng, Minjie; Zhao, Zhenli; Fan, Guoqiang

    2016-01-01

    Polyploidy plays a very important role in speciation and plant evolution by way of genomic merging and doubling. In the process of polyploidy, rapid genomic, and transcriptomic changes have been observed and researched. However, proteomic divergence caused by the effects of polyploidization is still poorly understood. In the present study, we used iTRAQ coupled with mass spectrometry to quantitatively analyze proteomic changes in the leaves of autotetraploid Paulownia and its diploid parent. A total of 2963 proteins were identified and quantified. Among them, 463 differentially abundant proteins were detected between autotetraploid Paulownia and its diploid parent, and 198 proteins were found to be non-additively abundant in autotetraploid Paulownia, suggesting the presence of non-additive protein regulation during genomic merger and doubling. We also detected 1808 protein-encoding genes in previously published RNA sequencing data. We found that 59 of the genes that showed remarkable changes at mRNA level encoded proteins with consistant changes in their abundance levels, while a further 48 genes that showed noteworthy changes in their expression levels encoded proteins with opposite changes in their abundance levels. Proteins involved in posttranslational modification, protein turnover, and response to stimulus, were significantly enriched among the non-additive proteins, which may provide some of the driving power for variation and adaptation in autopolyploids. Quantitative real-time PCR analysis verified the expression patterns of related protein-coding genes. In addition, we found that the percentage of differentially abundant proteins that matched previously reported differentially expressed genes was relatively low.

  11. Ex vivo measures of muscle mitochondrial capacity reveal quantitative limits of oxygen delivery by the circulation during exercise

    DEFF Research Database (Denmark)

    Boushel, Robert; Saltin, Bengt

    2013-01-01

    of the body mass will be discussed in relation to mitochondrial capacity measured ex vivo. These analyses reveal that as the mass of muscle engaged in exercise increases from one-leg knee extension, to 2-arm cranking, to 2-leg cycling and x-country skiing, the magnitude of blood flow and oxygen delivery...... decrease. Accordingly, a 2-fold higher oxygen delivery and oxygen uptake per unit muscle mass are seen in vivo during 1-leg exercise compared to 2-leg cycling indicating a significant limitation of the circulation during exercise with a large muscle mass. This analysis also reveals that mitochondrial......Muscle mitochondrial respiratory capacity measured ex vivo provides a physiological reference to assess cellular oxidative capacity as a component in the oxygen cascade in vivo. In this article, the magnitude of muscle blood flow and oxygen uptake during exercise involving a small-to-large fraction...

  12. Proteome Differences between Hepatitis B Virus Genotype-B- and Genotype-C-Induced Hepatocellular Carcinoma Revealed by iTRAQ-Based Quantitative Proteomics.

    Science.gov (United States)

    Wei, Dahai; Zeng, Yongyi; Xing, Xiaohua; Liu, Hongzhi; Lin, Minjie; Han, Xiao; Liu, Xiaolong; Liu, Jingfeng

    2016-02-05

    Hepatitis B virus (HBV) is the main cause of hepatocellular carcinoma (HCC) in southeast Asia where HBV genotype B and genotype C are the most prevalent. Viral genotypes have been reported to significantly affect the clinical outcomes of HCC. However, the underlying molecular differences among different genotypes of HBV virus infected HCC have not been revealed. Here, we applied isobaric tags for relative and absolute quantitation (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify the proteome differences between the HBV genotypes B- and C-induced HCC. In brief, a total of 83 proteins in the surrounding noncancerous tissues and 136 proteins in the cancerous tissues between HBV genotype-B- and genotype-C-induced HCC were identified, respectively. This information revealed that there might be different molecular mechanisms of the tumorigenesis and development of HBV genotypes B- and C-induced HCC. Furthermore, our results indicate that the two proteins ARFIP2 and ANXA1 might be potential biomarkers for distinguishing the HBV genotypes B- and C-induced HCC. Thus, the quantitative proteomic analysis revealed molecular differences between the HBV genotypes B- and C-induced HCC, and might provide fundamental information for further deep study.

  13. Quantitative Proteomic Analysis of Mosquito C6/36 Cells Reveals Host Proteins Involved in Zika Virus Infection.

    Science.gov (United States)

    Xin, Qi-Lin; Deng, Cheng-Lin; Chen, Xi; Wang, Jun; Wang, Shao-Bo; Wang, Wei; Deng, Fei; Zhang, Bo; Xiao, Gengfu; Zhang, Lei-Ke

    2017-06-15

    Zika virus (ZIKV) is an emerging arbovirus belonging to the genus Flavivirus of the family Flaviviridae During replication processes, flavivirus manipulates host cell systems to facilitate its replication, while the host cells activate antiviral responses. Identification of host proteins involved in the flavivirus replication process may lead to the discovery of antiviral targets. The mosquitoes Aedes aegypti and Aedes albopictus are epidemiologically important vectors for ZIKV, and effective restrictions of ZIKV replication in mosquitoes will be vital in controlling the spread of virus. In this study, an iTRAQ-based quantitative proteomic analysis of ZIKV-infected Aedes albopictus C6/36 cells was performed to investigate host proteins involved in the ZIKV infection process. A total of 3,544 host proteins were quantified, with 200 being differentially regulated, among which CHCHD2 can be upregulated by ZIKV infection in both mosquito C6/36 and human HeLa cells. Our further study indicated that CHCHD2 can promote ZIKV replication and inhibit beta interferon (IFN-β) production in HeLa cells, suggesting that ZIKV infection may upregulate CHCHD2 to inhibit IFN-I production and thus promote virus replication. Bioinformatics analysis of regulated host proteins highlighted several ZIKV infection-regulated biological processes. Further study indicated that the ubiquitin proteasome system (UPS) plays roles in the ZIKV entry process and that an FDA-approved inhibitor of the 20S proteasome, bortezomib, can inhibit ZIKV infection in vivo Our study illustrated how host cells respond to ZIKV infection and also provided a candidate drug for the control of ZIKV infection in mosquitoes and treatment of ZIKV infection in patients.IMPORTANCE ZIKV infection poses great threats to human health, and there is no FDA-approved drug available for the treatment of ZIKV infection. During replication, ZIKV manipulates host cell systems to facilitate its replication, while host cells activate

  14. On translation equivalence

    Institute of Scientific and Technical Information of China (English)

    石雏凤

    2009-01-01

    Nida's translation theories, especially for his "Dynamic equivalence theory", are highly praised and adopted in Chinese translation circle. Howev-er, there are a lot of criticism and misunderstanding at the same time. This paper explores the issue on translation equivalence so as to benefit our translation studies on both theory and practice level.

  15. Equivalence principles exotica

    Institute of Scientific and Technical Information of China (English)

    C.S. UNNIKRISHNAN; George T. GILLIES

    2008-01-01

    This is a short review of the different prin-ciples of equivalence stated and used in the context of the gravitational interaction. We emphasize the need for precision in stating and differentiating these different equivalence principles, especially in the context of preva-lent confusion regarding the applicability of the weak equivalence principle in quantum mechanics. We discuss several empirical results pertaining to the validity of the equivalence principle in exotic physical sitautions not di-rectly amenable to experimental tests. We conclude with a section on the physical basis of the universal validity of the equivalence principle, as manifest in the universality of free fall, and discuss its link to cosmic gravity.

  16. Quantitative Proteomic Analysis of Mitochondrial Proteins Reveals Pro-Survival Mechanisms in the Perpetuation of Radiation-Induced Genomic Instability

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Stefani N.; Waters, Katrina M.; Morgan, William F.; Yang, Austin; Baulch, Janet E.

    2012-07-26

    Radiation induced genomic instability is a well-studied phenomenon that is measured as mitotically heritable genetic alterations observed in the progeny of an irradiated cell. The mechanisms that perpetuate this instability are unclear, however, a role for chronic oxidative stress has consistently been demonstrated. In the chromosomally unstable LS12 cell line, oxidative stress and genomic instability were correlated with mitochondrial dysfunction. To clarify this mitochondrial dysfunction and gain insight into the mechanisms underlying radiation induced genomic instability we have evaluated the mitochondrial sub-proteome and performed quantitative mass spectrometry (MS) analysis of LS12 cells. Of 98 quantified mitochondrial proteins, 17 met criteria for fold changes and reproducibility; and 11 were statistically significant in comparison with the stable parental GM10115 cell line. Previous observations implicated defects in the electron transport chain (ETC) in the LS12 cell mitochondrial dysfunction. Proteomic analysis supports these observations, demonstrating significantly reduced levels of mitochondrial cytochrome c, the intermediary between complexes III and IV of the ETC. Results also suggest that LS12 cells compensate for ETC dysfunction and oxidative stress through increased levels of tricarboxylic acid cycle enzymes and up-regulation of proteins that protect against oxidative stress and apoptosis. More than one cellular defect is likely to contribute to the genomic instability phenotype. These data suggest that LS12 cells have adapted mechanisms that allow survival under sub-optimal conditions of oxidative stress and compromised mitochondrial function to perpetuate genomic instability.

  17. Quantitative imaging reveals real-time Pou5f3–Nanog complexes driving dorsoventral mesendoderm patterning in zebrafish

    Science.gov (United States)

    Perez-Camps, Mireia; Tian, Jing; Chng, Serene C; Sem, Kai Pin; Sudhaharan, Thankiah; Teh, Cathleen; Wachsmuth, Malte; Korzh, Vladimir; Ahmed, Sohail; Reversade, Bruno

    2016-01-01

    Formation of the three embryonic germ layers is a fundamental developmental process that initiates differentiation. How the zebrafish pluripotency factor Pou5f3 (homologous to mammalian Oct4) drives lineage commitment is unclear. Here, we introduce fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy to assess the formation of Pou5f3 complexes with other transcription factors in real-time in gastrulating zebrafish embryos. We show, at single-cell resolution in vivo, that Pou5f3 complexes with Nanog to pattern mesendoderm differentiation at the blastula stage. Later, during gastrulation, Sox32 restricts Pou5f3–Nanog complexes to the ventrolateral mesendoderm by binding Pou5f3 or Nanog in prospective dorsal endoderm. In the ventrolateral endoderm, the Elabela / Aplnr pathway limits Sox32 levels, allowing the formation of Pou5f3–Nanog complexes and the activation of downstream BMP signaling. This quantitative model shows that a balance in the spatiotemporal distribution of Pou5f3–Nanog complexes, modulated by Sox32, regulates mesendoderm specification along the dorsoventral axis. DOI: http://dx.doi.org/10.7554/eLife.11475.001 PMID:27684073

  18. Cancer-associated p53 tetramerization domain mutants: quantitative analysis reveals a low threshold for tumor suppressor inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Kamada, R.; Anderson, C.; Nomura, T.; Sakaguchi, K.

    2011-01-07

    The tumor suppressor p53, a 393-amino acid transcription factor, induces cell cycle arrest and apoptosis in response to genotoxic stress. Its inactivation via the mutation of its gene is a key step in tumor progression, and tetramer formation is critical for p53 post-translational modification and its ability to activate or repress the transcription of target genes vital in inhibiting tumor growth. About 50% of human tumors have TP53 gene mutations; most are missense ones that presumably lower the tumor suppressor activity of p53. In this study, we explored the effects of known tumor-derived missense mutations on the stability and oligomeric structure of p53; our comprehensive, quantitative analyses encompassed the tetramerization domain peptides representing 49 such substitutions in humans. Their effects on tetrameric structure were broad, and the stability of the mutant peptides varied widely ({Delta}T{sub m} = 4.8 {approx} -46.8 C). Because formation of a tetrameric structure is critical for protein-protein interactions, DNA binding, and the post-translational modification of p53, a small destabilization of the tetrameric structure could result in dysfunction of tumor suppressor activity. We suggest that the threshold for loss of tumor suppressor activity in terms of the disruption of the tetrameric structure of p53 could be extremely low. However, other properties of the tetramerization domain, such as electrostatic surface potential and its ability to bind partner proteins, also may be important.

  19. Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes

    Directory of Open Access Journals (Sweden)

    David Llères

    2017-02-01

    Full Text Available How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer-based fluorescence lifetime imaging microscopy (FLIM approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells. Using RNAi and repetitive extrachromosomal array approaches, we defined the heterochromatin state and showed that its architecture presents a nanoscale-compacted organization controlled by Heterochromatin Protein-1 (HP1 and SETDB1 H3-lysine-9 methyltransferase homologs in vivo. Next, we functionally explored condensin complexes. We found that condensin I and condensin II are essential for heterochromatin compaction and that condensin I additionally controls lowly compacted regions. Our data show that, in living animals, nanoscale chromatin compaction is controlled not only by histone modifiers and readers but also by condensin complexes.

  20. Quantitative Label-Free Phosphoproteomics Reveals Differentially Regulated Protein Phosphorylation Involved in West Nile Virus-Induced Host Inflammatory Response.

    Science.gov (United States)

    Zhang, Hao; Sun, Jun; Ye, Jing; Ashraf, Usama; Chen, Zheng; Zhu, Bibo; He, Wen; Xu, Qiuping; Wei, Yanming; Chen, Huanchun; Fu, Zhen F; Liu, Rong; Cao, Shengbo

    2015-12-01

    West Nile virus (WNV) can cause neuro-invasive and febrile illness that may be fatal to humans. The production of inflammatory cytokines is key to mediating WNV-induced immunopathology in the central nervous system. Elucidating the host factors utilized by WNV for productive infection would provide valuable insights into the evasion strategies used by this virus. Although attempts have been made to determine these host factors, proteomic data depicting WNV-host protein interactions are limited. We applied liquid chromatography-tandem mass spectrometry for label-free, quantitative phosphoproteomics to systematically investigate the global phosphorylation events induced by WNV infection. Quantifiable changes to 1,657 phosphoproteins were found; of these, 626 were significantly upregulated and 227 were downregulated at 12 h postinfection. The phosphoproteomic data were subjected to gene ontology enrichment analysis, which returned the inflammation-related spliceosome, ErbB, mitogen-activated protein kinase, nuclear factor kappa B, and mechanistic target of rapamycin signaling pathways. We used short interfering RNAs to decrease the levels of glycogen synthase kinase-3 beta, bifunctional polynucleotide phosphatase/kinase, and retinoblastoma 1 and found that the activity of nuclear factor kappa B (p65) is significantly decreased in WNV-infected U251 cells, which in turn led to markedly reduced inflammatory cytokine production. Our results provide a better understanding of the host response to WNV infection and highlight multiple targets for the development of antiviral and anti-inflammatory therapies.

  1. Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions.

    Science.gov (United States)

    Basnet, Ram K; Duwal, Anita; Tiwari, Dev N; Xiao, Dong; Monakhos, Sokrat; Bucher, Johan; Visser, Richard G F; Groot, Steven P C; Bonnema, Guusje; Maliepaard, Chris

    2015-01-01

    The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.

  2. Quantitative mass spectrometry analysis reveals similar substrate consensus motif for human Mps1 kinase and Plk1.

    Directory of Open Access Journals (Sweden)

    Zhen Dou

    Full Text Available BACKGROUND: Members of the Mps1 kinase family play an essential and evolutionarily conserved role in the spindle assembly checkpoint (SAC, a surveillance mechanism that ensures accurate chromosome segregation during mitosis. Human Mps1 (hMps1 is highly phosphorylated during mitosis and many phosphorylation sites have been identified. However, the upstream kinases responsible for these phosphorylations are not presently known. METHODOLOGY/PRINCIPAL FINDINGS: Here, we identify 29 in vivo phosphorylation sites in hMps1. While in vivo analyses indicate that Aurora B and hMps1 activity are required for mitotic hyper-phosphorylation of hMps1, in vitro kinase assays show that Cdk1, MAPK, Plk1 and hMps1 itself can directly phosphorylate hMps1. Although Aurora B poorly phosphorylates hMps1 in vitro, it positively regulates the localization of Mps1 to kinetochores in vivo. Most importantly, quantitative mass spectrometry analysis demonstrates that at least 12 sites within hMps1 can be attributed to autophosphorylation. Remarkably, these hMps1 autophosphorylation sites closely resemble the consensus motif of Plk1, demonstrating that these two mitotic kinases share a similar substrate consensus. CONCLUSIONS/SIGNIFICANCE: hMps1 kinase is regulated by Aurora B kinase and its autophosphorylation. Analysis on hMps1 autophosphorylation sites demonstrates that hMps1 has a substrate preference similar to Plk1 kinase.

  3. Fusion-related host proteins are actively regulated by NA during influenza infection as revealed by quantitative proteomics analysis.

    Directory of Open Access Journals (Sweden)

    Zhiwei Sui

    Full Text Available Three recombinant influenza A viruses with different neuraminidases (NAs in the background of A/PR/8/34 (PR8, named rPR8-H5N1NA, rPR8-H9N2NA, and rPR8-H1N1NA, derived from H5N1, H9N2, H1N1 (swine viruses, respectively, were constructed. We performed a quantitative proteomics analysis to investigate differential protein expression in Madin-Darby canine kidney (MDCK cells infected with recombinant and wild-type influenza viruses to determine whether NA replacement would alter host cell gene expression. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-TOF MS and two-dimensional gel electrophoresis (2-DE, we identified 12 up-regulated and 49 down-regulated protein spots, including cytoskeletal proteins, molecular biosynthesis proteins, ubiquitin-proteasome pathway proteins, and heat shock proteins. The most significant changes in infected cells were observed for molecular biosynthesis proteins. We found more differentially expressed protein spots in cells infected with rPR8-H5N1NA or rPR8-H9N2NA viruses than cells infected with wild-type virus. Many of those proteins are postulated to be involved in cell-cell fusion, but the full mechanism remains to be explored. Meanwhile, our data demonstrate that the wild-type virus has evolutionary advantages over recombinant viruses.

  4. Quantitative analysis reveals asynchronous and more than DSB-associated histone H2AX phosphorylation after exposure to ionizing radiation.

    Science.gov (United States)

    Han, Jianxun; Hendzel, Michael J; Allalunis-Turner, Joan

    2006-03-01

    Rapid phosphorylation of histone H2AX after exposure of cells to ionizing radiation occurs at DSB sites and extends to a region including as much as 30 Mbp of chromatin to form visible microscopic structures called gamma-H2AX foci. Although the kinetics of total cellular histone H2AX phosphorylation after irradiation has been characterized, we still know little about the phosphorylation kinetics of individual gamma-H2AX foci. In addition, there are hundreds of smaller gamma-H2AX foci that are not associated with DNA double-strand breaks. We refer to these sites as DSB-unrelated gamma-H2AX foci. By using indirect immunofluorescence microscopy, deconvolution and three-dimensional image analysis, we established an objective method to quantitatively analyze each gamma-H2AX focus as well as to discriminate DSB-related gamma-H2AX foci from DSB-unrelated gamma-H2AX foci. Using this method, we found that histone H2AX phosphorylation at different DSB sites was asynchronous after exposure to ionizing radiation. This may reflect the heterogeneous characteristic of free DNA ends that are generated under these conditions. In addition, we found that increased histone H2AX phosphorylation also occurred outside of DSB sites after exposure to ionizing radiation. The function of this DSB-unassociated phosphorylation is not known.

  5. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    Energy Technology Data Exchange (ETDEWEB)

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak P.; Woodruff, Teresa K.; O' Halloran, Thomas V.

    2014-12-15

    Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes

  6. New insights into the diets of harbor seals in the Salish Sea revealed by quantitative fatty acid signature analysis

    Science.gov (United States)

    Bromaghin, Jeffrey F.; Lance, Monique M.; Elliott, Elizabeth W.; Jeffries, Steven J.; Acevedo-Gutiérrez, Alejandro; Kennish, John M.

    2012-01-01

    Harbor seals (Phoca vitulina) are an abundant predator along the west coast of North America, and there is considerable interest in their diet composition, especially in regard to predation on valued fish stocks. Available information on harbor seal diets, primarily derived from scat analysis, suggests that adult salmon (Oncorhynchus spp.), Pacific Herring (Clupea pallasii), and gadids predominate. Because diet assessments based on scat analysis may be biased, we investigated diet composition through quantitative analysis of fatty acid signatures. Blubber samples from 49 harbor seals captured in western North America from haul-outs within the area of the San Juan Islands and southern Strait of Georgia in the Salish Sea were analyzed for fatty acid composition, along with 269 fish and squid specimens representing 27 potential prey classes. Diet estimates varied spatially, demographically, and among individual harbor seals. Findings confirmed the prevalence of previously identified prey species in harbor seal diets, but other species also contributed significantly. In particular, Black (Sebastes melanops) and Yellowtail (S. flavidus) Rockfish were estimated to compose up to 50% of some individual seal diets. Specialization and high predation rates on Black and Yellowtail Rockfish by a subset of harbor seals may play a role in the population dynamics of these regional rockfish stocks that is greater than previously realized.

  7. The Pseudomonas community in metal-contaminated sediments as revealed by quantitative PCR: a link with metal bioavailability.

    Science.gov (United States)

    Roosa, Stéphanie; Wauven, Corinne Vander; Billon, Gabriel; Matthijs, Sandra; Wattiez, Ruddy; Gillan, David C

    2014-10-01

    Pseudomonas bacteria are ubiquitous Gram-negative and aerobic microorganisms that are known to harbor metal resistance mechanisms such as efflux pumps and intracellular redox enzymes. Specific Pseudomonas bacteria have been quantified in some metal-contaminated environments, but the entire Pseudomonas population has been poorly investigated under these conditions, and the link with metal bioavailability was not previously examined. In the present study, quantitative PCR and cell cultivation were used to monitor and characterize the Pseudomonas population at 4 different sediment sites contaminated with various levels of metals. At the same time, total metals and metal bioavailability (as estimated using an HCl 1 m extraction) were measured. It was found that the total level of Pseudomonas, as determined by qPCR using two different genes (oprI and the 16S rRNA gene), was positively and significantly correlated with total and HCl-extractable Cu, Co, Ni, Pb and Zn, with high correlation coefficients (>0.8). Metal-contaminated sediments featured isolates of the Pseudomonas putida, Pseudomonas fluorescens, Pseudomonas lutea and Pseudomonas aeruginosa groups, with other bacterial genera such as Mycobacterium, Klebsiella and Methylobacterium. It is concluded that Pseudomonas bacteria do proliferate in metal-contaminated sediments, but are still part of a complex community.

  8. Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles.

    Directory of Open Access Journals (Sweden)

    Yvonne Förster

    Full Text Available Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.

  9. Quantitative phosphoproteomic analysis reveals system-wide signaling pathways downstream of SDF-1/CXCR4 in breast cancer stem cells.

    Science.gov (United States)

    Yi, Tingfang; Zhai, Bo; Yu, Yonghao; Kiyotsugu, Yoshikawa; Raschle, Thomas; Etzkorn, Manuel; Seo, Hee-Chan; Nagiec, Michal; Luna, Rafael E; Reinherz, Ellis L; Blenis, John; Gygi, Steven P; Wagner, Gerhard

    2014-05-27

    Breast cancer is the leading cause of cancer-related mortality in women worldwide, with an estimated 1.7 million new cases and 522,000 deaths around the world in 2012 alone. Cancer stem cells (CSCs) are essential for tumor reoccurrence and metastasis which is the major source of cancer lethality. G protein-coupled receptor chemokine (C-X-C motif) receptor 4 (CXCR4) is critical for tumor metastasis. However, stromal cell-derived factor 1 (SDF-1)/CXCR4-mediated signaling pathways in breast CSCs are largely unknown. Using isotope reductive dimethylation and large-scale MS-based quantitative phosphoproteome analysis, we examined protein phosphorylation induced by SDF-1/CXCR4 signaling in breast CSCs. We quantified more than 11,000 phosphorylation sites in 2,500 phosphoproteins. Of these phosphosites, 87% were statistically unchanged in abundance in response to SDF-1/CXCR4 stimulation. In contrast, 545 phosphosites in 266 phosphoproteins were significantly increased, whereas 113 phosphosites in 74 phosphoproteins were significantly decreased. SDF-1/CXCR4 increases phosphorylation in 60 cell migration- and invasion-related proteins, of them 43 (>70%) phosphoproteins are unrecognized. In addition, SDF-1/CXCR4 upregulates the phosphorylation of 44 previously uncharacterized kinases, 8 phosphatases, and 1 endogenous phosphatase inhibitor. Using computational approaches, we performed system-based analyses examining SDF-1/CXCR4-mediated phosphoproteome, including construction of kinase-substrate network and feedback regulation loops downstream of SDF-1/CXCR4 signaling in breast CSCs. We identified a previously unidentified SDF-1/CXCR4-PKA-MAP2K2-ERK signaling pathway and demonstrated the feedback regulation on MEK, ERK1/2, δ-catenin, and PPP1Cα in SDF-1/CXCR4 signaling in breast CSCs. This study gives a system-wide view of phosphorylation events downstream of SDF-1/CXCR4 signaling in breast CSCs, providing a resource for the study of CSC-targeted cancer therapy.

  10. Asynchrony of the early maturation of white matter bundles in healthy infants: Quantitative landmarks revealed noninvasively by diffusion tensor imaging

    Energy Technology Data Exchange (ETDEWEB)

    Dubois, J.; Perrin, M.; Mangin, J.F.; Cointepas, Y.; Duchesnay, E.; Le Bihan, D.; Hertz-Pannier, L. [CEA, Serv Hosp Frederic Joliot, UNAF, F-91406 Orsay (France); Dehaene-Lambertz, G. [INSERM, U562, Orsay (France); Dubois, J.; Dehaene-Lambertz, G.; Perrin, M.; Mangin, J.F.; Cointepas, Y.; Duchesnay, E.; Le Bihan, D.; Hertz-Pannier, L. [IFR49, Paris (France)

    2008-07-01

    Normal cognitive development in infants follows a well-known temporal sequence, which is assumed to be correlated with the structural maturation of underlying functional networks. Postmortem studies and, more recently, structural MR imaging studies have described qualitatively the heterogeneous spatio-temporal progression of white matter myelination. However, in vivo quantification of the maturation phases of fiber bundles is still lacking. We used noninvasive diffusion tensor MR imaging and tractography in twenty-three 1-4-month-old healthy infants to quantify the early maturation of the main cerebral fascicles. A specific maturation model, based on the respective roles of different maturational processes on the diffusion phenomena, was designed to highlight asynchronous maturation across bundles by evaluating the time-course of mean diffusivity and anisotropy changes over the considered developmental period. Using an original approach, a progression of maturation in four relative stages was determined in each tract by estimating the maturation state and speed, from the diffusion indices over the infants group compared with an adults group on one hand, and in each tract compared with the average over bundles on the other hand. Results were coherent with, and extended previous findings in 8 of 11 bundles, showing the anterior limb of the internal capsule and cingulum as the most immature, followed by the optic radiations, arcuate and inferior longitudinal fascicles, then the spino-thalamic tract and fornix, and finally the cortico-spinal tract as the most mature bundle. Thus, this approach provides new quantitative landmarks for further noninvasive research on brain-behavior relationships during normal and abnormal development. (authors)

  11. The CesA gene family of barley. Quantitative analysis of transcripts reveals two groups of co-expressed genes.

    Science.gov (United States)

    Burton, Rachel A; Shirley, Neil J; King, Brendon J; Harvey, Andrew J; Fincher, Geoffrey B

    2004-01-01

    Sequence data from cDNA and genomic clones, coupled with analyses of expressed sequence tag databases, indicate that the CesA (cellulose synthase) gene family from barley (Hordeum vulgare) has at least eight members, which are distributed across the genome. Quantitative polymerase chain reaction has been used to determine the relative abundance of mRNA transcripts for individual HvCesA genes in vegetative and floral tissues, at different stages of development. To ensure accurate expression profiling, geometric averaging of multiple internal control gene transcripts has been applied for the normalization of transcript abundance. Total HvCesA mRNA levels are highest in coleoptiles, roots, and stems and much lower in floral tissues, early developing grain, and in the elongation zone of leaves. In most tissues, HvCesA1, HvCesA2, and HvCesA6 predominate, and their relative abundance is very similar; these genes appear to be coordinately transcribed. A second group, comprising HvCesA4, HvCesA7, and HvCesA8, also appears to be coordinately transcribed, most obviously in maturing stem and root tissues. The HvCesA3 expression pattern does not fall into either of these two groups, and HvCesA5 transcript levels are extremely low in all tissues. Thus, the HvCesA genes fall into two general groups of three genes with respect to mRNA abundance, and the co-expression of the groups identifies their products as candidates for the rosettes that are involved in cellulose biosynthesis at the plasma membrane. Phylogenetic analysis allows the two groups of genes to be linked with orthologous Arabidopsis CesA genes that have been implicated in primary and secondary wall synthesis.

  12. Quantitative magnetic resonance analysis and a morphometric predictive model reveal lean body mass changes in migrating Nearctic-Neotropical passerines.

    Science.gov (United States)

    Seewagen, Chad L; Guglielmo, Christopher G

    2011-04-01

    Most studies of lean mass dynamics in free-living passerine birds have focused on Old World species at geographical barriers where they are challenged to make the longest non-stop flight of their migration. We examined lean mass variation in New World passerines in an area where the distribution of stopover habitat does not require flights to exceed more than a few hours and most migrants stop flying well before fat stores near exhaustion. We used either quantitative magnetic resonance (QMR) analysis or a morphometric model to measure or estimate, respectively, the fat and lean body mass of migrants during stopovers in New York, USA. With these data, we examined (1) variance in total body mass explained by lean body mass, (2) hourly rates of fat and lean body mass change in single-capture birds, and (3) net changes in fat and lean mass in recaptured birds. Lean mass contributed to 50% of the variation in total body mass among white-throated sparrows Zonotrichia albicollis and hermit thrushes Catharus guttatus. Lean mass of refueling gray catbirds Dumetella carolinensis and white-throated sparrows, respectively, increased 1.123 and 0.320 g h(-1). Lean mass of ovenbirds Seiurus aurocapillus accounted for an estimated 33-40% of hourly gains in total body mass. On average 35% of the total mass gained among recaptured birds was lean mass. Substantial changes in passerine lean mass are not limited to times when birds are forced to make long, non-stop flights across barriers. Protein usage during migration is common across broad taxonomic groups, migration systems, and migration strategies.

  13. iTRAQ-based quantitative proteomics of stratum corneum of dandruff scalp reveals new insights into its aetiology and similarities with atopic dermatitis.

    Science.gov (United States)

    Cavusoglu, Nükhet; Delattre, Caroline; Donovan, Mark; Bourassa, Sylvie; Droit, Arnaud; El Rawadi, Charles; Jourdain, Roland; Bernard, Dominique

    2016-11-01

    The study aimed at detecting differentially expressed proteins in the stratum corneum of dandruff versus non-dandruff scalps to better understand dandruff aetiology. iTRAQ-based quantitative proteomic analysis revealed a total of 68 differentially expressed biomarkers. A detailed analysis of their known physiological functions provided new insights into the affected metabolic pathways of a dandruff scalp. Dandruff scalp showed (1) profound changes in the expression and maturation of structural and epidermal differentiation related proteins, that are responsible for the integrity of the skin, (2) altered relevant factors that regulate skin hydration, and (3) an imbalanced physiological protease-protease inhibitor ratio. Stratum corneum proteins with antimicrobial activity, mainly those derived from sweat and sebaceous glands were also found modified. Comparing our data with those reported for atopic dermatitis revealed that about 50 % of the differentially expressed proteins in the superficial layers of the stratum corneum from dandruff and atopic dermatitis are identical.

  14. Quantitative lipidomics reveals age-dependent perturbations of whole-body lipid metabolism in ACBP deficient mice

    DEFF Research Database (Denmark)

    Gallego, Sandra F; Sprenger, Richard R; Neess, Ditte

    2017-01-01

    and delayed weaning, the physiological process where newborns transit from a fat-based milk diet to a carbohydrate-rich diet. To gain insights into how ACBP impinges on weaning and the concomitant remodeling of whole-body lipid metabolism we performed a comparative lipidomics analysis charting the absolute......The acyl-CoA binding protein (ACBP) plays a key role in chaperoning long-chain acyl-CoAs into lipid metabolic processes and acts as an important regulatory hub in mammalian physiology. This is highlighted by the recent finding that mice devoid of ACBP suffer from a compromised epidermal barrier...... abundance of 613 lipid molecules in liver, muscle and plasma from weaning and adult Acbp knockout and wild type mice. Our results reveal that ACBP deficiency affects primarily lipid metabolism of liver and plasma during weaning. Specifically, we show that ACBP deficient mice have elevated levels of hepatic...

  15. Quantitative lipidomics reveals age-dependent perturbations of whole-body lipid metabolism in ACBP deficient mice

    DEFF Research Database (Denmark)

    Gallego, Sandra Fernandez; Sprenger, Richard; Neess, Ditte;

    2016-01-01

    The acyl-CoA binding protein (ACBP) plays a key role in chaperoning long-chain acyl-CoAs into lipid metabolic processes and acts as an important regulatory hub in mammalian physiology. This is highlighted by the recent finding that mice devoid of ACBP suffer from a compromised epidermal barrier...... and delayed weaning, the physiological process where newborns transit from a fat-based milk diet to a carbohydrate-rich diet. To gain insights into how ACBP impinges on weaning and the concomitant remodeling of whole-body lipid metabolism we performed a comparative lipidomics analysis charting the absolute...... abundance of 613 lipid molecules in liver, muscle and plasma from weaning and adult Acbp knockout and wild type mice. Our results reveal that ACBP deficiency affects primarily lipid metabolism of liver and plasma during weaning. Specifically, we show that ACBP deficient mice have elevated levels of hepatic...

  16. Quantitative analysis of Nipah virus proteins released as virus-like particles reveals central role for the matrix protein

    Directory of Open Access Journals (Sweden)

    Eaton Bryan T

    2007-01-01

    Full Text Available Abstract Background Nipah virus (NiV is an emerging paramyxovirus distinguished by its ability to cause fatal disease in both animal and human hosts. Together with Hendra virus (HeV, they comprise the genus Henipavirus in the Paramyxoviridae family. NiV and HeV are also restricted to Biosafety Level-4 containment and this has hampered progress towards examining details of their replication and morphogenesis. Here, we have established recombinant expression systems to study NiV particle assembly and budding through the formation of virus-like particles (VLPs. Results When expressed by recombinant Modified Vaccinia virus Ankara (rMVA or plasmid transfection, individual NiV matrix (M, fusion (F and attachment (G proteins were all released into culture supernatants in a membrane-associated state as determined by sucrose density gradient flotation and immunoprecipitation. However, co-expression of F and G along with M revealed a shift in their distribution across the gradient, indicating association with M in VLPs. Protein release was also altered depending on the context of viral proteins being expressed, with F, G and nucleocapsid (N protein reducing M release, and N release dependent on the co-expression of M. Immunoelectron microscopy and density analysis revealed VLPs that were similar to authentic virus. Differences in the budding dynamics of NiV proteins were also noted between rMVA and plasmid based strategies, suggesting that over-expression by poxvirus may not be appropriate for studying the details of recombinant virus particle assembly and release. Conclusion Taken together, the results indicate that NiV M, F, and G each possess some ability to bud from expressing cells, and that co-expression of these viral proteins results in a more organized budding process with M playing a central role. These findings will aid our understanding of paramyxovirus particle assembly in general and could help facilitate the development of a novel vaccine

  17. A quantitative multiplex nuclease protection assay reveals immunotoxicity gene expression profiles in the rabbit model for vaginal drug safety evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Fichorova, Raina N., E-mail: rfichorova@rics.bwh.harvard.edu [Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States); Mendonca, Kevin; Yamamoto, Hidemi S.; Murray, Ryan [Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States); Chandra, Neelima; Doncel, Gustavo F. [CONRAD, Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, VA (United States)

    2015-06-15

    Any vaginal product that alters the mucosal environment and impairs the immune barrier increases the risk of sexually transmitted infections, especially HIV infection, which thrives on mucosal damage and inflammation. The FDA-recommended rabbit vaginal irritation (RVI) model serves as a first line selection tool for vaginal products; however, for decades it has been limited to histopathology scoring, insufficient to select safe anti-HIV microbicides. In this study we incorporate to the RVI model a novel quantitative nuclease protection assay (qNPA) to quantify mRNA levels of 25 genes representing leukocyte differentiation markers, toll-like receptors (TLR), cytokines, chemokines, epithelial repair, microbicidal and vascular markers, by designing two multiplex arrays. Tissue sections were obtained from 36 rabbits (6 per treatment arm) after 14 daily applications of a placebo gel, saline, 4% nonoxynol-9 (N-9), and three combinations of the anti-HIV microbicides tenofovir (TFV) and UC781 in escalating concentrations (highest: 10% TFV + 2.5%UC781). Results showed that increased expression levels of toll-like receptor (TLR)-4, interleukin (IL)-1β, CXCL8, epithelial membrane protein (EMP)-1 (P < 0.05), and decreased levels of TLR2 (P < 0.05), TLR3 and bactericidal permeability increasing protein (BPI) (P < 0.001) were associated with cervicovaginal mucosal alteration (histopathology). Seven markers showed a significant linear trend predicting epithelial damage (up with CD4, IL-1β, CXCL8, CCL2, CCL21, EMP1 and down with BPI). Despite the low tissue damage RVI scores, the high-dose microbicide combination gel caused activation of HIV host cells (SLC and CD4) while N-9 caused proinflammatory gene upregulation (IL-8 and TLR4) suggesting a potential for increasing risk of HIV via different mechanisms depending on the chemical nature of the test product. - Highlights: • A transcriptome nuclease protection assay assessed microbicides for vaginal safety. • Biomarkers were

  18. Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue

    Directory of Open Access Journals (Sweden)

    Woodfine Kathryn

    2011-01-01

    Full Text Available Abstract Background Genes subject to genomic imprinting are mono-allelically expressed in a parent-of-origin dependent manner. Each imprinted locus has at least one differentially methylated region (DMR which has allele specific DNA methylation and contributes to imprinted gene expression. Once DMRs are established, they are potentially able to withstand normal genome reprogramming events that occur during cell differentiation and germ-line DMRs are stably maintained throughout development. These DMRs, in addition to being either maternally or paternally methylated, have differences in whether methylation was acquired in the germ-line or post fertilization and are present in a variety of genomic locations with different Cytosine-phosphate guanine (CpG densities and CTCF binding capacities. We therefore examined the stability of maintenance of DNA methylation imprints and determined the normal baseline DNA methylation levels in several adult tissues for all imprinted genes. In order to do this, we first developed and validated 50 highly specific, quantitative DNA methylation pyrosequencing assays for the known DMRs associated with human imprinted genes. Results Remarkable stability of the DNA methylation imprint was observed in all germ-line DMRs and paternally methylated somatic DMRs (which maintained average methylation levels of between 35% - 65% in all somatic tissues, independent of gene expression. Maternally methylated somatic DMRs were found to have more variation with tissue specific methylation patterns. Most DMRs, however, showed some intra-individual variability for DNA methylation levels in peripheral blood, suggesting that more than one DMR needs to be examined in order to get an overall impression of the epigenetic stability in a tissue. The plasticity of DNA methylation at imprinted genes was examined in a panel of normal and cancer cell lines. All cell lines showed changes in DNA methylation, especially at the paternal germ

  19. Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling.

    Science.gov (United States)

    Kauko, Otto; Laajala, Teemu Daniel; Jumppanen, Mikael; Hintsanen, Petteri; Suni, Veronika; Haapaniemi, Pekka; Corthals, Garry; Aittokallio, Tero; Westermarck, Jukka; Imanishi, Susumu Y

    2015-08-17

    Hyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set, and synergistic relationship between CIP2A and KRAS depletion in colony growth assays.

  20. Quantitative lipidomics reveals age-dependent perturbations of whole-body lipid metabolism in ACBP deficient mice.

    Science.gov (United States)

    Gallego, Sandra F; Sprenger, Richard R; Neess, Ditte; Pauling, Josch K; Færgeman, Nils J; Ejsing, Christer S

    2017-02-01

    The acyl-CoA binding protein (ACBP) plays a key role in chaperoning long-chain acyl-CoAs into lipid metabolic processes and acts as an important regulatory hub in mammalian physiology. This is highlighted by the recent finding that mice devoid of ACBP suffer from a compromised epidermal barrier and delayed weaning, the physiological process where newborns transit from a fat-based milk diet to a carbohydrate-rich diet. To gain insights into how ACBP impinges on weaning and the concomitant remodeling of whole-body lipid metabolism we performed a comparative lipidomics analysis charting the absolute abundance of 613 lipid molecules in liver, muscle and plasma from weaning and adult Acbp knockout and wild type mice. Our results reveal that ACBP deficiency affects primarily lipid metabolism of liver and plasma during weaning. Specifically, we show that ACBP deficient mice have elevated levels of hepatic cholesteryl esters, and that lipids featuring an 18:1 fatty acid moiety are increased in Acbp depleted mice across all tissues investigated. Our results also show that the perturbation of systemic lipid metabolism in Acbp knockout mice is transient and becomes normalized and similar to that of wild type as mice grow older. These findings demonstrate that ACBP serves crucial functions in maintaining lipid metabolic homeostasis in mice during weaning.

  1. Quantitative superresolution microscopy reveals differences in nuclear DNA organization of multiple myeloma and monoclonal gammopathy of undetermined significance.

    Science.gov (United States)

    Sathitruangsak, Chirawadee; Righolt, Christiaan H; Klewes, Ludger; Tammur, Pille; Ilus, Tiiu; Tamm, Anu; Punab, Mari; Olujohungbe, Adebayo; Mai, Sabine

    2015-05-01

    The mammalian nucleus has a distinct substructure that cannot be visualized directly by conventional microscopy. In this study, the organization of the DNA within the nucleus of multiple myeloma (MM) cells, their precursor cells (monoclonal gammopathy of undetermined significance; MGUS) and control lymphocytes of the representative patients is visualized and quantified by superresolution microscopy. Three-dimensional structured illumination microscopy (3D-SIM) increases the spatial resolution beyond the limits of conventional widefield fluorescence microscopy. 3D-SIM reveals new insights into the nuclear architecture of cancer as we show for the first time that it resolves organizational differences in intranuclear DNA organization of myeloma cells in MGUS and in MM patients. In addition, we report a significant increase in nuclear submicron DNA structure and structure of the DNA-free space in myeloma nuclei compared to normal lymphocyte nuclei. Our study provides previously unknown details of the nanoscopic DNA architecture of interphase nuclei of the normal lymphocytes, MGUS and MM cells. This study opens new avenues to understanding the disease progression from MGUS to MM. © 2014 Wiley Periodicals, Inc.

  2. Topics in orbit equivalence

    CERN Document Server

    Kechris, Alexander S

    2004-01-01

    This volume provides a self-contained introduction to some topics in orbit equivalence theory, a branch of ergodic theory. The first two chapters focus on hyperfiniteness and amenability. Included here are proofs of Dye's theorem that probability measure-preserving, ergodic actions of the integers are orbit equivalent and of the theorem of Connes-Feldman-Weiss identifying amenability and hyperfiniteness for non-singular equivalence relations. The presentation here is often influenced by descriptive set theory, and Borel and generic analogs of various results are discussed. The final chapter is a detailed account of Gaboriau's recent results on the theory of costs for equivalence relations and groups and its applications to proving rigidity theorems for actions of free groups.

  3. Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level.

    Science.gov (United States)

    Smati, Mounira; Clermont, Olivier; Bleibtreu, Alexandre; Fourreau, Frédéric; David, Anthony; Daubié, Anne-Sophie; Hignard, Cécile; Loison, Odile; Picard, Bertrand; Denamur, Erick

    2015-08-01

    The primary habitat of the Escherichia coli species is the gut of warm-blooded vertebrates. The E. coli species is structured into four main phylogenetic groups A, B1, B2, and D. We estimated the relative proportions of these phylogroups in the feces of 137 wild and domesticated animals with various diets living in the Ile de France (Paris) region by real-time PCR. We distinguished three main clusters characterized by a particular abundance of two or more phylogroups within the E. coli animal commensal populations, which we called "enterocolitypes" by analogy with the enterotypes defined in the human gut microbiota at the genus level. These enterocolitypes were characterized by a dominant (>50%) B2, B1, or A phylogroup and were associated with different host species, diets, and habitats: wild and herbivorous species (wild rabbits and deer), domesticated herbivorous species (domesticated rabbits, horses, sheep, and cows), and omnivorous species (boar, pigs, and chickens), respectively. By analyzing retrospectively the data obtained using the same approach from 98 healthy humans living in Ile de France (Smati et al. 2013, Appl. Environ. Microbiol. 79, 5005-5012), we identified a specific human enterocolitype characterized by the dominant and/or exclusive (>90%) presence of phylogroup B2. We then compared B2 strains isolated from animals and humans, and revealed that human and animal strains differ regarding O-type and B2 subgroup. Moreover, two genes, sfa/foc and clbQ, were associated with the exclusive character of strains, observed only in humans. In conclusion, a complex network of interactions exists at several levels (genus and intra-species) within the intestinal microbiota. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  4. Real-time PCR for quantitative analysis of human commensal Escherichia coli populations reveals a high frequency of subdominant phylogroups.

    Science.gov (United States)

    Smati, Mounira; Clermont, Olivier; Le Gal, Frédéric; Schichmanoff, Olivier; Jauréguy, Françoise; Eddi, Alain; Denamur, Erick; Picard, Bertrand

    2013-08-01

    Escherichia coli is divided into four main phylogenetic groups, which each exhibit ecological specialization. To understand the population structure of E. coli in its primary habitat, we directly assessed the relative proportions of these phylogroups from the stools of 100 healthy human subjects using a new real-time PCR method, which allows a large number of samples to be studied. The detection threshold for our technique was 0.1% of the E. coli population, i.e., 10(5) CFU/g of feces; in other methods based on individual colony analysis, the threshold is 10%. One, two, three, or four phylogenetic groups were simultaneously found in 21%, 48%, 21%, and 8% of the subjects, respectively. Phylogroups present at a threshold of less than 10% of the population were found in 40% of the subjects, revealing high within-individual diversity. Phylogroups A and B2 were detected in 74% and 70% of the subjects, respectively; phylogroups B1 and D were detected in 36% and 32%, respectively. When phylogroup B2 was dominant, it tended not to cooccur with other phylogroups. In contrast, other phylogroups were present when phylogroup A was dominant. These data indicate a complex pattern of interactions between the members of a single species within the human gut and identify a reservoir of clones that are present at a low frequency. The presence of these minor clones could explain the fluctuation in the composition of the E. coli microbiota within single individuals that may be seen over time. They could also constitute reservoirs of virulent and/or resistant strains.

  5. CeleST: computer vision software for quantitative analysis of C. elegans swim behavior reveals novel features of locomotion.

    Science.gov (United States)

    Restif, Christophe; Ibáñez-Ventoso, Carolina; Vora, Mehul M; Guo, Suzhen; Metaxas, Dimitris; Driscoll, Monica

    2014-07-01

    In the effort to define genes and specific neuronal circuits that control behavior and plasticity, the capacity for high-precision automated analysis of behavior is essential. We report on comprehensive computer vision software for analysis of swimming locomotion of C. elegans, a simple animal model initially developed to facilitate elaboration of genetic influences on behavior. C. elegans swim test software CeleST tracks swimming of multiple animals, measures 10 novel parameters of swim behavior that can fully report dynamic changes in posture and speed, and generates data in several analysis formats, complete with statistics. Our measures of swim locomotion utilize a deformable model approach and a novel mathematical analysis of curvature maps that enable even irregular patterns and dynamic changes to be scored without need for thresholding or dropping outlier swimmers from study. Operation of CeleST is mostly automated and only requires minimal investigator interventions, such as the selection of videotaped swim trials and choice of data output format. Data can be analyzed from the level of the single animal to populations of thousands. We document how the CeleST program reveals unexpected preferences for specific swim "gaits" in wild-type C. elegans, uncovers previously unknown mutant phenotypes, efficiently tracks changes in aging populations, and distinguishes "graceful" from poor aging. The sensitivity, dynamic range, and comprehensive nature of CeleST measures elevate swim locomotion analysis to a new level of ease, economy, and detail that enables behavioral plasticity resulting from genetic, cellular, or experience manipulation to be analyzed in ways not previously possible.

  6. Quantitative morphometry of electrophysiologically identified CA3b interneurons reveals robust local geometry and distinct cell classes.

    Science.gov (United States)

    Ascoli, Giorgio A; Brown, Kerry M; Calixto, Eduardo; Card, J Patrick; Galván, E J; Perez-Rosello, T; Barrionuevo, Germán

    2009-08-20

    The morphological and electrophysiological diversity of inhibitory cells in hippocampal area CA3 may underlie specific computational roles and is not yet fully elucidated. In particular, interneurons with somata in strata radiatum (R) and lacunosum-moleculare (L-M) receive converging stimulation from the dentate gyrus and entorhinal cortex as well as within CA3. Although these cells express different forms of synaptic plasticity, their axonal trees and connectivity are still largely unknown. We investigated the branching and spatial patterns, plus the membrane and synaptic properties, of rat CA3b R and L-M interneurons digitally reconstructed after intracellular labeling. We found considerable variability within but no difference between the two layers, and no correlation between morphological and biophysical properties. Nevertheless, two cell types were identified based on the number of dendritic bifurcations, with significantly different anatomical and electrophysiological features. Axons generally branched an order of magnitude more than dendrites. However, interneurons on both sides of the R/L-M boundary revealed surprisingly modular axodendritic arborizations with consistently uniform local branch geometry. Both axons and dendrites followed a lamellar organization, and axons displayed a spatial preference toward the fissure. Moreover, only a small fraction of the axonal arbor extended to the outer portion of the invaded volume, and tended to return toward the proximal region. In contrast, dendritic trees demonstrated more limited but isotropic volume occupancy. These results suggest a role of predominantly local feedforward and lateral inhibitory control for both R and L-M interneurons. Such a role may be essential to balance the extensive recurrent excitation of area CA3 underlying hippocampal autoassociative memory function.

  7. Quantitative phosphoproteomic study of pressure-overloaded mouse heart reveals dynamin-related protein 1 as a modulator of cardiac hypertrophy.

    Science.gov (United States)

    Chang, Yu-Wang; Chang, Ya-Ting; Wang, Qinchuan; Lin, Jim Jung-Ching; Chen, Yu-Ju; Chen, Chien-Chang

    2013-11-01

    Pressure-overload stress to the heart causes pathological cardiac hypertrophy, which increases the risk of cardiac morbidity and mortality. However, the detailed signaling pathways induced by pressure overload remain unclear. Here we used phosphoproteomics to delineate signaling pathways in the myocardium responding to acute pressure overload and chronic hypertrophy in mice. Myocardial samples at 4 time points (10, 30, 60 min and 2 weeks) after transverse aortic banding (TAB) in mice underwent quantitative phosphoproteomics assay. Temporal phosphoproteomics profiles showed 360 phosphorylation sites with significant regulation after TAB. Multiple mechanical stress sensors were activated after acute pressure overload. Gene ontology analysis revealed differential phosphorylation between hearts with acute pressure overload and chronic hypertrophy. Most interestingly, analysis of the cardiac hypertrophy pathway revealed phosphorylation of the mitochondrial fission protein dynamin-related protein 1 (DRP1) by prohypertrophic kinases. Phosphorylation of DRP1 S622 was confirmed in TAB-treated mouse hearts and phenylephrine (PE)-treated rat neonatal cardiomyocytes. TAB-treated mouse hearts showed phosphorylation-mediated mitochondrial translocation of DRP1. Inhibition of DRP1 with the small-molecule inhibitor mdivi-1 reduced the TAB-induced hypertrophic responses. Mdivi-1 also prevented PE-induced hypertrophic growth and oxygen consumption in rat neonatal cardiomyocytes. We reveal the signaling responses of the heart to pressure stress in vivo and in vitro. DRP1 may be important in the development of cardiac hypertrophy.

  8. Quantitative proteomic analysis reveals that anti-cancer effects of selenium-binding protein 1 in vivo are associated with metabolic pathways.

    Science.gov (United States)

    Ying, Qi; Ansong, Emmanuel; Diamond, Alan M; Lu, Zhaoxin; Yang, Wancai; Bie, Xiaomei

    2015-01-01

    Previous studies have shown the tumor-suppressive role of selenium-binding protein 1 (SBP1), but the underlying mechanisms are unclear. In this study, we found that induction of SBP1 showed significant inhibition of colorectal cancer cell growth and metastasis in mice. We further employed isobaric tags for relative and absolute quantitation (iTRAQ) to identify proteins that were involved in SBP1-mediated anti-cancer effects in tumor tissues. We identified 132 differentially expressed proteins, among them, 53 proteins were upregulated and 79 proteins were downregulated. Importantly, many of the differentially altered proteins were associated with lipid/glucose metabolism, which were also linked to Glycolysis, MAPK, Wnt, NF-kB, NOTCH and epithelial-mesenchymal transition (EMT) signaling pathways. These results have revealed a novel mechanism that SBP1-mediated cancer inhibition is through altering lipid/glucose metabolic signaling pathways.

  9. Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH(c) in Saccharomyces cerevisiae.

    Science.gov (United States)

    Orij, Rick; Urbanus, Malene L; Vizeacoumar, Franco J; Giaever, Guri; Boone, Charles; Nislow, Corey; Brul, Stanley; Smits, Gertien J

    2012-09-10

    Because protonation affects the properties of almost all molecules in cells, cytosolic pH (pH(c)) is usually assumed to be constant. In the model organism yeast, however, pH(c) changes in response to the presence of nutrients and varies during growth. Since small changes in pH(c) can lead to major changes in metabolism, signal transduction, and phenotype, we decided to analyze pH(c) control. Introducing a pH-sensitive reporter protein into the yeast deletion collection allowed quantitative genome-wide analysis of pH(c) in live, growing yeast cultures. pH(c) is robust towards gene deletion; no single gene mutation led to a pH(c) of more than 0.3 units lower than that of wild type. Correct pH(c) control required not only vacuolar proton pumps, but also strongly relied on mitochondrial function. Additionally, we identified a striking relationship between pH(c) and growth rate. Careful dissection of cause and consequence revealed that pH(c) quantitatively controls growth rate. Detailed analysis of the genetic basis of this control revealed that the adequate signaling of pH(c) depended on inositol polyphosphates, a set of relatively unknown signaling molecules with exquisitely pH sensitive properties. While pH(c) is a very dynamic parameter in the normal life of yeast, genetically it is a tightly controlled cellular parameter. The coupling of pH(c) to growth rate is even more robust to genetic alteration. Changes in pH(c) control cell division rate in yeast, possibly as a signal. Such a signaling role of pH(c) is probable, and may be central in development and tumorigenesis.

  10. Current Conveyor Equivalent Circuits

    Directory of Open Access Journals (Sweden)

    Tejmal S. Rathore

    2012-02-01

    Full Text Available An equivalence between a class of (current conveyor CC II+ and CC II- circuits is established. CC IIequivalent circuit uses one extra element. However, under certain condition, the extra element can be eliminated. As an illustration of the application of this equivalence, minimal first and second order all-pass filters are derived. Incertain cases, it is possible to compensate the effect of the input resistor of CC at port X. At the end, an open problem of realizing an Nth order (N > 2 minimal all-pass filter is stated.

  11. Quantitative Transcriptomics Reveals the Growth- and Nutrient-Dependent Response of a Streamlined Marine Methylotroph to Methanol and Naturally Occurring Dissolved Organic Matter.

    Science.gov (United States)

    Gifford, Scott M; Becker, Jamie W; Sosa, Oscar A; Repeta, Daniel J; DeLong, Edward F

    2016-11-22

    substantial influence on marine organic matter flux, yet the carbon components targeted by specific bacterial groups, as well as how those groups' metabolic activities change under different conditions, are not well understood. Gene expression studies of model organisms can identify these responses under defined conditions, which can then be compared to environmental transcriptomes to elucidate in situ activities. This integration, however, is limited by the data's relative nature. Here, we report the fully quantitative transcriptome of a marine bacterium, providing a genome-wide survey of cellular transcript abundances and how they change with different states of growth, nutrient conditions, and carbon substrates. The results revealed the dynamic metabolic strategies this methylotroph has for processing both simple one-carbon compounds and the complex multicarbon substrates of naturally derived marine organic matter and provide baseline quantitative data for identifying their in situ activities and impact on the marine carbon cycle.

  12. Mass Equivalent Dyads

    NARCIS (Netherlands)

    van der Wijk, V.; Bai, Shaoping; Ceccarelli, Marco

    2015-01-01

    In this paper it is shown how a general 2-DoF dyad can be designed mass equivalent to a general (1-DoF) link element. This is useful in the synthesis of balanced mechanisms, for instance to increase or reduce the number of DoFs of a balanced mechanism maintaining its balance. Also it can be used as

  13. Mass equivalent triads

    NARCIS (Netherlands)

    van der Wijk, V.

    2015-01-01

    In this paper it is shown how a general 3-DoF triad can be designed mass equivalent to a general (1-DoF) link element. This is useful in the synthesis of shaking force balanced and statically balanced mechanisms, for instance to add or remove a number of DoFs of a balanced mechanism maintaining its

  14. Equivalence of Differential System

    Institute of Scientific and Technical Information of China (English)

    Zheng-xin Zhou

    2004-01-01

    Using refiecting function of Mironenko we construct some differential systems which are equivalent to the given differential system.This gives us an opportunity to find out the monodromic matrix of these periodi csystems which are not integrable in finite terms.

  15. Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition.

    Science.gov (United States)

    Hoffmann, Thomas; Krackhardt, Angela M; Antes, Iris

    2015-07-01

    T-cell receptors (TCR) play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response. Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy. However, the molecular mechanisms behind T-cell signaling are still predominantly unknown. For small sets of TCRs it was observed that the angle between their Vα- and Vβ-domains, which bind the epitope, can vary and might be important for epitope recognition. Here we present a comprehensive, quantitative study of the variation in the Vα/Vβ interdomain-angle and its influence on epitope recognition, performing a systematic bioinformatics analysis based on a representative set of experimental TCR structures. For this purpose we developed a new, cuboid-based superpositioning method, which allows a unique, quantitative analysis of the Vα/Vβ-angles. Angle-based clustering led to six significantly different clusters. Analysis of these clusters revealed the unexpected result that the angle is predominantly influenced by the TCR-clonotype, whereas the bound epitope has only a minor influence. Furthermore we could identify a previously unknown center of rotation (CoR), which is shared by all TCRs. All TCR geometries can be obtained by rotation around this center, rendering it a new, common TCR feature with the potential of improving the accuracy of TCR structure prediction considerably. The importance of Vα/Vβ rotation for signaling was confirmed as we observed larger variances in the Vα/Vβ-angles in unbound TCRs compared to epitope-bound TCRs. Our results strongly support a two-step mechanism for TCR-epitope: First, preformation of a flexible TCR geometry in the unbound state and second, locking of the Vα/Vβ-angle in a TCR-type specific geometry upon epitope-MHC association, the latter being driven by rotation around the unique center of rotation.

  16. From equivalence to adaptation

    Directory of Open Access Journals (Sweden)

    Paulina Borowczyk

    2009-01-01

    Full Text Available The aim of this paper is to illustrate in which cases the translators use the adaptation when they are confronted with a term related to sociocultural aspects. We will discuss the notions of equivalence and adaptation and their limits in the translation. Some samples from Arte TV news and from the American film Shrek translated into Polish, German and French will be provided as a support for this article.

  17. Equivalence Relations of -Algebra Extensions

    Indian Academy of Sciences (India)

    Changguo Wei

    2010-04-01

    In this paper, we consider equivalence relations of *-algebra extensions and describe the relationship between the isomorphism equivalence and the unitary equivalence. We also show that a certain group homomorphism is the obstruction for these equivalence relations to be the same.

  18. In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism.

    Directory of Open Access Journals (Sweden)

    Maria S Robles

    2014-01-01

    Full Text Available Circadian clocks are endogenous oscillators that drive the rhythmic expression of a broad array of genes, orchestrating metabolism and physiology. Recent evidence indicates that post-transcriptional and post-translational mechanisms play essential roles in modulating temporal gene expression for proper circadian function, particularly for the molecular mechanism of the clock. Due to technical limitations in large-scale, quantitative protein measurements, it remains unresolved to what extent the circadian clock regulates metabolism by driving rhythms of protein abundance. Therefore, we aimed to identify global circadian oscillations of the proteome in the mouse liver by applying in vivo SILAC mouse technology in combination with state of the art mass spectrometry. Among the 3000 proteins accurately quantified across two consecutive cycles, 6% showed circadian oscillations with a defined phase of expression. Interestingly, daily rhythms of one fifth of the liver proteins were not accompanied by changes at the transcript level. The oscillations of almost half of the cycling proteome were delayed by more than six hours with respect to the corresponding, rhythmic mRNA. Strikingly we observed that the length of the time lag between mRNA and protein cycles varies across the day. Our analysis revealed a high temporal coordination in the abundance of proteins involved in the same metabolic process, such as xenobiotic detoxification. Apart from liver specific metabolic pathways, we identified many other essential cellular processes in which protein levels are under circadian control, for instance vesicle trafficking and protein folding. Our large-scale proteomic analysis reveals thus that circadian post-transcriptional and post-translational mechanisms play a key role in the temporal orchestration of liver metabolism and physiology.

  19. iTRAQ-based quantitative proteomic analysis reveals potential factors associated with the enhancement of phenazine-1-carboxamide production in Pseudomonas chlororaphis P3.

    Science.gov (United States)

    Jin, Xue-Jie; Peng, Hua-Song; Hu, Hong-Bo; Huang, Xian-Qing; Wang, Wei; Zhang, Xue-Hong

    2016-06-07

    Phenazine-1-carboxamide (PCN), a phenazine derivative, is strongly antagonistic to fungal phytopathogens. Pseudomonas chlororaphis HT66 is a PCN-producing, non-pathogenic biocontrol strain, and we obtained the mutant P. chlororaphis P3, which produces 4.7 times more PCN than the wild-type HT66 strain. To reveal the cause of PCN production enhancement in P3 and find potential factors related to PCN biosynthesis, an iTRAQ-based quantitative proteomic analysis was used to study the expression changes between the two strains. Of the 452 differentially expressed proteins, most were functionally mapped into PCN biosynthesis pathway or other related metabolisms. The upregulation of proteins, including PhzA/B, PhzD, PhzF, PhzG, and PhzH, involved in PCN biosynthesis was in agreement with the efficient production of PCN in P3. A number of proteins that function primarily in energy production, amino acid metabolism, and secondary metabolism played important roles in PCN biosynthesis. Notably, proteins involved in the uptake and conversion of phosphate, inorganic nitrogen sources, and iron improved the PCN production. Furthermore, the type VI secretion system may participate in the secretion or/and indirect biosynthetic regulation of PCN in P. chlororaphis. This study provides valuable clues to better understand the biosynthesis, excretion and regulation of PCN in Pseudomonas and also provides potential gene targets for further engineering high-yield strains.

  20. Quantitative Analysis of the Human Milk Whey Proteome Reveals Developing Milk and Mammary-Gland Functions across the First Year of Lactation

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    2013-09-01

    Full Text Available In-depth understanding of the changing functions of human milk (HM proteins and the corresponding physiological adaptions of the lactating mammary gland has been inhibited by incomplete knowledge of the HM proteome. We analyzed the HM whey proteome (n = 10 women with samples at 1 week and 1, 3, 6, 9 and 12 months using a quantitative proteomic approach. One thousand three hundred and thirty three proteins were identified with 615 being quantified. Principal component analysis revealed a transition in the HM whey proteome-throughout the first year of lactation. Abundance changes in IgG, sIgA and sIgM display distinct features during the first year. Complement components and other acute-phase proteins are generally at higher levels in early lactation. Proteomic analysis further suggests that the sources of milk fatty acids (FA shift from more direct blood influx to more de novo mammary synthesis over lactation. The abundances of the majority of glycoproteins decline over lactation, which is consistent with increased enzyme expression in glycoprotein degradation and decreased enzyme expression in glycoprotein synthesis. Cellular detoxification machinery may be transformed as well, thereby accommodating increased metabolic activities in late lactation. The multiple developing functions of HM proteins and the corresponding mammary adaption become more apparent from this study.

  1. Quantitative Analysis of the Human Milk Whey Proteome Reveals Developing Milk and Mammary-Gland Functions across the First Year of Lactation.

    Science.gov (United States)

    Zhang, Qiang; Cundiff, Judy K; Maria, Sarah D; McMahon, Robert J; Woo, Jessica G; Davidson, Barbara S; Morrow, Ardythe L

    2013-09-03

    In-depth understanding of the changing functions of human milk (HM) proteins and the corresponding physiological adaptions of the lactating mammary gland has been inhibited by incomplete knowledge of the HM proteome. We analyzed the HM whey proteome (n = 10 women with samples at 1 week and 1, 3, 6, 9 and 12 months) using a quantitative proteomic approach. One thousand three hundred and thirty three proteins were identified with 615 being quantified. Principal component analysis revealed a transition in the HM whey proteome-throughout the first year of lactation. Abundance changes in IgG, sIgA and sIgM display distinct features during the first year. Complement components and other acute-phase proteins are generally at higher levels in early lactation. Proteomic analysis further suggests that the sources of milk fatty acids (FA) shift from more direct blood influx to more de novo mammary synthesis over lactation. The abundances of the majority of glycoproteins decline over lactation, which is consistent with increased enzyme expression in glycoprotein degradation and decreased enzyme expression in glycoprotein synthesis. Cellular detoxification machinery may be transformed as well, thereby accommodating increased metabolic activities in late lactation. The multiple developing functions of HM proteins and the corresponding mammary adaption become more apparent from this study.

  2. Comments on TNT Equivalence

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, P.W.

    1994-07-01

    The term ``TNT Equivalence`` is used throughout the explosives and related industries to compare the effects of the output of a given explosive to that of TNT. This is done for technical design reasons in scaling calculation such as for the prediction of blast waves, craters, and structural response, and is also used as a basis for government regulations controlling the shipping, handling and storage of explosive materials, as well as for the siting and design of explosive facilities. TNT equivalence is determined experimentally by several different types of tests, the most common of which include: plate dent, ballistic mortar, trauzl, sand crush, and air blast. All of these tests do not necessarily measure the same output property of the sample explosive. As examples of this, some tests depend simply upon the CJ pressure, some depend upon the PV work in the CJ zone and in the Taylor wave behind the CJ plane, some are functions of the total work which includes that from secondary combustion in the air mixing region of the fireball and are acutely effected by the shape of the pressure-time profile of the wave. Some of the tests incorporate systematic errors which are not readily apparent, and which have a profound effect upon skewing the resultant data. Further, some of the tests produce different TNT Equivalents for the same explosive which are a function of the conditions at which the test is run. This paper describes the various tests used, discusses the results of each test and makes detailed commentary on what the test is actually measuring, how the results may be interpreted, and if and how these results can be predicted by first principals based calculations. Extensive data bases are referred to throughout the paper and used in examples for each point in the commentaries.

  3. Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition.

    Directory of Open Access Journals (Sweden)

    Thomas Hoffmann

    2015-07-01

    Full Text Available T-cell receptors (TCR play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response. Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy. However, the molecular mechanisms behind T-cell signaling are still predominantly unknown. For small sets of TCRs it was observed that the angle between their Vα- and Vβ-domains, which bind the epitope, can vary and might be important for epitope recognition. Here we present a comprehensive, quantitative study of the variation in the Vα/Vβ interdomain-angle and its influence on epitope recognition, performing a systematic bioinformatics analysis based on a representative set of experimental TCR structures. For this purpose we developed a new, cuboid-based superpositioning method, which allows a unique, quantitative analysis of the Vα/Vβ-angles. Angle-based clustering led to six significantly different clusters. Analysis of these clusters revealed the unexpected result that the angle is predominantly influenced by the TCR-clonotype, whereas the bound epitope has only a minor influence. Furthermore we could identify a previously unknown center of rotation (CoR, which is shared by all TCRs. All TCR geometries can be obtained by rotation around this center, rendering it a new, common TCR feature with the potential of improving the accuracy of TCR structure prediction considerably. The importance of Vα/Vβ rotation for signaling was confirmed as we observed larger variances in the Vα/Vβ-angles in unbound TCRs compared to epitope-bound TCRs. Our results strongly support a two-step mechanism for TCR-epitope: First, preformation of a flexible TCR geometry in the unbound state and second, locking of the Vα/Vβ-angle in a TCR-type specific geometry upon epitope-MHC association, the latter being driven by rotation around the unique center of rotation.

  4. Establishing Substantial Equivalence: Proteomics

    Science.gov (United States)

    Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

    Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

  5. Reverse transcription quantitative PCR revealed persistency of thermophilic lactic acid bacteria metabolic activity until the end of the ripening of Emmental cheese.

    Science.gov (United States)

    Falentin, Hélène; Henaff, Nadine; Le Bivic, Pierre; Deutsch, Stéphanie-Marie; Parayre, Sandrine; Richoux, Romain; Sohier, Daniele; Thierry, Anne; Lortal, Sylvie; Postollec, Florence

    2012-02-01

    For Emmental manufacture two kinds of adjunct culture are added: (i) thermophilic lactic acid bacteria (starters) such as Lactobacillus helveticus (LH), and Streptococcus thermophilus (ST) growing the first day of the manufacture and (ii) ripening culture. ST and LH have a key role in curd acidification and proteolysis at the beginning of the manufacture but are considered to be lyzed for a great part of them at the ripening step. The aim of this work was to assess the metabolic activity of these bacteria throughout manufacture and ripening. During Emmental cheesemaking, LH and ST were subjected to i) population quantification by numerations and by quantitative PCR (qPCR) ii) reverse transcription (RT) Temporal Temperature Gel Electrophoresis (TTGE) iii) transcript quantification by RT-qPCR targeting 16S rRNA, tuf and groL mRNAs to evaluate bacterial metabolic activity. During ripening, ST and LH numerations showed a 2.5 log(10) loss of culturability whereas qPCR on pelleted cells revealed only one log(10) of decrease for both of these species. 10(9) ST and 10(8) LH cells/g of cheese still remained. They contained a stable number of 16S transcript and at least 10(6) copies of mRNAs per 10(9) cells until the end of ripening. These results prove the unexpected persistency of thermophilic lactic acid bacteria starters (ST and LH) metabolic activity until the end of ripening and open new perspectives in term of their involvement in the quality of cheeses during ripening.

  6. In vivo organization of the FtsZ-ring by ZapA and ZapB revealed by quantitative super-resolution microscopy.

    Science.gov (United States)

    Buss, Jackson; Coltharp, Carla; Huang, Tao; Pohlmeyer, Chris; Wang, Shih-Chin; Hatem, Christine; Xiao, Jie

    2013-09-01

    In most bacterial cells, cell division is dependent on the polymerization of the FtsZ protein to form a ring-like structure (Z-ring) at the midcell. Despite its essential role, the molecular architecture of the Z-ring remains elusive. In this work we examine the roles of two FtsZ-associated proteins, ZapA and ZapB, in the assembly dynamics and structure of the Z-ring in Escherichia coli cells. In cells deleted of zapA or zapB, we observed abnormal septa and highly dynamic FtsZ structures. While details of these FtsZ structures are difficult to discern under conventional fluorescence microscopy, single-molecule-based super-resolution imaging method Photoactivated Localization Microscopy (PALM) reveals that these FtsZ structures arise from disordered arrangements of FtsZ clusters. Quantitative analysis finds these clusters are larger and comprise more molecules than a single FtsZ protofilament, and likely represent a distinct polymeric species that is inherent to the assembly pathway of the Z-ring. Furthermore, we find these clusters are not due to the loss of ZapB-MatP interaction in ΔzapA and ΔzapB cells. Our results suggest that the main function of ZapA and ZapB in vivo may not be to promote the association of individual protofilaments but to align FtsZ clusters that consist of multiple FtsZ protofilaments. © 2013 John Wiley & Sons Ltd.

  7. Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability.

    Science.gov (United States)

    Miller, Christopher B; Bartlett, Delwyn J; Mullins, Anna E; Dodds, Kirsty L; Gordon, Christopher J; Kyle, Simon D; Kim, Jong Won; D'Rozario, Angela L; Lee, Rico S C; Comas, Maria; Marshall, Nathaniel S; Yee, Brendon J; Espie, Colin A; Grunstein, Ronald R

    2016-11-01

    To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative (q)-EEG and heart rate variability (HRV). Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P clusters by retaining the I-NSD and splitting the I-SSD cluster into two: I-SSD A (n = 29): defined by high WASO and I-SSD B (n = 14): a second I-SSD cluster with high SOL and medium WASO. The I-SSD B cluster performed worse than I-SSD A and I-NSD for sustained attention (P ≤ 0.05). In an exploratory analysis, q-EEG revealed reduced spectral power also in I-SSD B before (Delta, Alpha, Beta-1) and after sleep-onset (Beta-2) compared to I-SSD A and I-NSD (P ≤ 0.05). Two insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q-EEG. Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742.

  8. Quantitative meta-analysis of fMRI and PET studies reveals consistent activation in fronto-striatal-parietal regions and cerebellum during antisaccades and prosaccades

    Directory of Open Access Journals (Sweden)

    Sharna eJamadar

    2013-10-01

    Full Text Available The antisaccade task is a classic task of oculomotor control that requires participants to inhibit a saccade to a target and instead make a voluntary saccade to the mirror opposite location. By comparison, the prosaccade task requires participants to make a visually-guided saccade to the target. These tasks have been studied extensively using behavioural oculomotor, electrophysiological and neuroimaging in both non-human primates and humans. In humans, the antisaccade task is under active investigation as a potential endophenotype or biomarker for multiple psychiatric and neurological disorders. A large and growing body of literature has used functional magnetic resonance imaging (fMRI and positron emission tomography (PET to study the neural correlates of the antisaccade and prosaccade tasks. We present a quantitative meta-analysis of all published voxel-wise fMRI and PET studies (18 of the antisaccade task and show that consistent activation for antisaccades and prosaccades is obtained in a fronto-subcortical-parietal network encompassing frontal and supplementary eye fields, thalamus, striatum and intraparietal cortex. This network is strongly linked to oculomotor control and was activated to a greater extent for antisaccade than prosaccade trials. Antisaccade but not prosaccade trials additionally activated dorsolateral and ventrolateral prefrontal cortices. We also found that a number of additional regions not classically linked to oculomotor control were activated to a greater extent for antisaccade versus prosaccade trials; these regions are often reported in antisaccade studies but rarely commented upon. While the number of studies eligible to be included in this meta-analysis was small, the results of this systematic review reveal that antisaccade and prosaccade trials consistently activate a distributed network of regions both within and outside the classic definition of the oculomotor network.

  9. Stuttering Equivalence for Parity Games

    CERN Document Server

    Cranen, Sjoerd; Willemse, Tim A C

    2011-01-01

    We study the process theoretic notion of stuttering equivalence in the setting of parity games. We demonstrate that stuttering equivalent vertices have the same winner in the parity game. This means that solving a parity game can be accelerated by minimising the game graph with respect to stuttering equivalence. While, at the outset, it might not be clear that this strategy should pay off, our experiments using typical verification problems illustrate that stuttering equivalence speeds up solving parity games in many cases.

  10. Male fertility versus sterility, cytotype, and DNA quantitative variation in seed production in diploid and tetraploid sea lavenders (Limonium sp., Plumbaginaceae) reveal diversity in reproduction modes.

    Science.gov (United States)

    Róis, Ana Sofia; Teixeira, Generosa; Sharbel, Timothy F; Fuchs, Jörg; Martins, Sérgio; Espírito-Santo, Dalila; Caperta, Ana D

    2012-12-01

    The genus Limonium Miller, a complex taxonomic group, comprises annuals and perennials that can produce sexual and/or asexual seeds (apomixis). In this study, we used diverse cytogenetic and cytometric approaches to analyze male sporogenesis and gametogenesis for characterizing male reproductive output on seed production in Limonium ovalifolium and Limonium multiflorum. We showed here that the first species is mostly composed of diploid cytotypes with 2n = 16 chromosomes and the latter species by tetraploid cytotypes with 2n = 32, 34, 35, 36 chromosomes and had a genome roughly twice as big as the former one. In both species, euploid and aneuploid cytotypes with large metacentric chromosomes having decondensed interstitial sites were found within and among populations, possibly involved in chromosomal reconstructions. L. ovalifolium diploids showed regular meiosis resulting in normal tetrads, while diverse chromosome pairing and segregation irregularities leading to the formation of abnormal meiotic products are found in balanced and non-balanced L. multiflorum tetraploids. Before anther dehiscence, the characteristic unicellular, bicellular, or tricellular pollen grains showing the typical Limonium micro- or macro-reticulate exine ornamentation patterns were observed in L. ovalifolium using scanning electron microscopy. Most of these grains were viable and able to produce pollen tubes in vitro. In both balanced and unbalanced L. multiflorum tetraploids, microspores only developed until the "ring-vacuolate stage" with a collapsed morphology without the typical exine patterns, pointing to a sporophytic defect. These microspores were unviable and therefore never germinated in vitro. L. ovalifolium individuals presented larger pollen grains than those of L. multiflorum, indicating that pollen size and ploidy levels are not correlated in the Limonium system. Cytohistological studies in mature seeds from both species revealed that an embryo and a residual endosperm

  11. Why scalar-tensor equivalent theories are not physically equivalent?

    CERN Document Server

    Sk., Nayem

    2016-01-01

    Whether Jordan's and Einstein's frame descriptions of F(R) theory of gravity are physically equivalent, is a long standing debate. However, none questioned on true mathematical equivalence, since classical field equations may be translated from one frame to the other following a transformation relation. Nevertheless, true mathematical equivalence is only established, if all the mathematical results derived from one frame may be translated to the other. Here we show that, neither Noether equations, nor quantum equations may be translated from one frame to the other. The reason being the momenta can't be translated. This appears to be the cause for dynamical in-equivalence.

  12. Equivalent Effect in the Translation of Culture-Bound Terms

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    In the book Toward a Science of Translation,Eugene Nida brings out two important concepts:formal-equivalence(to reveal as much as possible of the form and content of the original message) and dynamic-equivalence(the closest natural equivalent to the source-language message).(Nida,1964) When we translate from poetry to poetry,prose to prose,novel to novel,we try to achieve F-E as much as possible

  13. Testing statistical hypotheses of equivalence

    CERN Document Server

    Wellek, Stefan

    2010-01-01

    Equivalence testing has grown significantly in importance over the last two decades, especially as its relevance to a variety of applications has become understood. Yet published work on the general methodology remains scattered in specialists' journals, and for the most part, it focuses on the relatively narrow topic of bioequivalence assessment.With a far broader perspective, Testing Statistical Hypotheses of Equivalence provides the first comprehensive treatment of statistical equivalence testing. The author addresses a spectrum of specific, two-sided equivalence testing problems, from the

  14. Temporary inactivation reveals that the CA1 region of the mouse dorsal hippocampus plays an equivalent role in the retrieval of long-term object memory and spatial memory.

    Science.gov (United States)

    Stackman, Robert W; Cohen, Sarah J; Lora, Joan C; Rios, Lisa M

    2016-09-01

    Recognition of a previously experienced item or object depends upon the successful retrieval of memory for the object. The neural mechanisms that support object recognition memory in the mammalian brain are not well understood. The rodent hippocampus plays a well-established role in spatial memory, and we previously demonstrated that temporary inactivation of the mouse hippocampus impairs object memory, as assessed with a novel object preference (NOP) test. The present studies were designed to test some remaining issues regarding the contribution of the CA1 sub-region of the mouse dorsal hippocampus to long-term object memory. Specifically, we examined whether the retrieval of spatial memory (as assessed by the Morris water maze; MWM) and object recognition memory are differentially sensitive to inactivation of the CA1 region. The current study used pre-test local microinfusion of muscimol directly into the CA1 region of dorsal hippocampus to temporarily interrupt its function during the respective retrieval phases of both behavioral tasks, in order to compare the contribution of the CA1 to object memory and spatial memory. Histological analyses revealed that local intra-CA1 injection of muscimol diffused within, and not beyond, the CA1 region of dorsal hippocampus. The degree of memory retrieval impairment induced by muscimol was comparable in the two tasks, supporting the view that object memory and spatial memory depend similarly on the CA1 region of rodent hippocampus. Further, we confirmed that the muscimol-induced impairment of CA1 function is temporary. First, mice that exhibited impaired object memory retrieval immediately after intra-CA1 muscimol, subsequently exhibited unimpaired retrieval of object memory when tested 24h later. Secondly, a cohort of mice that exhibited impaired object memory retrieval after intra-CA1 muscimol later acquired spatial memory in the MWM comparable to that of control mice. Together, these results offer further support for the

  15. Quantitative Detection of Chlamydia psittaci and C. pecorum by High-Sensitivity Real-Time PCR Reveals High Prevalence of Vaginal Infection in Cattle

    OpenAIRE

    DeGraves, Fred J.; Gao, Dongya; Hehnen, Hans-Robert; Schlapp, Tobias; Kaltenboeck, Bernhard

    2003-01-01

    Bovine vaginal cytobrush specimens were analyzed for the presence of Chlamydia spp. by a high-sensitivity, high-specificity quantitative PCR. The 53% prevalence of low-level Chlamydia psittaci and C. pecorum genital infection detected in virgin heifers suggests predominantely extragenital transmission of Chlamydia in cattle and conforms to the high seroprevalence of anti-Chlamydia antibodies.

  16. Saponification equivalent of dasamula taila.

    Science.gov (United States)

    Saxena, R B

    1994-07-01

    Saponification equivalent values of Dasamula taila are very useful for the technical and analytical work. It gives the mean molecular weight of the glycerides and acids present in Dasamula Taila. Saponification equivalent values of Dasamula taila are reported in different packings.

  17. Unitary equivalence of quantum walks

    Energy Technology Data Exchange (ETDEWEB)

    Goyal, Sandeep K., E-mail: sandeep.goyal@ucalgary.ca [School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, 4000 Durban (South Africa); Konrad, Thomas [School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, 4000 Durban (South Africa); National Institute for Theoretical Physics (NITheP), KwaZulu-Natal (South Africa); Diósi, Lajos [Wigner Research Centre for Physics, Institute for Particle and Nuclear Physics, H-1525 Budapest 114, P.O.B. 49 (Hungary)

    2015-01-23

    Highlights: • We have found unitary equivalent classes in coined quantum walks. • A single parameter family of coin operators is sufficient to realize all simple one-dimensional quantum walks. • Electric quantum walks are unitarily equivalent to time dependent quantum walks. - Abstract: A simple coined quantum walk in one dimension can be characterized by a SU(2) operator with three parameters which represents the coin toss. However, different such coin toss operators lead to equivalent dynamics of the quantum walker. In this manuscript we present the unitary equivalence classes of quantum walks and show that all the nonequivalent quantum walks can be distinguished by a single parameter. Moreover, we argue that the electric quantum walks are equivalent to quantum walks with time dependent coin toss operator.

  18. Quantitative Assessment of Chromatin Immunoprecipitation Grade Antibodies Directed against Histone Modifications Reveals Patterns of Co-occurring Marks on Histone Protein Molecules*

    OpenAIRE

    Peach, Sally E.; Rudomin, Emily L.; Udeshi, Namrata D.; Carr, Steven A.; Jaffe, Jacob D.

    2012-01-01

    The defining step in most chromatin immunoprecipitation (ChIP) assays is the use of an antibody to enrich for a particular protein or histone modification state associated with segments of chromatin. The specificity of the antibody is critical to the interpretation of the experiment, yet this property is rarely reported. Here, we present a quantitative method using mass spectrometry to characterize the specificity of key histone H3 modification-targeting antibodies that have previously been u...

  19. Quantitative weaknesses of the Marcus-Hush theory of electrode kinetics revealed by Reverse Scan Square Wave Voltammetry: The reduction of 2-methyl-2-nitropropane at mercury microelectrodes

    Science.gov (United States)

    Laborda, Eduardo; Wang, Yijun; Henstridge, Martin C.; Martínez-Ortiz, Francisco; Molina, Angela; Compton, Richard G.

    2011-08-01

    The Marcus-Hush and Butler-Volmer kinetic electrode models are compared experimentally by studying the reduction of 2-methyl-2-nitropropane in acetonitrile at mercury microelectrodes using Reverse Scan Square Wave Voltammetry. This technique is found to be very sensitive to the electrode kinetics and to permit critical comparison of the two models. The Butler-Volmer model satisfactorily fits the experimental data whereas Marcus-Hush does not quantitatively describe this redox system.

  20. Dominant Microbial Composition and Its Vertical Distribution in Saline Meromictic Lake Kaiike (Japan) as Revealed by Quantitative Oligonucleotide Probe Membrane Hybridization

    OpenAIRE

    Koizumi, Yoshikazu; Kojima, Hisaya; Fukui, Manabu

    2004-01-01

    Vertical distributions of dominant bacterial populations in saline meromictic Lake Kaiike were investigated throughout the water column and sediment by quantitative oligonucleotide probe membrane hybridization. Three oligonucleotide probes specific for the small-subunit (SSU) rRNA of three groups of Chlorobiaceae were newly designed. In addition, three general domain (Bacteria, Archaea, and Eukarya)-specific probes, two δ-Proteobacteria-specific probes, a Chlorobiaceae-specific probe, and a C...

  1. Population average T2 MRI maps reveal quantitative regional transformations in the degenerating rabbit intervertebral disc that vary by lumbar level.

    Science.gov (United States)

    Martin, John T; Collins, Christopher M; Ikuta, Kensuke; Mauck, Robert L; Elliott, Dawn M; Zhang, Yeija; Anderson, D Greg; Vaccaro, Alexander R; Albert, Todd J; Arlet, Vincent; Smith, Harvey E

    2015-01-01

    Magnetic resonance imaging (MRI) with T2-weighting is routinely performed to assess intervertebral disc degeneration. Standard clinical evaluations of MR images are qualitative, however, and do not focus on region-specific alterations in the disc. Utilizing a rabbit needle puncture model, T2 mapping was performed on injured discs to develop a quantitative description of the degenerative process following puncture. To do so, an 18G needle was inserted into four discs per rabbit (L3/L4 to L6/L7) and T2 maps were generated pre- and 4 weeks post-injury. Individual T2 maps were normalized to a disc-specific coordinate system and then averaged for pre- and post-injury population composite T2 maps. We also developed a method to automatically segment the nucleus pulposus by fitting the NP region of the T2 maps with modified 2-D and 3-D Gaussian distribution functions. Puncture injury produced alterations in MR signal intensity in a region-specific manner mirroring human degeneration. Population average T2 maps provided a quantitative representation of the injury response, and identified deviations of individual degenerate discs from the pre-injury population. We found that the response to standardized injury was modest at lower lumbar levels, likely as a result of increased disc dimensions. These tools will be valuable for the quantitative characterization of disc degeneration in future clinical and pre-clinical studies. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  2. Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

    Science.gov (United States)

    Bonnet, Timothée; Wandeler, Peter; Camenisch, Glauco; Postma, Erik

    2017-01-01

    In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called "stasis paradox" highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is

  3. Spatial maping of statistical information by using the concept of equivalence

    Directory of Open Access Journals (Sweden)

    Nadejda Yu. Gubanova

    2011-05-01

    Full Text Available The article focuses on the problems of the use of statistical tests for revealing equivalence. The combined application of equivalence and statistical difference tests in spatial maping is discussed.

  4. TRI12 based quantitative real-time PCR assays reveal the distribution of trichothecene genotype of F. graminearum and F. culmorum isolates in Danish small grain cereals

    DEFF Research Database (Denmark)

    Nielsen, L. K.; Jensen, J. D.; Rodríguez, A.

    2012-01-01

    Quantitative real-time PCR assays, based on polymorphisms in the TRI12 gene of the trichothecene pathway, were developed to identify and quantify the trichothecene genotypes producing 3-acetyl-deoxynivalenol (3ADON), 15-acetyl-deoxynivalenol (15ADON) or nivalenol (NIV) in the Fusarium graminearum...... in the sample representing the years from 1997 to 2000. Detection of low amounts of the 15ADON genotype in these historical samples and the relatively high amounts of 15ADON genotype in 2003 and following years correspond well with the occurrence of F. graminearum and indicates that the 15ADON genotype...

  5. The calcium-dependent protein kinase 3 of toxoplasma influences basal calcium levels and functions beyond egress as revealed by quantitative phosphoproteome analysis.

    OpenAIRE

    Moritz Treeck; Sanders, John L.; Rajshekhar Y Gaji; Kacie A LaFavers; Child, Matthew A.; Gustavo Arrizabalaga; Elias, Joshua E.; John C Boothroyd

    2014-01-01

    Calcium-dependent protein kinases (CDPKs) are conserved in plants and apicomplexan parasites. In Toxoplasma gondii, TgCDPK3 regulates parasite egress from the host cell in the presence of a calcium-ionophore. The targets and the pathways that the kinase controls, however, are not known. To identify pathways regulated by TgCDPK3, we measured relative phosphorylation site usage in wild type and TgCDPK3 mutant and knock-out parasites by quantitative mass-spectrometry using stable isotope-labelin...

  6. Full Static Output Feedback Equivalence

    Directory of Open Access Journals (Sweden)

    Aristotle G. Yannakoudakis

    2013-01-01

    Full Text Available We present a constructive solution to the problem of full output feedback equivalence, of linear, minimal, time-invariant systems. The equivalence relation on the set of systems is transformed to another on the set of invertible block Bezout/Hankel matrices using the isotropy subgroups of the full state feedback group and the full output injection group. The transformation achieving equivalence is calculated solving linear systems of equations. We give a polynomial version of the results proving that two systems are full output feedback equivalent, if and only if they have the same family of generalized Bezoutians. We present a new set of output feedback invariant polynomials that generalize the breakaway polynomial of scalar systems.

  7. Tissue Engineered Human Skin Equivalents

    Directory of Open Access Journals (Sweden)

    Zheng Zhang

    2012-01-01

    Full Text Available Human skin not only serves as an important barrier against the penetration of exogenous substances into the body, but also provides a potential avenue for the transport of functional active drugs/reagents/ingredients into the skin (topical delivery and/or the body (transdermal delivery. In the past three decades, research and development in human skin equivalents have advanced in parallel with those in tissue engineering and regenerative medicine. The human skin equivalents are used commercially as clinical skin substitutes and as models for permeation and toxicity screening. Several academic laboratories have developed their own human skin equivalent models and applied these models for studying skin permeation, corrosivity and irritation, compound toxicity, biochemistry, metabolism and cellular pharmacology. Various aspects of the state of the art of human skin equivalents are reviewed and discussed.

  8. Quantitative proteome profiling of dystrophic dog skeletal muscle reveals a stabilized muscular architecture and protection against oxidative stress after systemic delivery of MuStem cells.

    Science.gov (United States)

    Lardenois, Aurélie; Jagot, Sabrina; Lagarrigue, Mélanie; Guével, Blandine; Ledevin, Mireille; Larcher, Thibaut; Dubreil, Laurence; Pineau, Charles; Rouger, Karl; Guével, Laëtitia

    2016-07-01

    Proteomic profiling plays a decisive role in the elucidation of molecular signatures representative of a specific clinical context. MuStem cell based therapy represents a promising approach for clinical applications to cure Duchenne muscular dystrophy (DMD). To expand our previous studies collected in the clinically relevant DMD animal model, we decided to investigate the skeletal muscle proteome 4 months after systemic delivery of allogenic MuStem cells. Quantitative proteomics with isotope-coded protein labeling was used to compile quantitative changes in the protein expression profiles of muscle in transplanted Golden Retriever muscular dystrophy (GRMD) dogs as compared to Golden Retriever muscular dystrophy dogs. A total of 492 proteins were quantified, including 25 that were overrepresented and 46 that were underrepresented after MuStem cell transplantation. Interestingly, this study demonstrates that somatic stem cell therapy impacts on the structural integrity of the muscle fascicle by acting on fibers and its connections with the extracellular matrix. We also show that cell infusion promotes protective mechanisms against oxidative stress and favors the initial phase of muscle repair. This study allows us to identify putative candidates for tissue markers that might be of great value in objectively exploring the clinical benefits resulting from our cell-based therapy for DMD. All MS data have been deposited in the ProteomeXchange with identifier PXD001768 (http://proteomecentral.proteomexchange.org/dataset/PXD001768).

  9. Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease.

    Science.gov (United States)

    Mayers, Michael D; Moon, Clara; Stupp, Gregory S; Su, Andrew I; Wolan, Dennis W

    2017-02-03

    Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across two mouse cohorts as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control, thereby limiting genetic and environmental variables that influence microbiome composition. The data generated highlight quantitative alterations in both host and microbial proteins due to intestinal inflammation and corroborates the observed phylogenetic changes in bacteria that accompany IBD in humans and mouse models. The combination of isotope labeling with shotgun proteomics resulted in the total identification of 4434 protein clusters expressed in the microbial proteomic environment, 276 of which demonstrated differential abundance between control and IBD mice. Notably, application of a novel cysteine-reactive probe uncovered several microbial proteases and hydrolases overrepresented in the IBD mice. Implementation of these methods demonstrated that substantial insights into the identity and dysregulation of host and microbial proteins altered in IBD can be accomplished and can be used in the interrogation of other microbiome-related diseases.

  10. Quantitative measurements of alternating finger tapping in Parkinson's disease correlate with UPDRS motor disability and reveal the improvement in fine motor control from medication and deep brain stimulation.

    Science.gov (United States)

    Taylor Tavares, Ana Lisa; Jefferis, Gregory S X E; Koop, Mandy; Hill, Bruce C; Hastie, Trevor; Heit, Gary; Bronte-Stewart, Helen M

    2005-10-01

    The Unified Parkinson's Disease Rating Scale (UPDRS) is the primary outcome measure in most clinical trials of Parkinson's disease (PD) therapeutics. Each subscore of the motor section (UPDRS III) compresses a wide range of motor performance into a coarse-grained scale from 0 to 4; the assessment of performance can also be subjective. Quantitative digitography (QDG) is an objective, quantitative assessment of digital motor control using a computer-interfaced musical keyboard. In this study, we show that the kinematics of a repetitive alternating finger-tapping (RAFT) task using QDG correlate with the UPDRS motor score, particularly with the bradykinesia subscore, in 33 patients with PD. We show that dopaminergic medication and an average of 9.5 months of bilateral subthalamic nucleus deep brain stimulation (B-STN DBS) significantly improve UPDRS and QDG scores but may have different effects on certain kinematic parameters. This study substantiates the use of QDG to measure motor outcome in trials of PD therapeutics and shows that medication and B-STN DBS both improve fine motor control.

  11. Quantitative proteomics of fractionated membrane and lumen exosome proteins from isogenic metastatic and nonmetastatic bladder cancer cells reveal differential expression of EMT factors.

    Science.gov (United States)

    Jeppesen, Dennis Kjølhede; Nawrocki, Arkadiusz; Jensen, Steffen Grann; Thorsen, Kasper; Whitehead, Bradley; Howard, Kenneth A; Dyrskjøt, Lars; Ørntoft, Torben Falck; Larsen, Martin R; Ostenfeld, Marie Stampe

    2014-03-01

    Cancer cells secrete soluble factors and various extracellular vesicles, including exosomes, into their tissue microenvironment. The secretion of exosomes is speculated to facilitate local invasion and metastatic spread. Here, we used an in vivo metastasis model of human bladder carcinoma cell line T24 without metastatic capacity and its two isogenic derivate cell lines SLT4 and FL3, which form metastases in the lungs and liver of mice, respectively. Cultivation in CLAD1000 bioreactors rather than conventional culture flasks resulted in a 13- to 16-fold increased exosome yield and facilitated quantitative proteomics of fractionated exosomes. Exosomes from T24, SLT4, and FL3 cells were partitioned into membrane and luminal fractions and changes in protein abundance related to the gain of metastatic capacity were identified by quantitative iTRAQ proteomics. We identified several proteins linked to epithelial-mesenchymal transition, including increased abundance of vimentin and hepatoma-derived growth factor in the membrane, and casein kinase II α and annexin A2 in the lumen of exosomes, respectively, from metastatic cells. The change in exosome protein abundance correlated little, although significant for FL3 versus T24, with changes in cellular mRNA expression. Our proteomic approach may help identification of proteins in the membrane and lumen of exosomes potentially involved in the metastatic process.

  12. Quantitative profiling of glucosinolates by LC-MS analysis reveals several cultivars of cabbage and kale as promising sources of sulforaphane.

    Science.gov (United States)

    Sasaki, Katsunori; Neyazaki, Makiko; Shindo, Kazutoshi; Ogawa, Toshiya; Momose, Masaki

    2012-08-15

    Sulforaphane is an isothiocyanate well known for its potential health benefits. With the aim of finding sulforaphane supply sources, its precursor, glucoraphanin, was widely searched for among Brassica oleracea varieties. Quantitative profiling of seven glucosinolates by LC-MS analysis was performed on 6 cultivars of broccoli, 32 of cabbage and 24 cultivars of kale. The glucoraphanin levels found in three cultivars of cabbage and six cultivars of kale were comparable with, or even higher than, the highest of broccoli (119.4 mg/100g FW). The most promising group belonged to the black kale, Cavolo nero. Use of a C30 column and an ammonium formate buffer in LC-MS and a micro plate solid phase extraction technique was highly effective.

  13. An anti-phospholipase A2 receptor quantitative immunoassay and epitope analysis in membranous nephropathy reveals different antigenic domains of the receptor.

    Science.gov (United States)

    Behnert, Astrid; Fritzler, Marvin J; Teng, Beina; Zhang, Meifeng; Bollig, Frank; Haller, Hermann; Skoberne, Andrej; Mahler, Michael; Schiffer, Mario

    2013-01-01

    The phospholipase A2 receptor (PLA2R) was recently discovered as a target autoantigen in patients with idiopathic membranous nephropathy (IMN). Published evidence suggests that the autoantibodies directed towards a conformation dependent epitope are currently effectively detected by a cell based assay (CBA) utilizing indirect immunofluorescence (IIF) on tissue culture cells transfected with the PLA2R cDNA. Limitations of such IIF-CBA assays include observer dependent subjective evaluation of semi-quantitative test results and the protocols are not amenable to high throughput diagnostic testing. We developed a quantitative, observer independent, high throughput capture immunoassay for detecting PLA2R autoantibodies on an addressable laser bead immunoassay (ALBIA) platform. Since reactive domains of PLA2R (i.e. epitopes) could be used to improve diagnostic tests by using small peptides in various high throughput diagnostic platforms, we identified PLA2R epitopes that bound autoantibodies of IMN patients. These studies confirmed that inter-molecular epitope spreading occurs in IMN but use of the cognate synthetic peptides in immunoassays was unable to conclusively distinguish between IMN patients and normal controls. However, combinations of these peptides were able to effectively absorb anti-PLA2R reactivity in IIF-CBA and an immunoassay that employed a lysate derived from HEK cells tranfected with and overexpressing PLA2R. While we provide evidence of intermolecular epitope spreading, our data indicates that in addition to conformational epitopes, human anti-PLA2R reactivity in a commercially available CBA and an addressable laser bead immunoassay is significantly absorbed by peptides representing epitopes of PLA2R.

  14. An anti-phospholipase A2 receptor quantitative immunoassay and epitope analysis in membranous nephropathy reveals different antigenic domains of the receptor.

    Directory of Open Access Journals (Sweden)

    Astrid Behnert

    Full Text Available The phospholipase A2 receptor (PLA2R was recently discovered as a target autoantigen in patients with idiopathic membranous nephropathy (IMN. Published evidence suggests that the autoantibodies directed towards a conformation dependent epitope are currently effectively detected by a cell based assay (CBA utilizing indirect immunofluorescence (IIF on tissue culture cells transfected with the PLA2R cDNA. Limitations of such IIF-CBA assays include observer dependent subjective evaluation of semi-quantitative test results and the protocols are not amenable to high throughput diagnostic testing. We developed a quantitative, observer independent, high throughput capture immunoassay for detecting PLA2R autoantibodies on an addressable laser bead immunoassay (ALBIA platform. Since reactive domains of PLA2R (i.e. epitopes could be used to improve diagnostic tests by using small peptides in various high throughput diagnostic platforms, we identified PLA2R epitopes that bound autoantibodies of IMN patients. These studies confirmed that inter-molecular epitope spreading occurs in IMN but use of the cognate synthetic peptides in immunoassays was unable to conclusively distinguish between IMN patients and normal controls. However, combinations of these peptides were able to effectively absorb anti-PLA2R reactivity in IIF-CBA and an immunoassay that employed a lysate derived from HEK cells tranfected with and overexpressing PLA2R. While we provide evidence of intermolecular epitope spreading, our data indicates that in addition to conformational epitopes, human anti-PLA2R reactivity in a commercially available CBA and an addressable laser bead immunoassay is significantly absorbed by peptides representing epitopes of PLA2R.

  15. Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36

    DEFF Research Database (Denmark)

    Jung, Hye Ryung; Pasini, Diego; Helin, Kristian

    2010-01-01

    SUZ12 is a core component of the polycomb repressive complex 2 (PRC2) and is required for the differentiation of mouse embryonic stem cells (ESCs). PRC2 is associated with transcriptional repression via methylation of H3 Lys-27. We applied quantitative mass spectrometry to investigate the effects....... The combined use of ETD and CID MS/MS increased the total number of identified modified peptides. Comparative quantitative analysis of histones from wild type and Suz12-deficient ESCs using stable isotope labeling with amino acids in cell culture and LC-MS/MS revealed a dramatic reduction of H3K27me2 and H3K27...... analysis of the dynamics of coexisting post-translational modifications in proteins....

  16. Morita Equivalence for Factorisable Semigroups

    Institute of Scientific and Technical Information of China (English)

    Yu Qun CHEN; K. P. SHUM

    2001-01-01

    Recall that the semigroups S and R are said to be strongly Morita equivalent if there exists a unitary Morita context (S,R,S PR,RQs, <, []) with < and [] surjective. For a factorisable semigroup S, we denote s = {(s1, s2) ∈ S× S | ss1 =ss2,s ∈ S}, S' = S/s and US-FAct= {sM ∈S- Act|SM = M and SHoms(S, M) ≌ M}. We show that, for factorisable semigroups S and R, the categories US-FAct and UR-FAct are equivalent if and only if the semigroups S' and R' are strongly Morita equivalent. Some conditions for a factorisable semigroup to be strongly Morita equivalent to a sandwich semigroup, local units semigroup, monoid and group separately are also given. Moreover, we show that a semigroup S is completely simple if and only if S is strongly Morita equivalent to a group and for any index set I, S SHoms(S,Ⅱi∈ S)→Ⅱi∈S, s t·f→(st)f is an S-isomorphism.

  17. Matching of equivalent field regions

    DEFF Research Database (Denmark)

    Appel-Hansen, Jørgen; Rengarajan, S.B.

    2005-01-01

    screen, having the same homogeneous medium on both sides and an impressed current on one aide, an alternative procedure is relevant. We make use of the fact that in the aperture the tangential component of the magnetic field due to the induced currents in the screen is zero. The use of such a procedure......In aperture problems, integral equations for equivalent currents are often found by enforcing matching of equivalent fields. The enforcement is made in the aperture surface region adjoining the two volumes on each side of the aperture. In the case of an aperture in a planar perfectly conducting...... shows that equivalent currents can be found by a consideration of only one of the two volumes into which the aperture plane divides the space. Furthermore, from a consideration of an automatic matching at the aperture, additional information about tangential as well as normal field components...

  18. Teleparallel Equivalent of Lovelock Gravity

    CERN Document Server

    Gonzalez, P A

    2015-01-01

    There is a growing interest in modified gravity theories based on torsion due to these theories prove to exhibit interesting cosmological implications. In this work, inspired by the teleparallel formulation of General Relativity we present its extension to Lovelock Gravity known as the most natural extension of general relativity in higher-dimensional spacetimes. First, we review Teleparallel Equivalent of General Relativity and Teleparallel Equivalent of Gauss-Bonnet Gravity, and then we construct Teleparallel Equivalent of Lovelock Gravity. In order to achieve this goal we use the vielbein and the connection, without imposing the Weitzenb\\"ock connection. Then, we extract the teleparallel formulation of the theory by setting the curvature to be null.

  19. Mathematically Equivalent, Computationally Non-equivalent Formulas and Software Comprehensibility

    Science.gov (United States)

    2016-06-07

    and Software Comprehensibility Marvin J. Goldstein Surface Ship Sonar Department Approved for public release; distribution unlimited Report...equivalent Formulas and Software Comprehensibility 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Marvin Goldstein...13. SUPPLEMENTARY NOTES NUWC2015 14. ABSTRACT In the development of mathematical software , often the formula that defines the mathematical purpose

  20. Quantitative proteomics reveals significant changes in cell shape and an energy shift after IPTG induction via an optimized SILAC approach for Escherichia coli.

    Science.gov (United States)

    Ping, Lingyan; Zhang, Heng; Zhai, Linhui; Dammer, Eric B; Duong, Duc M; Li, Ning; Yan, Zili; Wu, Junzhu; Xu, Ping

    2013-12-01

    Stable isotope labeling by amino acids in cell culture (SILAC) has been widely used in yeast, mammalian cells, and even some multicellular organisms. However, the lack of optimized SILAC media limits its application in Escherichia coli, the most commonly used model organism. We optimized SILACE medium (SILAC medium created in this study for E. coli) for nonauxotrophic E. coli with high growth speed and complete labeling efficiency of the whole proteome in 12 generations. We applied a swapped SILAC workflow and pure null experiment with the SILACE medium using E. coli BL21 (DE3) cells hosting a recombinant plasmid coding for glutathione-S-transferase (GST) and ubiquitin binding domain before and after isopropyl thiogalactoside (IPTG) induction. Finally, we identified 1251 proteins with a significant change in abundance. Pathway analysis suggested that cell growth and fissiparism were inhibited accompanied by the down-regulation of proteins related to energy and metabolism, cell division, and the cell cycle, resulting in the size and shape change of the induced cells. Taken together, the results confirm the development of SILACE medium suitable for efficient and complete labeling of E. coli cells and a data filtering strategy for SILAC-based quantitative proteomics studies of E. coli.

  1. Quantitative shotgun proteomics reveals extensive changes to the proteome of the orbitofrontal cortex in rats that are hyperactive following withdrawal from a high sugar diet.

    Science.gov (United States)

    Franklin, Jane L; Mirzaei, Mehdi; Wearne, Travis A; Sauer, Melanie K; Homewood, Judi; Goodchild, Ann K; Haynes, Paul A; Cornish, Jennifer L

    2016-02-01

    In most Westernized societies, there has been an alarming increase in the consumption of sugar-sweetened drinks. For many adults these drinks represent a substantial proportion of their total daily caloric intake. Here we investigated whether extended exposure to sugar changes behavior and protein expression in the orbitofrontal cortex (OFC). Male adult Sprague-Dawley rats (n = 8 per group) were treated for 26 days with either water or a 10% sucrose solution. Locomotor behavior was measured on the first and last day of treatment, then 1 week after treatment. Following the 1-week period free from treatment, sucrose treated rats were significantly more active than the control. Two hours following final behavioral testing, brains were rapidly removed and prepared for proteomic analysis of the OFC. Label free quantitative shotgun proteomic analyses of three rats from each group found 290 proteins were differentially expressed in the sucrose treated group when compared to the control group. Major changes in the proteome were seen in proteins related to energy metabolism, mitochondrial function and the cellular response to stress. This research does not seek to suggest that sugar will cause specific neurological disorders, however similar changes in proteins have been seen in neurological disorders such as Alzheimer's disease, Parkinson's disease and schizophrenia.

  2. Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.

    Science.gov (United States)

    Resjö, Svante; Ali, Ashfaq; Meijer, Harold J G; Seidl, Michael F; Snel, Berend; Sandin, Marianne; Levander, Fredrik; Govers, Francine; Andreasson, Erik

    2014-04-04

    The oomycete Phytophthora infestans is the causal agent of late blight in potato and tomato. Since the underlying processes that govern pathogenicity and development in P. infestans are largely unknown, we have performed a large-scale phosphoproteomics study of six different P. infestans life stages. We have obtained quantitative data for 2922 phosphopeptides and compared their abundance. Life-stage-specific phosphopeptides include ATP-binding cassette transporters and a kinase that only occurs in appressoria. In an extended data set, we identified 2179 phosphorylation sites and deduced 22 phosphomotifs. Several of the phosphomotifs matched consensus sequences of kinases that occur in P. infestans but not Arabidopsis. In addition, we detected tyrosine phosphopeptides that are potential targets of kinases resembling mammalian tyrosine kinases. Among the phosphorylated proteins are members of the RXLR and Crinkler effector families. The latter are phosphorylated in several life stages and at multiple positions, in sites that are conserved between different members of the Crinkler family. This indicates that proteins in the Crinkler family have functions beyond their putative role as (necrosis-inducing) effectors. This phosphoproteomics data will be instrumental for studies on oomycetes and host-oomycete interactions. The data sets have been deposited to ProteomeXchange (identifier PXD000433).

  3. A quantitative label-free analysis of the extracellular proteome of human supraspinatus tendon reveals damage to the pericellular and elastic fibre niches in torn and aged tissue.

    Science.gov (United States)

    Hakimi, Osnat; Ternette, Nicola; Murphy, Richard; Kessler, Benedikt M; Carr, Andrew

    2017-01-01

    Tears of the human supraspinatus tendon are common and often cause painful and debilitating loss of function. Progressive failure of the tendon leading to structural abnormality and tearing is accompanied by numerous cellular and extra-cellular matrix (ECM) changes in the tendon tissue. This proteomics study aimed to compare torn and aged rotator cuff tissue to young and healthy tissue, and provide the first ECM inventory of human supraspinatus tendon generated using label-free quantitative LC-MS/MS. Employing two digestion protocols (trypsin and elastase), we analysed grain-sized tendon supraspinatus biopsies from older patients with torn tendons and from healthy, young controls. Our findings confirm measurable degradation of collagen fibrils and associated proteins in old and torn tendons, suggesting a significant loss of tissue organisation. A particularly marked reduction of cartilage oligomeric matrix protein (COMP) raises the possibility of using changes in levels of this glycoprotein as a marker of abnormal tissue, as previously suggested in horse models. Surprisingly, and despite using an elastase digestion for validation, elastin was not detected, suggesting that it is not highly abundant in human supraspinatus tendon as previously thought. Finally, we identified marked changes to the elastic fibre, fibrillin-rich niche and the pericellular matrix. Further investigation of these regions may yield other potential biomarkers and help to explain detrimental cellular processes associated with tendon ageing and tendinopathy.

  4. iTRAQ-based quantitative proteomic analysis reveals proteomic changes in leaves of cultivated tobacco (Nicotiana tabacum) in response to drought stress.

    Science.gov (United States)

    Xie, He; Yang, Da-Hai; Yao, Heng; Bai, Ge; Zhang, Yi-Han; Xiao, Bing-Guang

    2016-01-15

    Drought is one of the most severe forms of abiotic stresses that threaten the survival of plants, including crops. In turn, plants dramatically change their physiology to increase drought tolerance, including reconfiguration of proteomes. Here, we studied drought-induced proteomic changes in leaves of cultivated tobacco (Nicotiana tabacum), a solanaceous plant, using the isobaric tags for relative and absolute quantitation (iTRAQ)-based protein labeling technology. Of identified 5570 proteins totally, drought treatment increased and decreased abundance of 260 and 206 proteins, respectively, compared with control condition. Most of these differentially regulated proteins are involved in photosynthesis, metabolism, and stress and defense. Although abscisic acid (ABA) levels greatly increased in drought-treated tobacco leaves, abundance of detected ABA biosynthetic enzymes showed no obvious changes. In contrast, heat shock proteins (HSPs), thioredoxins, ascorbate-, glutathione-, and hydrogen peroxide (H2O2)-related proteins were up- or down-regulated in drought-treated tobacco leaves, suggesting that chaperones and redox signaling are important for tobacco tolerance to drought, and it is likely that redox-induced posttranslational modifications play an important role in modulating protein activity. This study not only provides a comprehensive dataset on overall protein changes in drought-treated tobacco leaves, but also shed light on the mechanism by which solanaceous plants adapt to drought stress.

  5. A genome-wide association study reveals a quantitative trait locus for days open on chromosome 2 in Japanese Black cattle.

    Science.gov (United States)

    Sasaki, Shinji; Ibi, Takayuki; Kojima, Takatoshi; Sugimoto, Yoshikazu

    2016-02-01

    Days open (DO), which is the interval from calving to conception, is an important trait related to reproductive performance in cattle. To identify quantitative trait loci for DO in Japanese Black cattle, we conducted a genome-wide association study with 33,303 single nucleotide polymorphisms (SNPs) using 459 animals with extreme DO values selected from a larger group of 15,488 animals. We identified a SNP on bovine chromosome 2 (BTA2) that was associated with DO. After imputation using phased haplotype data inferred from 586 812 SNPs of 1041 Japanese Black cattle, six SNPs associated with DO were located in an 8.5-kb region of high linkage disequilibrium on BTA2. These SNPs were located on the telomeric side at a distance of 177 kb from the parathyroid hormone 2 receptor (PTH2R) gene. The association was replicated in a sample of 1778 animals. In the replicated population, the frequency of the reduced-DO allele (Q) was 0.63, and it accounted for 1.72% of the total genetic variance. The effect of a Q-to-q allele substitution on DO was a decrease of 3.74 days. The results suggest that the Q allele could serve as a marker in Japanese Black cattle to select animals with superior DO performance.

  6. The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis.

    Science.gov (United States)

    Zhang, Yongjie; Skaar, Ida; Sulyok, Michael; Liu, Xingzhong; Rao, Mingyong; Taylor, John W

    2016-01-01

    Pu-erh is a tea produced in Yunnan, China by microbial fermentation of fresh Camellia sinensis leaves by two processes, the traditional raw fermentation and the faster, ripened fermentation. We characterized fungal and bacterial communities in leaves and both Pu-erhs by high-throughput, rDNA-amplicon sequencing and we characterized the profile of bioactive extrolite mycotoxins in Pu-erh teas by quantitative liquid chromatography-tandem mass spectrometry. We identified 390 fungal and 629 bacterial OTUs from leaves and both Pu-erhs. Major findings are: 1) fungal diversity drops and bacterial diversity rises due to raw or ripened fermentation, 2) fungal and bacterial community composition changes significantly between fresh leaves and both raw and ripened Pu-erh, 3) aging causes significant changes in the microbial community of raw, but not ripened, Pu-erh, and, 4) ripened and well-aged raw Pu-erh have similar microbial communities that are distinct from those of young, raw Ph-erh tea. Twenty-five toxic metabolites, mainly of fungal origin, were detected, with patulin and asperglaucide dominating and at levels supporting the Chinese custom of discarding the first preparation of Pu-erh and using the wet tea to then brew a pot for consumption.

  7. From beavis to beak color: a simulation study to examine how much qtl mapping can reveal about the genetic architecture of quantitative traits.

    Science.gov (United States)

    Slate, Jon

    2013-05-01

    Quantitative trait locus (QTL) mapping is frequently used in evolutionary studies to understand the genetic architecture of continuously varying traits. The majority of studies have been conducted in specially created crosses, in which genetic differences between parental lines are identified by linkage analysis. Detecting QTL segregating within populations is more problematic, especially in wild populations, because these populations typically have complicated and unbalanced multigenerational pedigrees. However, QTL mapping can still be conducted in such populations using a variance components mixed model approach, and the advent of appropriate statistical frameworks and better genotyping methods mean that the approach is gaining popularity. In this study it is shown that all studies described to date report evidence of QTL of major effect on trait variation, but that these findings are probably caused by inflated estimates of QTL effect sizes due to the Beavis effect. Using simulations I show that even the most powerful studies conducted to date are likely to give misleading descriptions of the genetic architecture of a trait. I show that an interpretation of a mapping study of beak color in the zebra finch (Taeniopygia guttata), that suggested genetic variation was determined by a small number of loci of large effect, which are possibly maintained by antagonistic pleiotropy, is likely to be incorrect. More generally, recommendations are made to how QTL mapping can be combined with other approaches to provide more accurate descriptions of a trait's genetic architecture.

  8. Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex

    Science.gov (United States)

    Nebl, Thomas; Prieto, Judith Helena; Kapp, Eugene; Smith, Brian J.; Williams, Melanie J.; Yates, John R.; Cowman, Alan F.; Tonkin, Christopher J.

    2011-01-01

    Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca2+-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of 32[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT) identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC)-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca2+-dependent phosphorylation patterns on three of its components - GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component. PMID:21980283

  9. Quantitative trait mapping reveals a regulatory axis involving peroxisome proliferator-activated receptors, PRDM16, transforming growth factor-β2 and FLT3 in hematopoiesis.

    Science.gov (United States)

    Avagyan, Serine; Aguilo, Francesca; Kamezaki, Kenjiro; Snoeck, Hans-Willem

    2011-12-01

    Hematopoiesis is the process whereby BM HSCs renew to maintain their number or to differentiate into committed progenitors to generate all blood cells. One approach to gain mechanistic insight into this complex process is the investigation of quantitative genetic variation in hematopoietic function among inbred mouse strains. We previously showed that TGF-β2 is a genetically determined positive regulator of hematopoiesis. In the presence of unknown nonprotein serum factors TGF-β2, but not TGF-β1 or -β3, enhances progenitor proliferation in vitro, an effect that is subject to mouse strain-dependent variation mapping to a locus on chr.4, Tb2r1. TGF-β2-deficient mice show hematopoietic defects, demonstrating the physiologic role of this cytokine. Here, we show that TGF-β2 specifically and predominantly cell autonomously enhances signaling by FLT3 in vitro and in vivo. A coding polymorphism in Prdm16 (PR-domain-containing 16) underlies Tb2r1 and differentially regulates transcriptional activity of peroxisome proliferator-activated receptor-γ (PPARγ), identifying lipid PPAR ligands as the serum factors required for regulation of FLT3 signaling by TGF-β2. We furthermore show that PPARγ agonists play a FLT3-dependent role in stress responses of progenitor cells. These observations identify a novel regulatory axis that includes PPARs, Prdm16, and TGF-β2 in hematopoiesis.

  10. Teleparallel equivalent of Lovelock gravity

    Science.gov (United States)

    González, P. A.; Vásquez, Yerko

    2015-12-01

    There is a growing interest in modified gravity theories based on torsion, as these theories exhibit interesting cosmological implications. In this work inspired by the teleparallel formulation of general relativity, we present its extension to Lovelock gravity known as the most natural extension of general relativity in higher-dimensional space-times. First, we review the teleparallel equivalent of general relativity and Gauss-Bonnet gravity, and then we construct the teleparallel equivalent of Lovelock gravity. In order to achieve this goal, we use the vielbein and the connection without imposing the Weitzenböck connection. Then, we extract the teleparallel formulation of the theory by setting the curvature to null.

  11. Representing Identity and Equivalence for Scientific Data

    Science.gov (United States)

    Wickett, K. M.; Sacchi, S.; Dubin, D.; Renear, A. H.

    2012-12-01

    Matters of equivalence and identity are central to the stewardship of scientific data. In order to properly prepare for and manage the curation, preservation and sharing of digitally-encoded data, data stewards must be able to characterize and assess the relationships holding between data-carrying digital resources. However, identity-related questions about resources and their information content may not be straightforward to answer: for example, what exactly does it mean to say that two files contain the same data, but in different formats? Information content is frequently distinguished from particular representations, but there is no adequately developed shared understanding of what this really means and how the relationship between content and its representations hold. The Data Concepts group at the Center for Informatics Research in Science and Scholarship (CIRSS), University of Illinois at Urbana Champaign, is developing a logic-based framework of fundamental concepts related to scientific data to support curation and integration. One project goal is to develop precise accounts of information resources carrying the same data. We present two complementary conceptual models for information representation: the Basic Representation Model (BRM) and the Systematic Assertion Model (SAM). We show how these models provide an analytical account of digitally-encoded scientific data and a precise understanding of identity and equivalence. The Basic Representation Model identifies the core entities and relationships involved in representing information carried by digital objects. In BRM, digital objects are symbol structures that express propositional content, and stand in layered encoding relationships. For example, an RDF description may be serialized as either XML or N3, and those expressions in turn may be encoded as either UTF-8 or UTF-16 sequences. Defining this encoding stack reveals distinctions necessary for a precise account of identity and equivalence

  12. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.

    Science.gov (United States)

    Peach, Sally E; Rudomin, Emily L; Udeshi, Namrata D; Carr, Steven A; Jaffe, Jacob D

    2012-05-01

    The defining step in most chromatin immunoprecipitation (ChIP) assays is the use of an antibody to enrich for a particular protein or histone modification state associated with segments of chromatin. The specificity of the antibody is critical to the interpretation of the experiment, yet this property is rarely reported. Here, we present a quantitative method using mass spectrometry to characterize the specificity of key histone H3 modification-targeting antibodies that have previously been used to characterize the "histone code." We further extend the use of these antibody reagents to the observation of long range correlations among disparate histone modifications. Using purified human histones representing the mixture of chromatin states present in living cells, we were able to quantify the degree of target enrichment and the specificity of several commonly used, commercially available ChIP grade antibodies. We found significant differences in enrichment efficiency among various reagents directed against four frequently studied chromatin marks: H3K4me2, H3K4me3, H3K9me3, and H3K27me3. For some antibodies, we also detected significant off target enrichment of alternate modifications at the same site (i.e., enrichment of H3K4me2 by an antibody directed against H3K4me3). Through cluster analysis, we were able to recognize patterns of co-enrichment of marks at different sites on the same histone protein. Surprisingly, these co-enrichments corresponded well to "canonical" chromatin states that are exemplary of activated and repressed regions of chromatin. Altogether, our findings suggest that 1) the results of ChIP experiments need to be evaluated with caution given the potential for cross-reactivity of the commonly used histone modification recognizing antibodies, 2) multiple marks with consistent biological interpretation exist on the same histone protein molecule, and 3) some components of the histone code may be transduced on single proteins in living cells.

  13. Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton.

    Science.gov (United States)

    Pauli, Duke; Andrade-Sanchez, Pedro; Carmo-Silva, A Elizabete; Gazave, Elodie; French, Andrew N; Heun, John; Hunsaker, Douglas J; Lipka, Alexander E; Setter, Tim L; Strand, Robert J; Thorp, Kelly R; Wang, Sam; White, Jeffrey W; Gore, Michael A

    2016-04-07

    The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010-2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars. Copyright © 2016 Pauli et al.

  14. Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton

    Directory of Open Access Journals (Sweden)

    Duke Pauli

    2016-04-01

    Full Text Available The application of high-throughput plant phenotyping (HTPP to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L. recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010–2012. Canopy temperature, normalized difference vegetation index (NDVI, height, and leaf area index (LAI displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars.

  15. iTRAQ-based quantitative proteomic analysis reveals Bai-Hu-Tang enhances phagocytosis and cross-presentation against LPS fever in rabbit.

    Science.gov (United States)

    Zhang, Shidong; Wang, Dongsheng; Dong, Shuwei; Yang, Zhiqiang; Yan, Zuoting

    2017-07-31

    Bai-Hu-Tang (BHT), a classical anti-febrile Chinese formula comprising of liquorice, anemarrhena rhizome, gypsum and rice, has been traditionally used to anti-febrile treatment and promote the production of body fluid to relieve thirst. In this paper, we aim to explore anti-febrile mechanism of BHT at protein level through analyzing alteration of differentially expressed proteins (DEPs) both lipopolysaccharide (LPS) fever syndrome and that was treated with BHT in rabbits. Febrile model was induced by LPS injection (i.v.) in rabbits, and BHT (750mg dry extract/kg body weight) was gavaged to another group of LPS fever rabbits. After sacrifice of animals, total protein of liver tissue was isolated, and two-dimensional liquid chromatography (LC) - tandem mass spectrometry (MS) coupled with isobaric tags for relative and absolute quantification (iTRAQ) labeling analysis was employed to quantitatively identify differentially expressed proteins in two group animals, which were compared with control group. Then bioinformatic analysis of DEPs was conducted through hierarchical Clustering, Venn analysis, gene ontology (GO) annotation enrichment, and kyoto encyclopedia of genes and genomes (KEGG) pathways enrichment. The results demonstrated there were 63 and 109 DEPs in LPS fever group and BHT-treated group, respectively. Enrichment analysis of GO annotations indicated that BHT mainly regulated expression of some extracellular structural proteins for response to stimulus and stress. KEGG analysis showed that ribosome and phagosome were the most significant pathways. Thereinto, several proteins in phagosome pathway were significantly up-regulated by BHT, including F-actin, coronin, Rac, and major histocompatibility complex class I (MHC I), which work in phagocytosis and cross-presentation CONCLUSION: BHT may contribute to pyrogen clearance by boosting antigenic phagocytosis, degradation, and cross presentation in the liver. Copyright © 2017. Published by Elsevier B.V.

  16. Dominant microbial composition and its vertical distribution in saline meromictic Lake Kaiike (Japan) as revealed by quantitative oligonucleotide probe membrane hybridization.

    Science.gov (United States)

    Koizumi, Yoshikazu; Kojima, Hisaya; Fukui, Manabu

    2004-08-01

    Vertical distributions of dominant bacterial populations in saline meromictic Lake Kaiike were investigated throughout the water column and sediment by quantitative oligonucleotide probe membrane hybridization. Three oligonucleotide probes specific for the small-subunit (SSU) rRNA of three groups of Chlorobiaceae were newly designed. In addition, three general domain (Bacteria, Archaea, and Eukarya)-specific probes, two delta-Proteobacteria-specific probes, a Chlorobiaceae-specific probe, and a Chloroflexi-specific probe were used after optimization of their washing conditions. The abundance of the sum of SSU rRNAs hybridizing with probes specific for three groups of Chlorobiaceae relative to total SSU rRNA peaked in the chemocline, accounting for up to 68%. The abundance of the delta-proteobacterial SSU rRNA relative to total SSU rRNA rapidly increased just below the chemocline up to 29% in anoxic water and peaked at the 2- to 3-cm sediment depth at ca. 34%. The abundance of SSU rRNAs hybridizing with the probe specific for the phylum Chloroflexi relative to total SSU rRNA was highest (31 to 54%) in the top of the sediment but then steeply declined with depth and became stable at 11 to 19%, indicating the robust coexistence of sulfate-reducing bacteria and Chloroflexi in the top of the sediment. Any SSU rRNA of Chloroflexi in the water column was under the detection limit. The summation of the signals of group-specific probes used in this study accounted for up to 89% of total SSU rRNA, suggesting that the DGGE-oligonucleotide probe hybridization approach, in contrast to conventional culture-dependent approaches, was very effective in covering dominant populations.

  17. Human mesenchymal stem cell expression program upon extended ex-vivo cultivation, as revealed by 2-DE-based quantitative proteomics.

    Directory of Open Access Journals (Sweden)

    Andreia Madeira

    Full Text Available Human mesenchymal stem cells (MSC have been on the focus of intense clinical-oriented research due to their multilineage differentiation potential and immunomodulatory properties. However, to reach the clinically meaningful cell numbers for cellular therapy and tissue engineering applications, MSC ex-vivo expansion is mandatory but sequential cell passaging results in loss of proliferative, clonogenic and differentiation potential. To get clues into the molecular mechanisms underlying cellular senescence resulting from extended ex-vivo cultivation of bone marrow (BM MSC, we explored a two-dimensional gel electrophoresis (2-DE based quantitative proteomics to compare the expression programs of Passage 3 cells (P3, commonly used in clinical studies with expanded MSC, and Passage 7 (P7 cells, which already demonstrated significant signs of culture-induced senescence. Proteins of the functional categories "Structural components and cellular cytoskeleton" and "Folding and stress response proteins" are less abundant in P7 cells, compared to P3, while proteins involved in "Energy metabolism", "Cell cycle regulation and aging" and "Apoptosis" are more abundant. The large number of multiple size and charge isoforms with an altered content that were identified in this study in P7 versus P3, namely the cytoskeleton components β-actin (7 forms and vimentin (24 forms, also emphasizes the importance of post-transcriptional modification upon long-term cultivation. The differential protein expression registered suggests that cellular senescence occurring during ex-vivo expansion of BM MSC is associated with the impairment of cytoskeleton remodeling and/or organization and the repair of damaged proteins resulting from cell exposure to culture stress. The genome-wide expression approach used in this study has proven useful for getting mechanistic insights into the observed decrease on the proliferative and clonogenic potential of P7 versus P3 cells and paves the

  18. Human mesenchymal stem cell expression program upon extended ex-vivo cultivation, as revealed by 2-DE-based quantitative proteomics.

    Science.gov (United States)

    Madeira, Andreia; da Silva, Cláudia L; dos Santos, Francisco; Camafeita, Emilio; Cabral, Joaquim M S; Sá-Correia, Isabel

    2012-01-01

    Human mesenchymal stem cells (MSC) have been on the focus of intense clinical-oriented research due to their multilineage differentiation potential and immunomodulatory properties. However, to reach the clinically meaningful cell numbers for cellular therapy and tissue engineering applications, MSC ex-vivo expansion is mandatory but sequential cell passaging results in loss of proliferative, clonogenic and differentiation potential. To get clues into the molecular mechanisms underlying cellular senescence resulting from extended ex-vivo cultivation of bone marrow (BM) MSC, we explored a two-dimensional gel electrophoresis (2-DE) based quantitative proteomics to compare the expression programs of Passage 3 cells (P3), commonly used in clinical studies with expanded MSC, and Passage 7 (P7) cells, which already demonstrated significant signs of culture-induced senescence. Proteins of the functional categories "Structural components and cellular cytoskeleton" and "Folding and stress response proteins" are less abundant in P7 cells, compared to P3, while proteins involved in "Energy metabolism", "Cell cycle regulation and aging" and "Apoptosis" are more abundant. The large number of multiple size and charge isoforms with an altered content that were identified in this study in P7 versus P3, namely the cytoskeleton components β-actin (7 forms) and vimentin (24 forms), also emphasizes the importance of post-transcriptional modification upon long-term cultivation. The differential protein expression registered suggests that cellular senescence occurring during ex-vivo expansion of BM MSC is associated with the impairment of cytoskeleton remodeling and/or organization and the repair of damaged proteins resulting from cell exposure to culture stress. The genome-wide expression approach used in this study has proven useful for getting mechanistic insights into the observed decrease on the proliferative and clonogenic potential of P7 versus P3 cells and paves the way to set

  19. Quantitative real-time reverse transcription-PCR analysis reveals stable and prolonged neurotoxin cluster gene activity in a Clostridium botulinum type E strain at refrigeration temperature.

    Science.gov (United States)

    Chen, Ying; Korkeala, Hannu; Lindén, Jere; Lindström, Miia

    2008-10-01

    The relative expression levels of six botulinum neurotoxin cluster genes in a group II Clostridium botulinum type E strain grown at 10 or 30 degrees C were investigated using quantitative real-time reverse transcription-PCR. An enzyme-linked immunosorbent assay was used to confirm neurotoxin expression. Distinct mRNA and toxin production patterns were observed at the two temperatures. The average relative mRNA levels at 10 degrees C were higher than (ntnh and p47), similar to (botE), or lower than (orfx1, orfx2, orfx3) those at 30 degrees C. The maximum botE expression levels and average neurotoxin levels at 10 degrees C were 45 to 65% of those at 30 degrees C. The relative mRNA levels at 10 degrees C declined generally slowly within 8 days, as opposed to the rapid decline observed at 30 degrees C within 24 h. Distinct expression patterns of the six genes at the two temperatures suggest that the type E neurotoxin cluster genes are transcribed as two tricistronic operons at 30 degrees C, whereas at 10 degrees C monocistronic (botE or orfx1 alone) and bicistronic (ntnh-p47 and orfx2-orfx3) transcription may dominate. Thus, type E botulinum neurotoxin production may be involved with various temperature-dependent regulatory events. In light of group II C. botulinum type E being a dangerous food-borne pathogen, these findings may be important in terms of the safety of refrigerated packaged foods of extended durability.

  20. Quantitative PCR reveals strong spatial and temporal variation of the wasting disease pathogen, Labyrinthula zosterae in northern European eelgrass (Zostera marina beds.

    Directory of Open Access Journals (Sweden)

    Anna-Christina Bockelmann

    Full Text Available Seagrass beds are the foundation species of functionally important coastal ecosystems worldwide. The world's largest losses of the widespread seagrass Zostera marina (eelgrass have been reported as a consequence of wasting disease, an infection with the endophytic protist Labyrinthula zosterae. During one of the most extended epidemics in the marine realm, ∼90% of East and Western Atlantic eelgrass beds died-off between 1932 and 1934. Today, small outbreaks continue to be reported, but the current extent of L. zosterae in European meadows is completely unknown. In this study we quantify the abundance and prevalence of the wasting disease pathogen among 19 Z. marina populations in northern European coastal waters, using quantitative PCR (QPCR with primers targeting a species specific portion of the internally transcribed spacer (ITS1 of L. zosterae. Spatially, we found marked variation among sites with abundances varying between 0 and 126 cells mg(-1 Z. marina dry weight (mean: 5.7 L. zosterae cells mg(-1 Z. marina dry weight ±1.9 SE and prevalences ranged from 0-88.9%. Temporarily, abundances varied between 0 and 271 cells mg(-1 Z. marina dry weight (mean: 8.5±2.6 SE, while prevalences ranged from zero in winter and early spring to 96% in summer. Field concentrations accessed via bulk DNA extraction and subsequent QPCR correlated well with prevalence data estimated via isolation and cultivation from live plant tissue. L. zosterae was not only detectable in black lesions, a sign of Labyrinthula-induced necrosis, but also occurred in green, apparently healthy tissue. We conclude that L. zosterae infection is common (84% infected populations in (northern European eelgrass populations with highest abundances during the summer months. In the light of global climate change and increasing rate of marine diseases our data provide a baseline for further studies on the causes of pathogenic outbreaks of L. zosterae.

  1. Quantitative profiling of the shedding rate of the three Marek's disease virus (MDV) serotypes reveals that challenge with virulent MDV markedly increases shedding of vaccinal viruses.

    Science.gov (United States)

    Islam, Aminul; Walkden-Brown, Stephen W

    2007-08-01

    The shedding profile of Marek's disease virus serotype 1 (MDV1, virulent), serotype 2 (MDV2, vaccinal) and herpesvirus of turkeys (HVT, vaccinal) in commercial broiler chickens was determined by measuring the daily rate of production of feather dander from chickens housed in isolators and by quantifying the viral load of each of these serotypes in the dander using quantitative real-time PCR (qPCR). MDV1 and HVT viruses were detectable in dander filtered from isolator exhaust air from day 7 and MDV2 from day 12 after infection and thereafter until the end of the experiment at 61 days of age of the chickens. There was no difference in shedding rate among the three MDV1 isolates. Daily shedding of MDV1 increased sharply between days 7 and 28 and stabilized thereafter at about 10(9) virus copies per chicken per day, irrespective of vaccination status. Challenge with the three different MDV1 isolates markedly increased shedding of the vaccinal viruses HVT and MDV2 in dander by 38- and 75-fold, respectively. These results demonstrate the utility of qPCR for the differentiation and quantification of different MDV serotypes in feather dander and have significant implications for the routine monitoring of Marek's disease using qPCR assays of dust, for epidemiological modelling of the behaviour and spread of MDVs in chicken populations and for studies into the evolution of virulence in MDV1 in the face of blanket vaccination with imperfect vaccines that ameliorate disease but do not prevent infection and replication of virulent virus.

  2. Quantitative proteomics analysis reveals perturbation of lipid metabolic pathways in the liver of Atlantic cod (Gadus morhua) treated with PCB 153.

    Science.gov (United States)

    Yadetie, Fekadu; Oveland, Eystein; Døskeland, Anne; Berven, Frode; Goksøyr, Anders; Karlsen, Odd André

    2017-04-01

    PCB 153 is one of the most abundant PCB congeners detected in biological samples. It is a persistent compound that is still present in the environment despite the ban on production and use of PCBs in the late 1970s. It has strong tendencies to bioaccumulate and biomagnify in biota, and studies have suggested that it is an endocrine and metabolic disruptor. In order to study mechanisms of toxicity, we exposed Atlantic cod (Gadus morhua) to various doses of PCB 153 (0, 0.5, 2 and 8mg/kg body weight) for two weeks and examined the effects on expression of liver proteins using label-free quantitative proteomics. Label-free liquid chromatography-mass spectrometry analysis of the liver proteome resulted in the quantification of 1272 proteins, of which 78 proteins were differentially regulated in the PCB 153-treated dose groups compared to the control group. Functional enrichment analysis showed that pathways significantly affected are related to lipid metabolism, cytoskeletal remodeling, cell cycle and cell adhesion. Importantly, the main effects appear to be on lipid metabolism, with up-regulation of enzymes in the de novo fatty acid synthesis pathway, consistent with previous transcriptomics results. Increased plasma triglyceride levels were also observed in the PCB 153 treated fish, in agreement with the induction of the lipogenic genes and proteins. The results suggest that PCB 153 perturbs lipid metabolism in the Atlantic cod liver. Elevated levels of lipogenic enzymes and plasma triglycerides further suggest increased synthesis of fatty acids and triglycerides. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A Novel Function for Arabidopsis CYCLASE1 in Programmed Cell Death Revealed by Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Analysis of Extracellular Matrix Proteins.

    Science.gov (United States)

    Smith, Sarah J; Kroon, Johan T M; Simon, William J; Slabas, Antoni R; Chivasa, Stephen

    2015-06-01

    Programmed cell death is essential for plant development and stress adaptation. A detailed understanding of the signal transduction pathways that regulate plant programmed cell death requires identification of the underpinning protein networks. Here, we have used a protagonist and antagonist of programmed cell death triggered by fumonisin B1 as probes to identify key cell death regulatory proteins in Arabidopsis. Our hypothesis was that changes in the abundance of cell death-regulatory proteins induced by the protagonist should be blocked or attenuated by concurrent treatment with the antagonist. We focused on proteins present in the mobile phase of the extracellular matrix on the basis that they are important for cell-cell communications during growth and stress-adaptive responses. Salicylic acid, a plant hormone that promotes programmed cell death, and exogenous ATP, which can block fumonisin B1-induced cell death, were used to treat Arabidopsis cell suspension cultures prior to isobaric-tagged relative and absolute quantitation analysis of secreted proteins. A total of 33 proteins, whose response to salicylic acid was suppressed by ATP, were identified as putative cell death-regulatory proteins. Among these was CYCLASE1, which was selected for further analysis using reverse genetics. Plants in which CYCLASE1 gene expression was knocked out by insertion of a transfer-DNA sequence manifested dramatically increased cell death when exposed to fumonisin B1 or a bacterial pathogen that triggers the defensive hypersensitive cell death. Although pathogen inoculation altered CYCLASE1 gene expression, multiplication of bacterial pathogens was indistinguishable between wild type and CYCLASE1 knockout plants. However, remarkably severe chlorosis symptoms developed on gene knockout plants in response to inoculation with either a virulent bacterial pathogen or a disabled mutant that is incapable of causing disease in wild type plants. These results show that CYCLASE1, which

  4. Quantitative analysis of viral load per haploid genome revealed the different biological features of Merkel cell polyomavirus infection in skin tumor.

    Directory of Open Access Journals (Sweden)

    Satoshi Ota

    Full Text Available Merkel cell polyomavirus (MCPyV has recently been identified in Merkel cell carcinoma (MCC, an aggressive cancer that occurs in sun-exposed skin. Conventional technologies, such as polymerase chain reaction (PCR and immunohistochemistry, have produced conflicting results for MCPyV infections in non-MCC tumors. Therefore, we performed quantitative analyses of the MCPyV copy number in various skin tumor tissues, including MCC (n = 9 and other sun exposure-related skin tumors (basal cell carcinoma [BCC, n = 45], actinic keratosis [AK, n = 52], Bowen's disease [n = 34], seborrheic keratosis [n = 5], primary cutaneous anaplastic large-cell lymphoma [n = 5], malignant melanoma [n = 5], and melanocytic nevus [n = 6]. In a conventional PCR analysis, MCPyV DNA was detected in MCC (9 cases; 100%, BCC (1 case; 2%, and AK (3 cases; 6%. We then used digital PCR technology to estimate the absolute viral copy number per haploid human genome in these tissues. The viral copy number per haploid genome was estimated to be around 1 in most MCC tissues, and there were marked differences between the MCC (0.119-42.8 and AK (0.02-0.07 groups. PCR-positive BCC tissue showed a similar viral load as MCC tissue (0.662. Immunohistochemistry with a monoclonal antibody against the MCPyV T antigen (CM2B4 demonstrated positive nuclear localization in most of the high-viral-load tumor groups (8 of 9 MCC and 1 BCC, but not in the low-viral-load or PCR-negative tumor groups. These results demonstrated that MCPyV infection is possibly involved in a minority of sun-exposed skin tumors, including BCC and AK, and that these tumors display different modes of infection.

  5. Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex.

    Directory of Open Access Journals (Sweden)

    Thomas Nebl

    2011-09-01

    Full Text Available Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca²⁺-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of ³²[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca²⁺-dependent phosphorylation patterns on three of its components--GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component.

  6. Acquired Equivalence Changes Stimulus Representations

    Science.gov (United States)

    Meeter, M.; Shohamy, D.; Myers, C. E.

    2009-01-01

    Acquired equivalence is a paradigm in which generalization is increased between two superficially dissimilar stimuli (or antecedents) that have previously been associated with similar outcomes (or consequents). Several possible mechanisms have been proposed, including changes in stimulus representations, either in the form of added associations or…

  7. USEPA PATHOGEN EQUIVALENCY COMMITTEE RETREAT

    Science.gov (United States)

    The Pathogen Equivalency Committee held its retreat from September 20-21, 2005 at Hueston Woods State Park in College Corner, Ohio. This presentation will update the PEC’s membership on emerging pathogens, analytical methods, disinfection techniques, risk analysis, preparat...

  8. Comments on field equivalence principles

    DEFF Research Database (Denmark)

    Appel-Hansen, Jørgen

    1987-01-01

    It is pointed Out that often-used arguments based on a short-circuit concept in presentations of field equivalence principles are not correct. An alternative presentation based on the uniqueness theorem is given. It does not contradict the results obtained by using the short-circuit concept...

  9. Quantitative Assessment of Chromatin Immunoprecipitation Grade Antibodies Directed against Histone Modifications Reveals Patterns of Co-occurring Marks on Histone Protein Molecules*

    Science.gov (United States)

    Peach, Sally E.; Rudomin, Emily L.; Udeshi, Namrata D.; Carr, Steven A.; Jaffe, Jacob D.

    2012-01-01

    The defining step in most chromatin immunoprecipitation (ChIP) assays is the use of an antibody to enrich for a particular protein or histone modification state associated with segments of chromatin. The specificity of the antibody is critical to the interpretation of the experiment, yet this property is rarely reported. Here, we present a quantitative method using mass spectrometry to characterize the specificity of key histone H3 modification-targeting antibodies that have previously been used to characterize the “histone code.” We further extend the use of these antibody reagents to the observation of long range correlations among disparate histone modifications. Using purified human histones representing the mixture of chromatin states present in living cells, we were able to quantify the degree of target enrichment and the specificity of several commonly used, commercially available ChIP grade antibodies. We found significant differences in enrichment efficiency among various reagents directed against four frequently studied chromatin marks: H3K4me2, H3K4me3, H3K9me3, and H3K27me3. For some antibodies, we also detected significant off target enrichment of alternate modifications at the same site (i.e., enrichment of H3K4me2 by an antibody directed against H3K4me3). Through cluster analysis, we were able to recognize patterns of co-enrichment of marks at different sites on the same histone protein. Surprisingly, these co-enrichments corresponded well to “canonical” chromatin states that are exemplary of activated and repressed regions of chromatin. Altogether, our findings suggest that 1) the results of ChIP experiments need to be evaluated with caution given the potential for cross-reactivity of the commonly used histone modification recognizing antibodies, 2) multiple marks with consistent biological interpretation exist on the same histone protein molecule, and 3) some components of the histone code may be transduced on single proteins in living

  10. A Quantitative Model of the GIRK1/2 Channel Reveals That Its Basal and Evoked Activities Are Controlled by Unequal Stoichiometry of Gα and Gβγ

    Science.gov (United States)

    Rubinstein, Moran; Farhy-Tselnicker, Isabella; Styr, Boaz; Keren-Raifman, Tal; Dessauer, Carmen W.; Dascal, Nathan

    2015-01-01

    G protein-gated K+ channels (GIRK; Kir3), activated by Gβγ subunits derived from Gi/o proteins, regulate heartbeat and neuronal excitability and plasticity. Both neurotransmitter-evoked (Ievoked) and neurotransmitter-independent basal (Ibasal) GIRK activities are physiologically important, but mechanisms of Ibasal and its relation to Ievoked are unclear. We have previously shown for heterologously expressed neuronal GIRK1/2, and now show for native GIRK in hippocampal neurons, that Ibasal and Ievoked are interrelated: the extent of activation by neurotransmitter (activation index, Ra) is inversely related to Ibasal. To unveil the underlying mechanisms, we have developed a quantitative model of GIRK1/2 function. We characterized single-channel and macroscopic GIRK1/2 currents, and surface densities of GIRK1/2 and Gβγ expressed in Xenopus oocytes. Based on experimental results, we constructed a mathematical model of GIRK1/2 activity under steady-state conditions before and after activation by neurotransmitter. Our model accurately recapitulates Ibasal and Ievoked in Xenopus oocytes, HEK293 cells and hippocampal neurons; correctly predicts the dose-dependent activation of GIRK1/2 by coexpressed Gβγ and fully accounts for the inverse Ibasal-Ra correlation. Modeling indicates that, under all conditions and at different channel expression levels, between 3 and 4 Gβγ dimers are available for each GIRK1/2 channel. In contrast, available Gαi/o decreases from ~2 to less than one Gα per channel as GIRK1/2's density increases. The persistent Gβγ/channel (but not Gα/channel) ratio support a strong association of GIRK1/2 with Gβγ, consistent with recruitment to the cell surface of Gβγ, but not Gα, by GIRK1/2. Our analysis suggests a maximal stoichiometry of 4 Gβγ but only 2 Gαi/o per one GIRK1/2 channel. The unique, unequal association of GIRK1/2 with G protein subunits, and the cooperative nature of GIRK gating by Gβγ, underlie the complex pattern of

  11. A quantitative, high-throughput reverse genetic screen reveals novel connections between Pre-mRNA splicing and 5' and 3' end transcript determinants.

    Directory of Open Access Journals (Sweden)

    Laura-Oana Albulescu

    Full Text Available Here we present the development and implementation of a genome-wide reverse genetic screen in the budding yeast, Saccharomyces cerevisiae, that couples high-throughput strain growth, robotic RNA isolation and cDNA synthesis, and quantitative PCR to allow for a robust determination of the level of nearly any cellular RNA in the background of ~5,500 different mutants. As an initial test of this approach, we sought to identify the full complement of factors that impact pre-mRNA splicing. Increasing lines of evidence suggest a relationship between pre-mRNA splicing and other cellular pathways including chromatin remodeling, transcription, and 3' end processing, yet in many cases the specific proteins responsible for functionally connecting these pathways remain unclear. Moreover, it is unclear whether all pathways that are coupled to splicing have been identified. As expected, our approach sensitively detects pre-mRNA accumulation in the vast majority of strains containing mutations in known splicing factors. Remarkably, however, several additional candidates were found to cause increases in pre-mRNA levels similar to that seen for canonical splicing mutants, none of which had previously been implicated in the splicing pathway. Instead, several of these factors have been previously implicated to play roles in chromatin remodeling, 3' end processing, and other novel categories. Further analysis of these factors using splicing-sensitive microarrays confirms that deletion of Bdf1, a factor that links transcription initiation and chromatin remodeling, leads to a global splicing defect, providing evidence for a novel connection between pre-mRNA splicing and this component of the SWR1 complex. By contrast, mutations in 3' end processing factors such as Cft2 and Yth1 also result in pre-mRNA splicing defects, although only for a subset of transcripts, suggesting that spliceosome assembly in S. cerevisiae may more closely resemble mammalian models of exon

  12. Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.

    Science.gov (United States)

    Woys, Ann Marie; Almeida, Aaron M; Wang, Lu; Chiu, Chi-Cheng; McGovern, Michael; de Pablo, Juan J; Skinner, James L; Gellman, Samuel H; Zanni, Martin T

    2012-11-21

    Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel β-sheets. Using a synthetic macrocycle that enforces a two stranded parallel β-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly (13)C═(18)O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies of the labels ranged from 1585 to 1595 cm(-1), with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the line widths and frequencies nearly quantitatively. Historically, the characteristic features of β-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through-space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel β-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm(-1) line width. Narrower line widths indicate that the amide I backbone is solvent

  13. Quantitative Persulfide Site Identification (qPerS-SID) Reveals Protein Targets of H2S Releasing Donors in Mammalian Cells.

    Science.gov (United States)

    Longen, Sebastian; Richter, Florian; Köhler, Yvette; Wittig, Ilka; Beck, Karl-Friedrich; Pfeilschifter, Josef

    2016-07-14

    H2S is an important signalling molecule involved in diverse biological processes. It mediates the formation of cysteine persulfides (R-S-SH), which affect the activity of target proteins. Like thiols, persulfides show reactivity towards electrophiles and behave similarly to other cysteine modifications in a biotin switch assay. In this manuscript, we report on qPerS-SID a mass spectrometry-based method allowing the isolation of persulfide containing peptides in the mammalian proteome. With this method, we demonstrated that H2S donors differ in their efficacy to induce persulfides in HEK293 cells. Furthermore, data analysis revealed that persulfide formation affects all subcellular compartments and various cellular processes. Negatively charged amino acids appeared more frequently adjacent to cysteines forming persulfides. We confirmed our proteomic data using pyruvate kinase M2 as a model protein and showed that several cysteine residues are prone to persulfide formation finally leading to its inactivation. Taken together, the site-specific identification of persulfides on a proteome scale can help to identify target proteins involved in H2S signalling and enlightens the biology of H2S and its releasing agents.

  14. Matching Derived Functionally-Same Stimulus Relations: Equivalence-Equivalence and Classical Analogies

    National Research Council Canada - National Science Library

    Carpentier, Franck; Smeets, Paul M; Barnes-Holmes, Dermot; Stewart, Ian

    2004-01-01

    ... (equivalence-equivalence). Similar performances are required in classical analogies (a : b :: c : d). Therefore, some researchers have argued that equivalence-equivalence can serve as a behavior analytic model for analogical reasoning...

  15. EQUIVALENCE VERSUS NON-EQUIVALENCE IN ECONOMIC TRANSLATION

    Directory of Open Access Journals (Sweden)

    Cristina, Chifane

    2012-01-01

    Full Text Available This paper aims at highlighting the fact that “equivalence” represents a concept worth revisiting and detailing upon when tackling the translation process of economic texts both from English into Romanian and from Romanian into English. Far from being exhaustive, our analysis will focus upon the problems arising from the lack of equivalence at the word level. Consequently, relevant examples from the economic field will be provided to account for the following types of non-equivalence at word level: culturespecific concepts; the source language concept is not lexicalised in the target language; the source language word is semantically complex; differences in physical and interpersonal perspective; differences in expressive meaning; differences in form; differences in frequency and purpose of using specific forms and the use of loan words in the source text. Likewise, we shall illustrate a number of translation strategies necessary to deal with the afore-mentioned cases of non-equivalence: translation by a more general word (superordinate; translation by a more neutral/less expressive word; translation by cultural substitution; translation using a loan word or loan word plus explanation; translation by paraphrase using a related word; translation by paraphrase using unrelated words; translation by omission and translation by illustration.

  16. MiRNA Analysis by Quantitative PCR in Preterm Human Breast Milk Reveals Daily Fluctuations of hsa-miR-16-5p.

    Directory of Open Access Journals (Sweden)

    Ilaria Floris

    Full Text Available Human breast milk is an extremely dynamic fluid containing many biologically-active components which change throughout the feeding period and throughout the day. We designed a miRNA assay on minimized amounts of raw milk obtained from mothers of preterm infants. We investigated changes in miRNA expression within month 2 of lactation and then over the course of 24 hours.Analyses were performed on pooled breast milk, made by combining samples collected at different clock times from the same mother donor, along with time series collected over 24 hours from four unsynchronized mothers. Whole milk, lipids or skim milk fractions were processed and analyzed by qPCR. We measured hsa-miR-16-5p, hsa-miR-21-5p, hsa-miR-146-5p, and hsa-let-7a, d and g (all -5p. Stability of miRNA endogenous controls was evaluated using RefFinder, a web tool integrating geNorm, Normfinder, BestKeeper and the comparative ΔΔCt method.MiR-21 and miR-16 were stably expressed in whole milk collected within month 2 of lactation from four mothers. Analysis of lipids and skim milk revealed that miR-146b and let-7d were better references in both fractions. Time series (5H-23H allowed the identification of a set of three endogenous reference genes (hsa-let-7d, hsa-let-7g and miR-146b to normalize raw quantification cycle (Cq data. We identified a daily oscillation of miR-16-5p.Our assay allows exploring miRNA levels of breast milk from mother with preterm baby collected in time series over 48-72 hours.

  17. A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences.

    Science.gov (United States)

    Conlan, Jessica A; Rocker, Melissa M; Francis, David S

    2017-01-01

    Lipids are involved in a host of biochemical and physiological processes in corals. Therefore, changes in lipid composition reflect changes in the ecology, nutrition, and health of corals. As such, accurate lipid extraction, quantification, and identification is critical to obtain comprehensive insight into a coral's condition. However, discrepancies exist in sample preparation methodology globally, and it is currently unknown whether these techniques generate analogous results. This study compared the two most common sample preparation techniques for lipid analysis in corals: (1) tissue isolation by air-spraying and (2) crushing the coral in toto. Samples derived from each preparation technique were subsequently analysed to quantify lipids and their constituent classes and fatty acids in four common, scleractinian coral species representing three distinct morphotypes (Acropora millepora, Montipora crassotuberculata, Porites cylindrica, and Pocillopora damicornis). Results revealed substantial amounts of organic material, including lipids, retained in the skeletons of all species following air-spraying, causing a marked underestimation of total lipid concentration using this method. Moreover, lipid class and fatty acid compositions between the denuded skeleton and sprayed tissue were substantially different. In particular, the majority of the total triacylglycerol and total fatty acid concentrations were retained in the skeleton (55-69% and 56-64%, respectively). As such, the isolated, sprayed tissue cannot serve as a reliable proxy for lipid quantification or identification in the coral holobiont. The in toto crushing method is therefore recommended for coral sample preparation prior to lipid analysis to capture the lipid profile of the entire holobiont, permitting accurate diagnoses of coral condition.

  18. Quantitative proteome-level analysis of paulownia witches’ broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes

    Directory of Open Access Journals (Sweden)

    Zhe Wang

    2017-07-01

    Full Text Available Paulownia witches’ broom (PaWB disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ to quantify and analyze the proteome-level changes among healthy P. fortunei (PF, PaWB-infected P. fortunei (PFI, and PaWB-infected P. fortunei treated with 20 mg L−1 or 60 mg L−1 methyl methane sulfonate (MMS (PFI-20 and PFI-60, respectively. A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process and PFI-20 vs. PFI-60 (recovered process, and further found that many of the MMS-response proteins mapped to “photosynthesis” and “ribosome” pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1 carbohydrate and energy metabolism, (2 protein synthesis and degradation, and (3 stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.

  19. Simulation-Based Prediction of Equivalent Continuous Noises during Construction Processes.

    Science.gov (United States)

    Zhang, Hong; Pei, Yun

    2016-08-12

    Quantitative prediction of construction noise is crucial to evaluate construction plans to help make decisions to address noise levels. Considering limitations of existing methods for measuring or predicting the construction noise and particularly the equivalent continuous noise level over a period of time, this paper presents a discrete-event simulation method for predicting the construction noise in terms of equivalent continuous level. The noise-calculating models regarding synchronization, propagation and equivalent continuous level are presented. The simulation framework for modeling the noise-affected factors and calculating the equivalent continuous noise by incorporating the noise-calculating models into simulation strategy is proposed. An application study is presented to demonstrate and justify the proposed simulation method in predicting the equivalent continuous noise during construction. The study contributes to provision of a simulation methodology to quantitatively predict the equivalent continuous noise of construction by considering the relevant uncertainties, dynamics and interactions.

  20. Simulation-Based Prediction of Equivalent Continuous Noises during Construction Processes

    Directory of Open Access Journals (Sweden)

    Hong Zhang

    2016-08-01

    Full Text Available Quantitative prediction of construction noise is crucial to evaluate construction plans to help make decisions to address noise levels. Considering limitations of existing methods for measuring or predicting the construction noise and particularly the equivalent continuous noise level over a period of time, this paper presents a discrete-event simulation method for predicting the construction noise in terms of equivalent continuous level. The noise-calculating models regarding synchronization, propagation and equivalent continuous level are presented. The simulation framework for modeling the noise-affected factors and calculating the equivalent continuous noise by incorporating the noise-calculating models into simulation strategy is proposed. An application study is presented to demonstrate and justify the proposed simulation method in predicting the equivalent continuous noise during construction. The study contributes to provision of a simulation methodology to quantitatively predict the equivalent continuous noise of construction by considering the relevant uncertainties, dynamics and interactions.

  1. Equivalence problem for Bishop surfaces

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The paper has two parts. We first briefly survey recent studies on the equivalence problem for real submanifolds in a complex space under the action of biholomorphic transformations. We will mainly focus on some of the recent studies of Bishop surfaces, which, in particular, includes the work of the authors. In the second part of the paper, we apply the general theory developed by the authors to explicitly classify an algebraic family of Bishop surfaces with a vanishing Bishop invariant. More precisely, we let M be a real submanifold of C 2 defined by an equation of the form w = zz + 2Re(z s + az s+1 ) with s≥ 3 and a a complex parameter. We will prove in the second part of the paper that for s≥ 4 two such surfaces are holomorphically equivalent if and only if the parameter differs by a certain rotation. When s = 3, we show that surfaces of this type with two different real parameters are not holomorphically equivalent.

  2. Equivalent statistics and data interpretation.

    Science.gov (United States)

    Francis, Gregory

    2016-10-14

    Recent reform efforts in psychological science have led to a plethora of choices for scientists to analyze their data. A scientist making an inference about their data must now decide whether to report a p value, summarize the data with a standardized effect size and its confidence interval, report a Bayes Factor, or use other model comparison methods. To make good choices among these options, it is necessary for researchers to understand the characteristics of the various statistics used by the different analysis frameworks. Toward that end, this paper makes two contributions. First, it shows that for the case of a two-sample t test with known sample sizes, many different summary statistics are mathematically equivalent in the sense that they are based on the very same information in the data set. When the sample sizes are known, the p value provides as much information about a data set as the confidence interval of Cohen's d or a JZS Bayes factor. Second, this equivalence means that different analysis methods differ only in their interpretation of the empirical data. At first glance, it might seem that mathematical equivalence of the statistics suggests that it does not matter much which statistic is reported, but the opposite is true because the appropriateness of a reported statistic is relative to the inference it promotes. Accordingly, scientists should choose an analysis method appropriate for their scientific investigation. A direct comparison of the different inferential frameworks provides some guidance for scientists to make good choices and improve scientific practice.

  3. 21 CFR 26.9 - Equivalence determination.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Equivalence determination. 26.9 Section 26.9 Food... Specific Sector Provisions for Pharmaceutical Good Manufacturing Practices § 26.9 Equivalence determination... document insufficient evidence of equivalence, lack of opportunity to assess equivalence or a determination...

  4. On the Translation Equivalence of Literature Works

    Institute of Scientific and Technical Information of China (English)

    吴娟

    2013-01-01

    As for translation principle, people have different opinions. The principle of equivalent translation may be is one of the most reason-able ones in today's translation world in my eyes. This paper focuses on the possibility and thec ondition to be achieved the biggest equivalence of the semantic, pragmatic and culture in order to get the conclusion that the translation equivalence is the proper principle. Besides,this paper has also discussed the pragmatic equivalence and cultural equivalence.

  5. On the Translation Equivalence of Literature Works

    Institute of Scientific and Technical Information of China (English)

    吴娟

    2013-01-01

    As for translation principle,people have different opinions.The principle of equivalent translation maybe is one of the most reasonable ones in today’s translation world in my eyes.This paper focuses on the possibility and the condition to be achieved the biggest equivalence of the semantic,pragmatic and culture in order to get the conclusion that the translation equivalence is the proper principle.Besides,this paper has also discussed the pragmatic equivalence and cultural equivalence.

  6. On an equivalence of fuzzy subgroups III

    Directory of Open Access Journals (Sweden)

    V. Murali

    2003-01-01

    Full Text Available This paper is the third in a series of papers studying equivalence classes of fuzzy subgroups of a given group under a suitable equivalence relation. We introduce the notion of a pinned flag in order to study the operations sum, intersection and union, and their behavior with respect to the equivalence. Further, we investigate the extent to which a homomorphism preserves the equivalence. Whenever the equivalences are not preserved, we have provided suitable counterexamples.

  7. Conformal dynamical equivalence and applications

    Science.gov (United States)

    Spyrou, N. K.

    2011-02-01

    The "Conformal Dynamical Equivalence" (CDE) approach is briefly reviewed, and some of its applications, at various astrophysical levels (Sun, Solar System, Stars, Galaxies, Clusters of Galaxies, Universe as a whole), are presented. According to the CDE approach, in both the Newtonian and general-relativistic theories of gravity, the isentropic hydrodynamic flows in the interior of a bounded gravitating perfect-fluid source are dynamically equivalent to geodesic motions in a virtual, fully defined fluid source. Equivalently, the equations of hydrodynamic motion in the former source are functionally similar to those of the geodesic motions in the latter, physically, fully defined source. The CDE approach is followed for the dynamical description of the motions in the fluid source. After an observational introduction, taking into account all the internal physical characteristics of the corresponding perfect-fluid source, and based on the property of the isentropic hydrodynamic flows (quite reasonable for an isolated physical system), we examine a number of issues, namely, (i) the classical Newtonian explanation of the celebrated Pioneer-Anomaly effect in the Solar System, (ii) the possibility of both the attractive gravity and the repulsive gravity in a non-quantum Newtonian framework, (iii) the evaluation of the masses - theoretical, dynamical, and missing - and of the linear dimensions of non-magnetized and magnetized large-scale cosmological structures, (iv) the explanation of the flat-rotation curves of disc galaxies, (v) possible formation mechanisms of winds and jets, and (vi) a brief presentation of a conventional approach - toy model to the dynamics of the Universe, characterized by the dominant collisional dark matter (with its subdominant luminous baryonic "contamination"), correctly interpreting the cosmological observational data without the need of the notions dark energy, cosmological constant, and universal accelerating expansion.

  8. Equivalence principle in Chameleon models .

    Science.gov (United States)

    Kraiselburd, L.; Landau, S.; Salgado, M.; Sudarsky, D.

    Most theories that predict time and/or space variation of fundamental constants also predict violations of the Weak Equivalence Principle (WEP). Khoury and Weltmann proposed the chameleon model in 2004 and claimed that this model avoids experimental bounds on WEP. We present a contrasting view based on an approximate calculation of the two body problem for the chameleon field and show that the force depends on the test body composition. Furthermore, we compare the prediction of the force on a test body with Eötvös type experiments and find that the chameleon field effect cannot account for current bounds.

  9. Thermodynamic equivalence of spin systems

    Energy Technology Data Exchange (ETDEWEB)

    Beltman, J.M. (Katholieke Universiteit Nijmegen (Netherlands))

    1975-01-01

    The thermodynamic equilibrium properties of systems composed of classical spin /sup 1///sub 2/ particles (Ising spins) are studied. Given an interaction pattern between the Ising spins the main problem is to calculate the equilibrium state(s) of the system. The point put forward here is the existence of many thermodynamical equivalent spin coordinate systems. As a consequence of this phenomenon the interaction pattern of a system may be very intricate when described with respect to one spin coordinate system whereas it may become simple with respect to another one and vice versa. A systematic investigation of this phenomenon is made. (FR)

  10. Blast Wave Characteristics and Equivalency

    OpenAIRE

    Sochet, Isabelle; Schneider, Helmut

    2010-01-01

    ISBN 978-5-94588-079-5; The characteristics of blast waves generated by detonation of gas clouds are studies theoretically and validated by both small-scale and large-scale experiments with ethylene-air mixtures of different equivalence ratio. The mixtures were confined in hemispherical or spherical balloons made from thin polyethylene foils of 0.75 m³ and 15 m³ in volume. The detonation of gas mixtures was initiated by a solid explosive. The characteristics of the blast wave in terms of over...

  11. Equivalence Principle in Chameleon Models

    CERN Document Server

    Kraiselburd, Lucila; Salgado, Marcelo; Sudarsky, Daniel

    2013-01-01

    Most theories that predict time and/or space variation of fundamental constants also predict violations of the Weak Equivalence Principle (WEP). Khoury and Weltmann proposed the chameleon model in 2004 and claimed that this model avoids experimental bounds on WEP. We present a contrasting view based on an approximate calculation of the two body problem for the chameleon field and show that the force depends on the test body composition. Furthermore, we compare the prediction of the force on a test body with E\\"otv\\"os type experiments and find that the chameleon field effect cannot account for current bounds.

  12. On Vasyliunas's equivalent conductivity formalism

    Science.gov (United States)

    Pontius, D. H., Jr.

    1992-01-01

    The Vasyliunas's (1972) equivalent conductivity formalism (ECF) for representing the coupling of the ionosphere and the magnetosphere is discussed, and a new, simpler, derivation is presented of the ECF, in which certain of the underlying assumptions and their implications are made transparent. The derivation presented indicates that the only role of the ions in the ECF is to insure quasi-neutrality. It is shown that the ECF is not as robust as usually assumed and that caution must be used to insure that reasonable results are obtained.

  13. Equivalent magnetization over the World's Ocean

    Science.gov (United States)

    Dyment, J.; Choi, Y.; Hamoudi, M.; Erwan, T.; Lesur, V.

    2014-12-01

    As a by-product of our recent work to build a candidate model over the oceans for the World Digital Magnetic Anomaly Map (WDMAM) version 2, we derived global distributions of the equivalent magnetization in oceanic domains. In a first step, we use classic point source forward modeling on a spherical Earth to build a forward model of the marine magnetic anomalies at sea-surface. We estimate magnetization vectors using the age map of the ocean floor, the relative plate motions, the apparent polar wander path for Africa, and a geomagnetic reversal time scale. As magnetized source geometry, we assume 1 km-thick layer bearing a 10 A/m magnetization following the topography of the oceanic basement as defined by the bathymetry and sedimentary thickness. Adding a present-day geomagnetic field model allows the computation of our initial magnetic anomaly model. In a second step, we adjust this model to the existing marine magnetic anomaly data, in order to make it consistent with these data. To do so, we extract synthetic magnetic along the ship tracks for which real data are available and we compare quantitatively the measured and computed anomalies on 100, 200 or 400 km-long sliding windows (depending the spreading rate). Among the possible comparison criteria, we discard the maximal range - too dependent on local values - and the correlation and coherency - the geographical adjustment between model and data being not accurate enough - to favor the standard deviation around the mean value. The ratio between the standard deviations of data and model on each sliding window represent an estimate of the magnetization ratio causing the anomalies, which we interpolate to adjust the initial magnetic anomaly model to the data and therefore compute a final model to be included in our WDMAM candidate over the oceanic regions lacking data. The above ratio, after division by the magnetization of 10 A/m used in the model, represents an estimate of the equivalent magnetization under the

  14. The hsp 16 Gene of the Probiotic Lactobacillus acidophilus Is Differently Regulated by Salt, High Temperature and Acidic Stresses, as Revealed by Reverse Transcription Quantitative PCR (qRT-PCR Analysis

    Directory of Open Access Journals (Sweden)

    Daniela Fiocco

    2011-08-01

    Full Text Available Small heat shock proteins (sHsps are ubiquitous conserved chaperone-like proteins involved in cellular proteins protection under stressful conditions. In this study, a reverse transcription quantitative PCR (RT-qPCR procedure was developed and used to quantify the transcript level of a small heat shock gene (shs in the probiotic bacterium Lactobacillus acidophilus NCFM, under stress conditions such as heat (45 °C and 53 °C, bile (0.3% w/v, hyperosmosis (1 M and 2.5 M NaCl, and low pH value (pH 4. The shs gene of L. acidophilus NCFM was induced by salt, high temperature and acidic stress, while repression was observed upon bile stress. Analysis of the 5' noncoding region of the hsp16 gene reveals the presence of an inverted repeat (IR sequence (TTAGCACTC-N9-GAGTGCTAA homologue to the controlling IR of chaperone expression (CIRCE elements found in the upstream regulatory region of Gram-positive heat shock operons, suggesting that the hsp16 gene of L. acidophilus might be transcriptionally controlled by HrcA. In addition, the alignment of several small heat shock proteins identified so far in lactic acid bacteria, reveals that the Hsp16 of L. acidophilus exhibits a strong evolutionary relationship with members of the Lactobacillus acidophilus group.

  15. The hsp 16 gene of the probiotic Lactobacillus acidophilus is differently regulated by salt, high temperature and acidic stresses, as revealed by reverse transcription quantitative PCR (qRT-PCR) analysis.

    Science.gov (United States)

    Capozzi, Vittorio; Arena, Mattia Pia; Crisetti, Elisabetta; Spano, Giuseppe; Fiocco, Daniela

    2011-01-01

    Small heat shock proteins (sHsps) are ubiquitous conserved chaperone-like proteins involved in cellular proteins protection under stressful conditions. In this study, a reverse transcription quantitative PCR (RT-qPCR) procedure was developed and used to quantify the transcript level of a small heat shock gene (shs) in the probiotic bacterium Lactobacillus acidophilus NCFM, under stress conditions such as heat (45 °C and 53 °C), bile (0.3% w/v), hyperosmosis (1 M and 2.5 M NaCl), and low pH value (pH 4). The shs gene of L. acidophilus NCFM was induced by salt, high temperature and acidic stress, while repression was observed upon bile stress. Analysis of the 5' noncoding region of the hsp16 gene reveals the presence of an inverted repeat (IR) sequence (TTAGCACTC-N9-GAGTGCTAA) homologue to the controlling IR of chaperone expression (CIRCE) elements found in the upstream regulatory region of Gram-positive heat shock operons, suggesting that the hsp16 gene of L. acidophilus might be transcriptionally controlled by HrcA. In addition, the alignment of several small heat shock proteins identified so far in lactic acid bacteria, reveals that the Hsp16 of L. acidophilus exhibits a strong evolutionary relationship with members of the Lactobacillus acidophilus group.

  16. Einstein's equivalence principle in cosmology

    CERN Document Server

    Kopeikin, Sergei M

    2013-01-01

    We study physical consequences of the Einstein equivalence principle (EEP) for a Hubble observer in FLRW universe. We introduce the local inertial coordinates with the help of a special conformal transformation. The local inertial metric is Minkowski flat and materialized by a congruence of time-like geodesics of static observers. The static observers are equipped with the ideal clocks measuring the proper time that is synchronized with the clocks of the Hubble observer. The local inertial metric is used for physical measurements of spacetime intervals with the ideal clocks and rulers. The special conformal transformation preserves null geodesics but does not keep invariant time-like geodesics. Moreover, it makes the rate of the local time coordinate dependent on velocity of the particle which makes impossible to rich the uniform parameterization of the world lines of static observers and light geodesics with a single parameter - they differ by the conformal factor of FLRW metric. The most convenient way to s...

  17. ROMANIC EQUIVALENTS FOR LATIN IDIOMS

    Directory of Open Access Journals (Sweden)

    Dr. Stefan DUMITRU

    2010-11-01

    Full Text Available In this study we set forth to present several of the most important aspects regarding the contrastive analysis of a well-defined number of Latin idioms in parallel with their Romanic counterparts (in French, Italian, Spanish and Romanian. Our intent was not to discover, in the Romanic space, all the equivalents of the phrases that form the corpus we work with, for reasons pertaining to material restrictions, but to discuss, based on a certain number of units, the different types of issues they may point to. The most important is to establish the relation between the idiomatic expressions in Latin and their correspondents in the above mentioned languages, regarding their inner form, their meaning and their structure.

  18. Electroweak Vortices and Gauge Equivalence

    Science.gov (United States)

    MacDowell, Samuel W.; Törnkvist, Ola

    Vortex configurations in the electroweak gauge theory are investigated. Two gauge-inequivalent solutions of the field equations, the Z and W vortices, have previously been found. They correspond to embeddings of the Abelian Nielsen-Olesen vortex solution into a U(1) subgroup of SU(2)×U(1). It is shown here that any electroweak vortex solution can be mapped into a solution of the same energy with a vanishing upper component of the Higgs field. The correspondence is a gauge equivalence for all vortex solutions except those for which the winding numbers of the upper and lower Higgs components add to zero. This class of solutions, which includes the W vortex, corresponds to a singular solution in the one-component gauge. The results, combined with numerical investigations, provide an argument against the existence of other vortex solutions in the gauge-Higgs sector of the Standard Model.

  19. Expanding the Interaction Equivalency Theorem

    Directory of Open Access Journals (Sweden)

    Brenda Cecilia Padilla Rodriguez

    2015-06-01

    Full Text Available Although interaction is recognised as a key element for learning, its incorporation in online courses can be challenging. The interaction equivalency theorem provides guidelines: Meaningful learning can be supported as long as one of three types of interactions (learner-content, learner-teacher and learner-learner is present at a high level. This study sought to apply this theorem to the corporate sector, and to expand it to include other indicators of course effectiveness: satisfaction, knowledge transfer, business results and return on expectations. A large Mexican organisation participated in this research, with 146 learners, 30 teachers and 3 academic assistants. Three versions of an online course were designed, each emphasising a different type of interaction. Data were collected through surveys, exams, observations, activity logs, think aloud protocols and sales records. All course versions yielded high levels of effectiveness, in terms of satisfaction, learning and return on expectations. Yet, course design did not dictate the types of interactions in which students engaged within the courses. Findings suggest that the interaction equivalency theorem can be reformulated as follows: In corporate settings, an online course can be effective in terms of satisfaction, learning, knowledge transfer, business results and return on expectations, as long as (a at least one of three types of interaction (learner-content, learner-teacher or learner-learner features prominently in the design of the course, and (b course delivery is consistent with the chosen type of interaction. Focusing on only one type of interaction carries a high risk of confusion, disengagement or missed learning opportunities, which can be managed by incorporating other forms of interactions.

  20. Equivalent damage of loads on pavements

    CSIR Research Space (South Africa)

    Prozzi, JA

    2009-05-26

    Full Text Available This report describes a new methodology for the determination of Equivalent Damage Factors (EDFs) of vehicles with multiple axle and wheel configurations on pavements. The basic premise of this new procedure is that "equivalent pavement response...

  1. Discovering Classes of Strongly Equivalent Logic Programs

    OpenAIRE

    Chen, Y.; Lin, F.

    2011-01-01

    In this paper we apply computer-aided theorem discovery technique to discover theorems about strongly equivalent logic programs under the answer set semantics. Our discovered theorems capture new classes of strongly equivalent logic programs that can lead to new program simplification rules that preserve strong equivalence. Specifically, with the help of computers, we discovered exact conditions that capture the strong equivalence between a rule and the empty set, between two rules, between t...

  2. Classroom Activities for Introducing Equivalence Relations

    Science.gov (United States)

    Brandt, Jim

    2013-01-01

    Equivalence relations and partitions are two interconnected ideas that play important roles in advanced mathematics. While students encounter the informal notion of equivalence in many courses, the formal definition of an equivalence relation is typically introduced in a junior level transition-to-proof course. This paper reports the results of a…

  3. Equivalence Principle in Chameleon Models

    CERN Document Server

    Kraiselburd, Lucila; Salgado, Marcelo; Sudarsky, Daniel; Vucetich, Héctor

    2015-01-01

    Most theories that predict time and(or) space variation of fundamental constants also predict violations of the Weak Equivalence Principle (WEP). Khoury and Weltman proposed the chameleon model in 2004 and claimed that this model avoids experimental bounds on the WEP. In this paper we present a contrasting view based on the analysis of the force between two bodies induced by the chameleon field using a particular approach in which the field due to both the large and the small bodies is obtained by appropriate series expansions in the various regions of interest and the corresponding matching conditions. We found that resulting force depends on the test body\\'{}s composition even when the chameleon coupling constants $\\beta_{i}$ are universal. In particular, we compared the resulting differential acceleration of test bodies made of Be and Al with the corresponding bounds obtained from E\\"otv\\"os type experiments and find that the predictions of the chameleon model are, in general, various orders of magnitude a...

  4. Testing the weak equivalence principle

    Science.gov (United States)

    Nobili, Anna M.; Comandi, Gian Luca; Pegna, Raffaello; Bramanti, Donato; Doravari, Suresh; Maccarone, Francesco; Lucchesi, David M.

    2010-01-01

    The discovery of Dark Energy and the fact that only about 5% of the mass of the universe can be explained on the basis of the current laws of physics have led to a serious impasse. Based on past history, physics might indeed be on the verge of major discoveries; but the challenge is enormous. The way to tackle it is twofold. On one side, scientists try to perform large scale direct observations and measurements - mostly from space. On the other, they multiply their efforts to put to the most stringent tests ever the physical theories underlying the current view of the physical world, from the very small to the very large. On the extremely small scale very exciting results are expected from one of the most impressive experiments in the history of mankind: the Large Hadron Collider. On the very large scale, the universe is dominated by gravity and the present impasse undoubtedly calls for more powerful tests of General Relativity - the best theory of gravity to date. Experiments testing the Weak Equivalence Principle, on which General Relativity ultimately lies, have the strongest probing power of them all; a breakthrough in sensitivity is possible with the “Galileo Galilei” (GG) satellite experiment to fly in low Earth orbit.

  5. Equivalent Simplification Method of Micro-Grid

    Directory of Open Access Journals (Sweden)

    Cai Changchun

    2013-09-01

    Full Text Available The paper concentrates on the equivalent simplification method for the micro-grid system connection into distributed network. The equivalent simplification method proposed for interaction study between micro-grid and distributed network. Micro-grid network, composite load, gas turbine synchronous generation, wind generation are equivalent simplification and parallel connect into the point of common coupling. A micro-grid system is built and three phase and single phase grounded faults are performed for the test of the equivalent model of micro-grid. The simulation results show that the equivalent model of micro-grid is effective, and the dynamic of equivalent model is similar with the detailed model of micro-grid. The equivalent simplification method for the micro-grid network and distributed components is suitable for the study of micro-grid.  

  6. Offsetting Ongoing Methane Emissions --- An Alternative to Emission Equivalence Metrics

    Science.gov (United States)

    Clisby, N.; Enting, I. G.; Lauder, A.; Carter, J.; Cowie, A.; Henry, B.; Raupach, M. R.

    2012-12-01

    The Global Warming Potential (GWP) has been widely adopted as a metric for comparing the climate impact of different greenhouse gases. As has been frequently noted, there are many problems with using GWPs to define emission equivalence in spite of the use of GWPs for this purpose in contexts such as the Kyoto Protocol. We propose that for methane, rather than define emission equivalence, the appropriate comparison is between ongoing emissions of 0.9 to 1.0 kg of CH4 per year and one-off emissions of 1 tonne of carbon. This approach represents an approximate solution to the inverse problem of defining a forcing equivalent index (FEI) that gives exact equivalence of radiative forcing over a range of timescales. In our approach, if ongoing methane emissions are offset by a one-off carbon removal that is built up with 40-year e-folding time, then the result is close to radiatively neutral over periods from years to centuries. In contrast, the GWP provides radiative equivalence (in integrated terms) only at a single time, with large discrepancies at other times. Our approach also follows from consideration of greenhouse gas stabilisation, since stabilising atmospheric CO2 requires an approximate cap on total emissions, while stabilising methane requires stabilisation of ongoing emissions. Our quantitative treatment recognises that, on time scales of centuries, removal of 1 tonne of carbon only lowers the atmospheric carbon content by 0.3 to 0.35 tonnes. We discuss the implications for rangeland grazing systems. In the absence of effective mitigation techniques for methane from rangeland systems, this approach may provide an attractive offset mechanism in spite of requiring that woody vegetation be established and maintained over about 15% of the landscape, or an equivalent amount of carbon storage in soil.

  7. Energy & Climate: Getting Quantitative

    Science.gov (United States)

    Wolfson, Richard

    2011-11-01

    A noted environmentalist claims that buying an SUV instead of a regular car is energetically equivalent to leaving your refrigerator door open for seven years. A fossil-fuel apologist argues that solar energy is a pie-in-the-sky dream promulgated by na"ive environmentalists, because there's nowhere near enough solar energy to meet humankind's energy demand. A group advocating shutdown of the Vermont Yankee nuclear plant claims that 70% of its electrical energy is lost in transmission lines. Around the world, thousands agitate for climate action, under the numerical banner ``350.'' Neither the environmentalist, the fossil-fuel apologist, the antinuclear activists, nor most of those marching under the ``350'' banner can back up their assertions with quantitative arguments. Yet questions about energy and its environmental impacts almost always require quantitative answers. Physics can help! This poster gives some cogent examples, based on the newly published 2^nd edition of the author's textbook Energy, Environment, and Climate.

  8. Metabolic equivalents during scooter exercise.

    Science.gov (United States)

    Kijima, Akira; Arimoto, Morio; Muramatsu, Shigeru

    2007-06-01

    The purpose of this study was to determine the metabolic equivalents (METs) for scooter exercise (riding a scooter, scootering) and to examine the energy expenditure and the heart rate response, so that the results can be used in health promotion activities. Eighteen young adults (10 males and 8 females) participated in scootering on a treadmill at three different speeds for six minutes each. Before, during, and after the exercise, pulmonary ventilation, oxygen uptake (VO(2)), carbon dioxide product, respiratory exchange ratio (R), and heart rate (HR) were measured. These measurements kept steady states from the 3rd to 6th minute of each different speed session. The MET values acquired during scootering at 80 m.min(-1), 110 m.min(-1), and 140 m.min(-1) were 3.9, 4.3, and 5.0, respectively. Calculated using VO(2) (ml.kg(-1).min(-1))x[4.0+R], the energy consumption for scootering at each speed was 67.0+/-10.6, 73.3+/-10.2, and 84.8+/-7.9 cal.kg(-1).min(-1), respectively. The regression equation between scootering speed (X, m.min(-1)) and VO(2) (Y, ml.kg(-1).min(-1)) is Y=0.062X+8.655, and the regression equation between HR (X, beats.min(-1)) and VO(2)reserve (Y, %) is Y=0.458X-11.264. These equations can be applied to both females and males. Thus, scootering at 80 to 140 m.min(-1) might not be sufficient to improve the cardiorespiratory fitness of young male adults similar to the participants, but it may contribute many healthy benefits to most female adults and even male adults, and improve their health and fitness at the faster speeds.

  9. INVARIANTS UNDER STABLE EQUIVALENCES OF MORITA TYPE

    Institute of Scientific and Technical Information of China (English)

    Li Fang; Sun Longgang

    2012-01-01

    The aim of this article is to study some invariants of associative algebras under stable equivalences of Morita type.First of all,we show that,if two finite-dimensional selfinjective k-algebras are stably equivalent of Morita type,then their orbit algebras are isomorphic.Secondly,it is verified that the quasitilted property of an algebra is invariant under stable equivalences of Morita type.As an application of this result,it is obtained that if an algebra is of finite representation type,then its tilted property is invariant under stable equivalences of Morita type; the other application to partial tilting modules is given in Section 4. Finally,we prove that when two finite-dimensional k-algebras are stably equivalent of Morita type,their repetitive algebras are also stably equivalent of Morita type under certain conditions.

  10. The Complexity of Identifying Large Equivalence Classes

    DEFF Research Database (Denmark)

    Skyum, Sven; Frandsen, Gudmund Skovbjerg; Miltersen, Peter Bro

    1999-01-01

    We prove that at least 3k−4/k(2k−3)(n/2) – O(k)equivalence tests and no more than 2/k (n/2) + O(n) equivalence tests are needed in the worst case to identify the equivalence classes with at least k members in set of n elements. The upper bound is an improvement by a factor 2 compared to known res...

  11. Homogeneous Dielectric Equivalents of Composite Material Shields

    Directory of Open Access Journals (Sweden)

    P. Tobola

    2009-04-01

    Full Text Available The paper deals with the methodology of replacing complicated parts of an airplane skin by simple homogeneous equivalents, which can exhibit similar shielding efficiency. On one hand, the airplane built from the virtual homogeneous equivalents can be analyzed with significantly reduced CPU-time demands and memory requirements. On the other hand, the equivalent model can estimate the internal fields satisfactory enough to evaluate the electromagnetic immunity of the airplane.

  12. Equivalent Simplification Method of Micro-Grid

    OpenAIRE

    Cai Changchun; Cao Xiangqin

    2013-01-01

    The paper concentrates on the equivalent simplification method for the micro-grid system connection into distributed network. The equivalent simplification method proposed for interaction study between micro-grid and distributed network. Micro-grid network, composite load, gas turbine synchronous generation, wind generation are equivalent simplification and parallel connect into the point of common coupling. A micro-grid system is built and three phase and single phase grounded faults are per...

  13. equivalency/majorly/market share,etc.

    Institute of Scientific and Technical Information of China (English)

    张福基

    1998-01-01

    equivalency n. a level of achievement equivalent to completion of an educational or trainingprogram。同等学历(相当于完成某一教育或训练计划的学业成绩水平):a highschool equivalency certificate中学同等学历证书。注意不能用equivalence。majorly[’meid??li]adv.[1956

  14. 21 CFR 26.6 - Equivalence assessment.

    Science.gov (United States)

    2010-04-01

    ... OF PHARMACEUTICAL GOOD MANUFACTURING PRACTICE REPORTS, MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS... Specific Sector Provisions for Pharmaceutical Good Manufacturing Practices § 26.6 Equivalence...

  15. Approximate equivalence in von Neumann algebras

    Institute of Scientific and Technical Information of China (English)

    DING; Huiru; Don; Hadwin

    2005-01-01

    One formulation of D. Voiculescu's theorem on approximate unitary equivalence is that two unital representations π and ρ of a separable C*-algebra are approximately unitarily equivalent if and only if rank o π = rank o ρ. We study the analog when the ranges of π and ρ are contained in a von Neumann algebra R, the unitaries inducing the approximate equivalence must come from R, and "rank" is replaced with "R-rank" (defined as the Murray-von Neumann equivalence of the range projection).

  16. Criteria equivalent to the Riemann Hypothesis

    Science.gov (United States)

    Cisło, J.; Wolf, M.

    2008-11-01

    We give a brief overview of a few criteria equivalent to the Riemann Hypothesis. Next we concentrate on the Riesz and Báez-Duarte criteria. We prove that they are equivalent and we provide some computer data to support them.

  17. EQUIVALENT MODELS IN COVARIANCE STRUCTURE-ANALYSIS

    NARCIS (Netherlands)

    LUIJBEN, TCW

    1991-01-01

    Defining equivalent models as those that reproduce the same set of covariance matrices, necessary and sufficient conditions are stated for the local equivalence of two expanded identified models M1 and M2 when fitting the more restricted model M0. Assuming several regularity conditions, the rank def

  18. Galeazzi-equivalent lesions in adolescence.

    Science.gov (United States)

    Kamano, Masayuki; Honda, Yoshinobu

    2002-07-01

    Two cases of a Galeazzi-equivalent lesion in adolescence are described. Accurate diagnosis of the epiphyseal injury of the distal ulna, rigid fixation of the distal radius, and stabilization of the distal radioulnar joint are keys in obtaining a good result in the treatment of Galeazzi-equivalent lesion in adolescence.

  19. Orientifold Planar Equivalence: The Chiral Condensate

    DEFF Research Database (Denmark)

    Armoni, Adi; Lucini, Biagio; Patella, Agostino

    2008-01-01

    The recently introduced orientifold planar equivalence is a promising tool for solving non-perturbative problems in QCD. One of the predictions of orientifold planar equivalence is that the chiral condensates of a theory with $N_f$ flavours of Dirac fermions in the symmetric (or antisymmetric...

  20. Flow equivalence and isotopy for subshifts

    DEFF Research Database (Denmark)

    Boyle, Mike; Carlsen, Toke Meier; Eilers, Søren

    2017-01-01

    We study basic properties of flow equivalence on one-dimensional compact metric spaces with a particular emphasis on isotopy in the group of (self-) flow equivalences on such a space. In particular, we show that such an orbit-preserving map is not always an isotopy, but that this always is the ca...

  1. The therapeutic equivalence of complex drugs

    NARCIS (Netherlands)

    Schellekens, H.; Klinger, E.; Muehlebach, S.; Brin, J-F.; Storm, G.; Crommelin, D.J.A.

    2011-01-01

    When the patent of a small molecule drug expires generics may be introduced. They are considered therapeutically equivalent once pharmaceutical equivalence (i.e. identical active substances) and bioequivalence (i.e. comparable pharmacokinetics) have been established in a cross-over volunteer study.

  2. A Discrete Equivalent of the Logistic Equation

    Directory of Open Access Journals (Sweden)

    Petropoulou EugeniaN

    2010-01-01

    Full Text Available A discrete equivalent and not analogue of the well-known logistic differential equation is proposed. This discrete equivalent logistic equation is of the Volterra convolution type, is obtained by use of a functional-analytic method, and is explicitly solved using the -transform method. The connection of the solution of the discrete equivalent logistic equation with the solution of the logistic differential equation is discussed. Also, some differences of the discrete equivalent logistic equation and the well-known discrete analogue of the logistic equation are mentioned. It is hoped that this discrete equivalent of the logistic equation could be a better choice for the modelling of various problems, where different versions of known discrete logistic equations are used until nowadays.

  3. Calabi-Yau completions and orbifold equivalences

    CERN Document Server

    Carqueville, Nils

    2015-01-01

    Calabi-Yau algebras are particularly symmetric differential graded algebras. There is a construction due to Keller called `Calabi-Yau completion' which produces a canonical Calabi-Yau algebra from any homologically smooth dg algebra. Homologically smooth dg algebras also form a 2-category to which the construction of `equivariant completion' can be applied. In this theory two objects are called `orbifold equivalent' if there is a 1-morphism with invertible quantum dimensions between them. Any such relation entails a whole family of equivalences between categories. We show that Calabi-Yau completion and equivariant completion are compatible. More precisely, we prove that any orbifold equivalence between two homologically smooth and proper dg algebras lifts to an orbifold equivalence between their Calabi-Yau completions. As a corollary we obtain orbifold equivalences between Ginzburg algebras of Dynkin quivers.

  4. Equivalence in Ventilation and Indoor Air Quality

    Energy Technology Data Exchange (ETDEWEB)

    Sherman, Max; Walker, Iain; Logue, Jennifer

    2011-08-01

    We ventilate buildings to provide acceptable indoor air quality (IAQ). Ventilation standards (such as American Society of Heating, Refrigerating, and Air-Conditioning Enginners [ASHRAE] Standard 62) specify minimum ventilation rates without taking into account the impact of those rates on IAQ. Innovative ventilation management is often a desirable element of reducing energy consumption or improving IAQ or comfort. Variable ventilation is one innovative strategy. To use variable ventilation in a way that meets standards, it is necessary to have a method for determining equivalence in terms of either ventilation or indoor air quality. This study develops methods to calculate either equivalent ventilation or equivalent IAQ. We demonstrate that equivalent ventilation can be used as the basis for dynamic ventilation control, reducing peak load and infiltration of outdoor contaminants. We also show that equivalent IAQ could allow some contaminants to exceed current standards if other contaminants are more stringently controlled.

  5. 77 FR 60985 - Ambient Air Monitoring Reference and Equivalent Methods: Designation of Three New Equivalent Methods

    Science.gov (United States)

    2012-10-05

    ... AGENCY Ambient Air Monitoring Reference and Equivalent Methods: Designation of Three New Equivalent... methods for monitoring ambient air quality. SUMMARY: Notice is hereby given that the Environmental... in the ambient air. FOR FURTHER INFORMATION CONTACT: Robert Vanderpool, Human Exposure...

  6. 78 FR 67360 - Ambient Air Monitoring Reference and Equivalent Methods: Designation of Five New Equivalent Methods

    Science.gov (United States)

    2013-11-12

    ... AGENCY Ambient Air Monitoring Reference and Equivalent Methods: Designation of Five New Equivalent... of the designation of five new equivalent methods for monitoring ambient air quality. SUMMARY: Notice... measuring concentrations of PM 10-2.5 , two for measuring PM 2.5, and one for measuring NO 2 in the...

  7. On Equivalence and Non-equivalence of Words and Phrases In Different Cultures

    Institute of Scientific and Technical Information of China (English)

    高新霞

    2008-01-01

    This paper is mainly focused on the study of the relationship among three concepts, namely, culture,psychological association and equivalence or non-equivalence of words and phrases with combination of Problems posed by my students and discuss three patterns of the relationship with an attempt to describe the importance of culture to equivalence.

  8. Quantitative research.

    Science.gov (United States)

    Watson, Roger

    2015-04-01

    This article describes the basic tenets of quantitative research. The concepts of dependent and independent variables are addressed and the concept of measurement and its associated issues, such as error, reliability and validity, are explored. Experiments and surveys – the principal research designs in quantitative research – are described and key features explained. The importance of the double-blind randomised controlled trial is emphasised, alongside the importance of longitudinal surveys, as opposed to cross-sectional surveys. Essential features of data storage are covered, with an emphasis on safe, anonymous storage. Finally, the article explores the analysis of quantitative data, considering what may be analysed and the main uses of statistics in analysis.

  9. Analytical and numerical construction of equivalent cables.

    Science.gov (United States)

    Lindsay, K A; Rosenberg, J R; Tucker, G

    2003-08-01

    The mathematical complexity experienced when applying cable theory to arbitrarily branched dendrites has lead to the development of a simple representation of any branched dendrite called the equivalent cable. The equivalent cable is an unbranched model of a dendrite and a one-to-one mapping of potentials and currents on the branched model to those on the unbranched model, and vice versa. The piecewise uniform cable, with a symmetrised tri-diagonal system matrix, is shown to represent the canonical form for an equivalent cable. Through a novel application of the Laplace transform it is demonstrated that an arbitrary branched model of a dendrite can be transformed to the canonical form of an equivalent cable. The characteristic properties of the equivalent cable are extracted from the matrix for the transformed branched model. The one-to-one mapping follows automatically from the construction of the equivalent cable. The equivalent cable is used to provide a new procedure for characterising the location of synaptic contacts on spinal interneurons.

  10. Analysis of affinely equivalent Boolean functions

    Institute of Scientific and Technical Information of China (English)

    MENG QingShu; ZHANG HuanGuo; YANG Min; WANG ZhangYi

    2007-01-01

    By some basic transforms and invariant theory, we give two results: 1) an algorithm,which can be used to judge if two Boolean functions are affinely equivalent and to obtain the equivalence relationship if they are equivalent. This is useful in studying Boolean functions and in engineering. For example, we classify all 8-variable homogeneous bent functions of degree 3 into two classes; 2) Reed-Muller codes R(4,6)/R(1,6), R(3,7)/R(1,7) are classified efficiently.

  11. Antireflection design concepts with equivalent layers.

    Science.gov (United States)

    Schallenberg, Uwe B

    2006-03-01

    Some novel concepts of designing antireflection (AR) coatings with equivalent layers are presented. As an introduction, essential papers concerning thin-film optics and AR designs are cited, and the AR problem and a previously introduced AR-hard design type are discussed. Based on the known matrix formalism, a potential AR region, an equivalent stack index, and an equivalent substrate index are defined to use the theory of stop-band suppression as a starting point for the design of broadband AR coatings. The known multicycle AR design type is identified as a typical solution to the AR problem if the presented approach is used.

  12. Equivalent circuit with complex physical constants and equivalent-parameters-expressed dissipation factors of piezoelectric materials

    Institute of Scientific and Technical Information of China (English)

    Chen Yu; Wen Yu-Mei; Li Ping

    2006-01-01

    The equivalent circuit with complex physical constants for a piezoelectric ceramic in thickness mode is established.In the equivalent circuit, electric components (equivalent circuit parameters) are connected to real and imaginary parts of complex physical coefficients of piezoelectric materials. Based on definitions of dissipation factors, three of them (dielectric, elastic and piezoelectric dissipation factors) are represented by equivalent circuit parameters. Since the equivalent circuit parameters are detectable, the dissipation factors can be easily obtained. In the experiments, the temperature and the stress responses of the three dissipation factors are measured.

  13. Comparison between ionospheric convection vortices and the associated equivalent currents

    Science.gov (United States)

    Liang, J.; Benkevitch, L.; Sofko, G. J.; Koustov, A. V.

    2004-12-01

    The equivalent current pattern derived from CANOPUS, NRCAN/GSC and MACCS magnetometers has been compared with the ionospheric convection pattern observed by SuperDARN HF radars. The discrepancies between the equivalent convection (EQC) and the SuperDARN-observed convection (SDC) patterns are explained in terms of the effect of day-night photoionization conductance gradient and the coupling between field-aligned currents (FACs) and ionospheric conductances. In particular, the agreement between the EQC and SDC patterns is usually worse for a counterclockwise convection vortex than for a clockwise cell, but a consistent pattern of discrepancy for counterclockwise convection vortices has been found. We suggest that the discrepancies are due to a downward FAC-conductance coupling process. Since the counterclockwise vortices and clockwise vortices occur predominantly in the dawn and dusk sectors, respectively, in accordance with the usual 2-cell global convection pattern, the asymmetry between the EQC and SDC patterns for counterclockwise vortices and clockwise vortices would naturally lead to a dawn-dusk asymmetry as well. This is revealed by a global statistical study of the deviation of direction between the magnetic equivalent convection and the SuperDARN convection in different time sectors and latitudes. In the dawn sector, the statistical results reveal that, at lower latitudes, the EQC direction deviation is slightly counterclockwise with respect to the SDC direction, whereas the deviation is significantly clockwise at high latitudes. These deviations are consistent with the discrepancy pattern for counterclockwise convection vortices, as found in the individual vortex event studies.

  14. Lexical Equivalence in Business English Translation

    Institute of Scientific and Technical Information of China (English)

    王淼

    2009-01-01

    Business English is English used in business contexts.It is a combination of knowledge in both business and language.Being faithful is of primary importance in business English translation,but a translation only faithful to the original is far from adequate if it is not appropriate to the original in style.Therefore,in doing business translation,the translators should always keep in mind the specific purposes and functions of the original texts and make attempts to render the closet natural equivalent in the target language.This article focuses on equivalence at lexical level in this chapter.Several major tendencies toward word choice are put forward and stylistic equivalence in each case is analyzed at some length.Three criteria are proposed here for choosing suitable words:preciseness,conciseness and gracefulness.If the three criteria are satisfied,stylistic equivalence will also be established.

  15. Lexical Equivalence in Business English Translation

    Institute of Scientific and Technical Information of China (English)

    王淼

    2009-01-01

    Business English is English used in business contexts.It is a combination of knowledge in both business and language.Being faithful is ofprimary importance in business English Iranslation,but a translation only faithful to the original is far from adequate if it is not appropriate to the original in style.Therefore,in doing business translation,the translators should always keep in mind the specific purposes and functions ofthe original texts and make attempts to render the closet natural equivalent in the target language.This atticle focuses on equivalence at lexical level in this chapter.Several major tendencies toward word choice arc put forward and stylistic equivalence in each case is analyzed at some length.Three criteria are proposed here for choosing suitable words:preciseness,concise-ness and gracefulness.1fthe three criteria are satisfied,stylistic equivalence will also be established.

  16. Equivalence Principle, Higgs Boson and Cosmology

    Directory of Open Access Journals (Sweden)

    Mauro Francaviglia

    2013-05-01

    Full Text Available We discuss here possible tests for Palatini f(R-theories together with their implications for different formulations of the Equivalence Principle. We shall show that Palatini f(R-theories obey the Weak Equivalence Principle and violate the Strong Equivalence Principle. The violations of the Strong Equivalence Principle vanish in vacuum (and purely electromagnetic solutions as well as on short time scales with respect to the age of the universe. However, we suggest that a framework based on Palatini f(R-theories is more general than standard General Relativity (GR and it sheds light on the interpretation of data and results in a way which is more model independent than standard GR itself.

  17. Equivalence relations and the reinforcement contingency.

    Science.gov (United States)

    Sidman, M

    2000-07-01

    Where do equivalence relations come from? One possible answer is that they arise directly from the reinforcement contingency. That is to say, a reinforcement contingency produces two types of outcome: (a) 2-, 3-, 4-, 5-, or n-term units of analysis that are known, respectively, as operant reinforcement, simple discrimination, conditional discrimination, second-order conditional discrimination, and so on; and (b) equivalence relations that consist of ordered pairs of all positive elements that participate in the contingency. This conception of the origin of equivalence relations leads to a number of new and verifiable ways of conceptualizing equivalence relations and, more generally, the stimulus control of operant behavior. The theory is also capable of experimental disproof.

  18. The effective theory of Borel equivalence relations

    DEFF Research Database (Denmark)

    Fokina, E.B.; Friedman, S.-D.; Törnquist, Asger Dag

    2010-01-01

    The study of Borel equivalence relations under Borel reducibility has developed into an important area of descriptive set theory. The dichotomies of Silver [20] and Harrington, Kechris and Louveau [6] show that with respect to Borel reducibility, any Borel equivalence relation strictly above...... under effectively Borel reducibility. The resulting structure is complex, even for equivalence relations with finitely many equivalence classes. However use of Kleene's O as a parameter is sufficient to restore the picture from the noneffective setting. A key lemma is that of the existence of two...... effectively Borel sets of reals, neither of which contains the range of the other under any effectively Borel function; the proof of this result applies Barwise compactness to a deep theorem of Harrington (see [5,16]) establishing for any recursive ordinal α the existence of Π singletons whose α...

  19. Equivalent boundary integral equations for plane elasticity

    Institute of Scientific and Technical Information of China (English)

    胡海昌; 丁皓江; 何文军

    1997-01-01

    Indirect and direct boundary integral equations equivalent to the original boundary value problem of differential equation of plane elasticity are established rigorously. The unnecessity or deficiency of some customary boundary integral equations is indicated by examples and numerical comparison.

  20. On the Notion of Equivalence in Translation

    Institute of Scientific and Technical Information of China (English)

    张颖

    2016-01-01

    Thanks to translations, varies cultures are allowed to exchange with one another. One the one hand, this has been promoting the studies of translation. On the other hand, this poses huge challenges on translators, because it is hard to define what is a good target translation when a source text is translated. There is a variety of standards to evaluate the quality of a translation, among which equivalence seems to be the most controversial one. On the analysis of studies on equivalence, this essay discusses the role of equivalence in the practice of translating with illustrations of Chinese-English and English-Chinese translation. Indeed, to translate a source text into a target one is based on the equivalence among languages. However, in the process of translating, it can be adjusted to some extent for the sake of the acceptability in the target culture.

  1. interpratation: of equivalences and cultural untranslatability

    African Journals Online (AJOL)

    jgmweri

    Interpretation: signs and meaning, diversity in language use, equivalences and ... movement of the hands, arms or body, and facial expressions to express ... people who belong to the same culture given the similar experiences they have gone.

  2. ON THE EQUIVALENCE OF THE ABEL EQUATION

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    This article uses the reflecting function of Mironenko to study some complicated differential equations which are equivalent to the Abel equation. The results are applied to discuss the behavior of solutions of these complicated differential equations.

  3. REFractions: The Representing Equivalent Fractions Game

    Science.gov (United States)

    Tucker, Stephen I.

    2014-01-01

    Stephen Tucker presents a fractions game that addresses a range of fraction concepts including equivalence and computation. The REFractions game also improves students' fluency with representing, comparing and adding fractions.

  4. Equivalence relations and the reinforcement contingency.

    OpenAIRE

    Sidman, M

    2000-01-01

    Where do equivalence relations come from? One possible answer is that they arise directly from the reinforcement contingency. That is to say, a reinforcement contingency produces two types of outcome: (a) 2-, 3-, 4-, 5-, or n-term units of analysis that are known, respectively, as operant reinforcement, simple discrimination, conditional discrimination, second-order conditional discrimination, and so on; and (b) equivalence relations that consist of ordered pairs of all positive elements that...

  5. EQUIVALENT EXCITATION METHOD FOR VIBRATION ISOLATION DESIGN:THEORETICAL ANALYSIS AND EXPERIMENTAL RESULTS

    Institute of Scientific and Technical Information of China (English)

    Huo Rui; Shi Yin

    2005-01-01

    In view of difficulties concerned with direct measurement of excitations inside source equipments and their significant influence on vibration isolation effectiveness, a dynamical model, for vibration isolation of a rigid machine with six-degree-of-freedom mounted on a flexible foundation through multiple mounts, is analyzed, in which the complicated and multiple disturbances inside the machine are described as an equivalent excitation spectrum. And a method for the estimation of the equivalent excitation spectrum according to system dynamic responses is discussed for the quantitative prediction of isolation effectiveness.Both theoretical analysis and experimental results are demonstrated. Further work shows the quantitative prediction of transmitted power flow in a flexible vibration isolation experiment system using the proposed equivalent excitation spectrum method, by comparison with its testing results.

  6. Regional Differences in Equivalence Scales in Turkey

    Directory of Open Access Journals (Sweden)

    Gianni Betti

    2017-03-01

    Full Text Available Equivalence scales have a crucial role in poverty measurement. For Turkey, there are no available up-todate equivalence scales, representing Turkish data. There were no efforts for calculation of equivalence scales at the regional level. The aim of the paper is to calculate and propose an equivalence scale for Turkey and estimate regional differences. Besides the models with Engel method, different equivalence scales were estimated by Almost Ideal Demand System. The results of the first model of AIDS approach composed of 5 age groups, is proposed for Turkey, but for simplicity the results of the second AIDS model could be used as well. In this model, the equivalence scale for Turkey is calculated as 0.65 for each additional adult after the first one and 0.35 for each child. For regional equivalence scales, we use two methods and comare the results. In the first one, regressions were run for each region separately and in the second one, dummy variables introduced. The highest difference in the results of the two methods was observed in Istanbul region. The findings for the regional scales are less reliable as the household size is bigger. This limitation is due to the relatively small size of the data sets. Having surveys with higher sample sizes would enable better results. After getting the results some conclusions could be drawn especially with regard to child cost differences among regions. It was expected to have higher costs for children in poorer regions and the regional results have confirmed this hypothesis.

  7. A Directional Dose Equivalent Monitor for Neutrons

    Energy Technology Data Exchange (ETDEWEB)

    D' Errico, F.; Alberts, W.G.; Curzio, G.; Matzke, M.; Nath, R.; Siebert, B.R.L

    2001-07-01

    A directional dose equivalent monitor is introduced which consists of a 30 cm diameter spherical phantom hosting a superheated drop detector embedded at a depth of 10 mm. The device relies on the similarity between the fluence response of neutron superheated drop detectors based on halocarbon-12 and the quality-factor-weighted kerma factor. This implies that these detectors can be used for in-phantom dosimetry and provide a direct reading of dose equivalent at depth. The directional dose equivalent monitor was characterised experimentally with fast neutron calibrations and numerically with Monte Carlo simulations. The fluence response was determined at angles of 0, 45, 90, 135 and 180 degrees for thermal to 20 MeV neutrons. The response of the device is closely proportional to the fluence-to-directional dose equivalent conversion coefficient, H'{sub F}(10;a,E). Therefore, our monitor is suitable for a direct measurement of neutron directional dose equivalent, H'(10), regardless of angle and energy distribution of the neutron fluence. (author)

  8. System Equivalent for Real Time Digital Simulator

    Science.gov (United States)

    Lin, Xi

    2011-07-01

    The purpose of this research is to develop a method of making system equivalents for the Real Time Digital Simulator (RTDS), which should enhance its capability of simulating large power systems. The proposed equivalent combines a Frequency Dependent Network Equivalent (FDNE) for the high frequency electromagnetic transients and a Transient Stability Analysis (TSA) type simulation block for the electromechanical transients. The frequency dependent characteristic for FDNE is obtained by curve-fitting frequency domain admittance characteristics using the Vector Fitting method. An approach for approximating the frequency dependent characteristic of large power networks from readily available typical power-flow data is also introduced. A new scheme of incorporating TSA solution in RTDS is proposed. This report shows how the TSA algorithm can be adapted to a real time platform. The validity of this method is confirmed with examples, including the study of a multi in-feed HVDC system based network.

  9. The New Wind Chill Equivalent Temperature Chart.

    Science.gov (United States)

    Osczevski, Randall; Bluestein, Maurice

    2005-10-01

    The formula used in the U.S. and Canada to express the combined effect of wind and low temperature on how cold it feels was changed in November 2001. Many had felt that the old formula for equivalent temperature, derived in the 1960s from Siple and Passel's flawed but quite useful Wind Chill Index, unnecessarily exaggerated the severity of the weather. The new formula is based on a mathematical model of heat flow from the upwind side of a head-sized cylinder moving at walking speed into the wind. The paper details the assumptions that were made in generating the new wind chill charts. It also points out weaknesses in the concept of wind chill equivalent temperature, including its steady-state character and a seemingly paradoxical effect of the internal thermal resistance of the cylinder on comfort and equivalent temperature. Some improvements and alternatives are suggested.

  10. Fiscal adjustments in Europe and Ricardian equivalence

    Directory of Open Access Journals (Sweden)

    V. DE BONIS

    1998-09-01

    Full Text Available According to the ‘Ricardian’ equivalence hypothesis, consumption is dependent on permanent disposable income and current deficits are equivalent to future tax payments. This hypothesis is tested on 14 European countries in the 1990s. The relationships between private sector savings and general government deficit, and the GDP growth rate and the unemployment rate are determined. The results show the change in consumers' behaviour with respect to government deficit, and that expectations of an increase in future wealth are no longer associated with a decrease in deficit.

  11. Equivalent circuit analysis of terahertz metamaterial filters

    KAUST Repository

    Zhang, Xueqian

    2011-01-01

    An equivalent circuit model for the analysis and design of terahertz (THz) metamaterial filters is presented. The proposed model, derived based on LMC equivalent circuits, takes into account the detailed geometrical parameters and the presence of a dielectric substrate with the existing analytic expressions for self-inductance, mutual inductance, and capacitance. The model is in good agreement with the experimental measurements and full-wave simulations. Exploiting the circuit model has made it possible to predict accurately the resonance frequency of the proposed structures and thus, quick and accurate process of designing THz device from artificial metamaterials is offered. ©2011 Chinese Optics Letters.

  12. Algebraic cobordism theory attached to algebraic equivalence

    CERN Document Server

    Krishna, Amalendu

    2012-01-01

    After the algebraic cobordism theory of Levine-Morel, we develop a theory of algebraic cobordism modulo algebraic equivalence. We prove that this theory can reproduce Chow groups modulo algebraic equivalence and the zero-th semi-topological K-groups. We also show that with finite coefficients, this theory agrees with the algebraic cobordism theory. We compute our cobordism theory for some low dimensional or special types of varieties. The results on infinite generation of some Griffiths groups by Clemens and on smash-nilpotence by Voevodsky and Voisin are also lifted and reinterpreted in terms of this cobordism theory.

  13. Atom interferometry and the Einstein equivalence principle

    CERN Document Server

    Wolf, Peter; Bordé, Christian J; Reynaud, Serge; Salomon, Christophe; Cohen-Tannoudji, Clande

    2011-01-01

    The computation of the phase shift in a symmetric atom interferometer in the presence of a gravitational field is reviewed. The difference of action-phase integrals between the two paths of the interferometer is zero for any Lagrangian which is at most quadratic in position and velocity. We emphasize that in a large class of theories of gravity the atom interferometer permits a test of the weak version of the equivalence principle (or universality of free fall) by comparing the acceleration of atoms with that of ordinary bodies, but is insensitive to that aspect of the equivalence principle known as the gravitational redshift or universality of clock rates.

  14. A model for equivalent axle load factors

    OpenAIRE

    Amorim, Sara I.R.; Pais, Jorge; Vale, Aline C.; Minhoto, Manuel

    2014-01-01

    Most design methods for road pavements require the design traffic, based on the transformation of the traffic spectrum, to be calculated into a number of equivalent passages of a standard axle using the equivalent axle load factors. Generally, these factors only consider the type of axle (single, tandem or tridem), but they do not consider the type of wheel on the axles, i.e., single or dual wheel. The type of wheel has an important influence on the calculation of the design traffic. The exis...

  15. Relative Derived Equivalences and Relative Homological Dimensions

    Institute of Scientific and Technical Information of China (English)

    Sheng Yong PAN

    2016-01-01

    Let A be a small abelian category. For a closed subbifunctor F of Ext1A (−,−), Buan has generalized the construction of Verdier’s quotient category to get a relative derived category, where he localized with respect to F-acyclic complexes. In this paper, the homological properties of relative derived categories are discussed, and the relation with derived categories is given. For Artin algebras, using relative derived categories, we give a relative version on derived equivalences induced by F-tilting complexes. We discuss the relationships between relative homological dimensions and relative derived equivalences.

  16. AN EQUIVALENT CONTINUUM METHOD OF LATTICE STRUCTURES

    Institute of Scientific and Technical Information of China (English)

    Fan Hualin; Yang Wei

    2006-01-01

    An equivalent continuum method is developed to analyze the effective stiffness of three-dimensional stretching dominated lattice materials. The strength and three-dimensional plastic yield surfaces are calculated for the equivalent continuum. A yielding model is formulated and compared with the results of other models. The bedding-in effect is considered to include the compliance of the lattice joints. The predicted stiffness and strength are in good agreement with the experimental data, validating the present model in the prediction of the mechanical properties of stretching dominated lattice structures.

  17. Quantitative Proteomics Reveals That the Specific Methyltransferases Txr1p and Ezl2p Differentially Affect the Mono-, Di- and Trimethylation States of Histone H3 Lysine 27 (H3K27)*

    OpenAIRE

    Zhang, Chunchao; Molascon, Anthony J.; Gao, Shan; Liu, Yifan; Andrews, Philip C.

    2012-01-01

    Nuclear DNA in eukaryotic cells is assembled into the hierarchical chromatin structure via a process that is dynamically affected by the combinatorial set of post-translational modifications (PTMs) of histones in a dynamic manner responsive to physiological and environmental changes. The precise quantification of these complex modifications is challenging. Here we present a robust MS-based quantitative proteomics method for studying histone PTMs using 15N metabolically labeled histones as the...

  18. Increased presence of monounsaturated fatty acids in the stratum corneum of human skin equivalents.

    Science.gov (United States)

    Thakoersing, Varsha S; van Smeden, Jeroen; Mulder, Aat A; Vreeken, Rob J; El Ghalbzouri, Abdoelwaheb; Bouwstra, Joke A

    2013-01-01

    Previous results showed that our in-house human skin equivalents (HSEs) differ in their stratum corneum (SC) lipid organization compared with human SC. To elucidate the cause of the altered SC lipid organization in the HSEs, a recently developed liquid chromatography/mass spectrometry method was used to study the free fatty acid (FFA) and ceramide composition in detail. In addition, the SC lipid composition of the HSEs and human skin was examined quantitatively with high-performance thin-layer chromatography. Our results reveal that all our HSEs have an increased presence of monounsaturated FFAs compared with human SC. Moreover, the HSEs display the presence of ceramide species with a monounsaturated acyl chain, which are not detected in human SC. All HSEs also exhibit an altered expression of stearoyl-CoA desaturase, the enzyme that converts saturated FFAs to monounsaturated FFAs. Furthermore, the HSEs show the presence of 12 ceramide subclasses, similar to native human SC. However, the HSEs have increased levels of ceramides EOS and EOH and ceramide species with short total carbon chains and a reduced FFA level compared with human SC. The presence of unsaturated lipid chains in HSE offers new opportunities to mimic the lipid properties of human SC more closely.

  19. 77 FR 55832 - Ambient Air Monitoring Reference and Equivalent Methods: Designation of a New Equivalent Method

    Science.gov (United States)

    2012-09-11

    ... AGENCY Ambient Air Monitoring Reference and Equivalent Methods: Designation of a New Equivalent Method... monitoring ambient air quality. SUMMARY: Notice is hereby given that the Environmental Protection Agency (EPA... concentrations of PM 2.5 in the ambient air. FOR FURTHER INFORMATION CONTACT: Robert Vanderpool, Human...

  20. Experimental Uncertainties of TEPC Dose Equivalent

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Wei-hua; XIAO; Xue-fu; WANG; Zhi-qiang; LIU; Yi-na; LI; Chun-juan; LUO; Hai-long

    2013-01-01

    The tissue-equivalent proportional counters(TEPC)are widely used for radiation protection in mixed radiation fields.The operational quantity H*(10)can be directly obtained by means of microdosimetric spectra measurements with TEPC.An empirical evaluation of uncertainties is reported in this paper.The sources of uncertainties involved in measuring microdosimetric spectra mainly are the sensitive

  1. Reading adn Auditory-Visual Equivalences

    Science.gov (United States)

    Sidman, Murray

    1971-01-01

    A retarded boy, unable to read orally or with comprehension, was taught to match spoken to printed words and was then capable of reading comprehension (matching printed words to picture) and oral reading (naming printed words aloud), demonstrating that certain learned auditory-visual equivalences are sufficient prerequisites for reading…

  2. Confluence Modulo Equivalence in Constraint Handling Rules

    DEFF Research Database (Denmark)

    Christiansen, Henning; Kirkeby, Maja Hanne

    2014-01-01

    Previous results on confluence for Constraint Handling Rules, CHR, are generalized to take into account user-defined state equivalence relations. This allows a much larger class of programs to enjoy the ad- vantages of confluence, which include various optimization techniques and simplified corre...

  3. Equivalence of Conformal Superalgebras to Hamiltonian Superoperators

    Institute of Scientific and Technical Information of China (English)

    Xiaoping Xu

    2001-01-01

    In this paper, we present a formal variational calculus of super functions in one real variable and find the conditions for a "matrix differential operator'' to be a Hamiltonian superoperator. Moreover, we prove that conformal superalgebras are equivalent to certain Hamiltonian superoperators.

  4. CP Violation, Neutral Currents, and Weak Equivalence

    Science.gov (United States)

    Fitch, V. L.

    1972-03-23

    Within the past few months two excellent summaries of the state of our knowledge of the weak interactions have been presented. Correspondingly, we will not attempt a comprehensive review but instead concentrate this discussion on the status of CP violation, the question of the neutral currents, and the weak equivalence principle.

  5. On the Leitmann equivalent problem approach

    NARCIS (Netherlands)

    F.O.O. Wagener

    2009-01-01

    The purpose of this paper is to show how Leitmann’s equivalent problem approach ties in with the classical notions of the calculus of variations and how it can be exploited to give a rapid and elegant approach to the Weierstrass theory of sufficient conditions. Fixed, free and constrained endpoint c

  6. On Functional Equivalence of Idiom Translation

    Institute of Scientific and Technical Information of China (English)

    管琴

    2008-01-01

    The aim of this article is to discuss the feasibility of functional equivalence in idiom translations in Chinese-English cultures,trying to find efficient ways to avoid both under-translation and over-translation.The more functions are reproduced,the better the version will be at achieving correspondence between meaning and function.

  7. Chameleonic equivalence postulate and wave function collapse

    CERN Document Server

    Zanzi, Andrea

    2014-01-01

    A chameleonic solution to the cosmological constant problem and the non-equivalence of different conformal frames at the quantum level have been recently suggested [Phys. Rev. D82 (2010) 044006]. In this article we further discuss the theoretical grounds of that model and we are led to a chameleonic equivalence postulate (CEP). Whenever a theory satisfies our CEP (and some other additional conditions), a density-dependence of the mass of matter fields is naturally present. Let us summarize the main results of this paper. 1) The CEP can be considered the microscopic counterpart of the Einstein's Equivalence Principle and, hence, a chameleonic description of quantum gravity is obtained: in our model, (quantum) gravitation is equivalent to a conformal anomaly. 2) To illustrate one of the possible applications of the CEP, we point out a connection between chameleon fields and quantum-mechanical wave function collapse. The collapse is induced by the chameleonic nature of the theory. We discuss the collapse for a S...

  8. On the Equivalence of Regularization Schemes

    Institute of Scientific and Technical Information of China (English)

    YANG Ji-Feng

    2002-01-01

    We illustrate via the sunset diagram that dimensional regularization ‘deforms' the nonlocal contentsof multi-loop diagrams with its equivalence to cutoff regularization scheme recovered only after sub-divergence wassubtracted. Then we employed a differential equation approach for calculating loop diagrams to verify that dimensionalare argued especially in nonperturbativc perspective.

  9. Equivalent thermal conductivity of heat pipes

    Institute of Scientific and Technical Information of China (English)

    Zesheng LU; Binghui MA

    2008-01-01

    In precision machining, the machining error from thermal distortion carries a high proportion of the total errors. If a precision machining tool can transfer heat fast, the thermal distortion will be reduced and the machining precision will be improved. A heat pipe working based on phase transitions of the inner working liquid transfers heat with high efficiency and is widely applied in spaceflight and chemical industries. In mechanics, applications of heat pipes are correspondingly less. When a heat pipe is applied to a hydrostatic motor-ized spindle, the thermal distortion cannot be solved dur-ing the heat transfer process because thermal conductivity or equivalent thermal conductivity should be provided first for special application in mechanics. An equivalent thermal conductivity model based on equivalent thermal resistances is established. Performance tests for a screen wick pipe, gravity pipe, and rotation heat pipe are done to validate the efficiency of the equivalent thermal conduc-tivity model. The proposed model provides a calculation method for the thermal distortion analysis of heat pipes applied in the motorized spindle.

  10. Beyond Language Equivalence on Visibly Pushdown Automata

    DEFF Research Database (Denmark)

    Srba, Jiri

    2009-01-01

    We study (bi)simulation-like preorder/equivalence checking on the class of visibly pushdown automata and its natural subclasses visibly BPA (Basic Process Algebra) and visibly one-counter automata. We describe generic methods for proving complexity upper and lower bounds for a number of studied...

  11. A Logical Characterisation of Static Equivalence

    DEFF Research Database (Denmark)

    Hüttel, Hans; Pedersen, Michael D.

    2007-01-01

    The work of Abadi and Fournet introduces the notion of a frame to describe the knowledge of the environment of a cryptographic protocol. Frames are lists of terms; two frames are indistinguishable under the notion of static equivalence if they satisfy the same equations on terms. We present a first...

  12. THE EQUIVALENCE THEORY OF NATIVE SPACES

    Institute of Scientific and Technical Information of China (English)

    Lin-Tian Luh

    2001-01-01

    In this paper some equivalence definitions are given for native spaces which were introduced by Madych and Nelson and have become influential in the theory of radial basis functions. The abstract elements in na tive spaces are interpreted. Moreaver, Weinrich and Iske's theonies are unified.

  13. Visual Equivalence and Amodal Completion in Cuttlefish.

    Science.gov (United States)

    Lin, I-Rong; Chiao, Chuan-Chin

    2017-01-01

    Modern cephalopods are notably the most intelligent invertebrates and this is accompanied by keen vision. Despite extensive studies investigating the visual systems of cephalopods, little is known about their visual perception and object recognition. In the present study, we investigated the visual processing of the cuttlefish Sepia pharaonis, including visual equivalence and amodal completion. Cuttlefish were trained to discriminate images of shrimp and fish using the operant conditioning paradigm. After cuttlefish reached the learning criteria, a series of discrimination tasks were conducted. In the visual equivalence experiment, several transformed versions of the training images, such as images reduced in size, images reduced in contrast, sketches of the images, the contours of the images, and silhouettes of the images, were used. In the amodal completion experiment, partially occluded views of the original images were used. The results showed that cuttlefish were able to treat the training images of reduced size and sketches as the visual equivalence. Cuttlefish were also capable of recognizing partially occluded versions of the training image. Furthermore, individual differences in performance suggest that some cuttlefish may be able to recognize objects when visual information was partly removed. These findings support the hypothesis that the visual perception of cuttlefish involves both visual equivalence and amodal completion. The results from this research also provide insights into the visual processing mechanisms used by cephalopods.

  14. The Nature of Dynamic Equivalence in Translating

    Science.gov (United States)

    Nida, Eugene A.

    1977-01-01

    A discussion of three types of translation: formal correspondence, cognitive content and emotive response-oriented. The latter two are dynamic-equivalent translations. Their purpose is to enable the receptors to understand the implications of the cognitive content or to make a corresponding emotive response without recourse to the original text.…

  15. An Equivalent Circuit for Landau Damping

    DEFF Research Database (Denmark)

    Pécseli, Hans

    1976-01-01

    An equivalent circuit simulating the effect of Landau damping in a stable plasma‐loaded parallel‐plate capacitor is presented. The circuit contains a double infinity of LC components. The transition from stable to unstable plasmas is simulated by the introduction of active elements into the circuit....

  16. Canonical equivalence between massive spin 1 theories

    CERN Document Server

    Arias, P J; Arias, Pio J.; Perez-Mosquera, Jean C.

    2004-01-01

    The model of Cremmer-Scherck and Proca are considered in dimensions greater than 3+1. It is obtained that the Proca model correspond to a gauged fixed version of the Cremmer-Scherck one, and we show their canonical equivalence.

  17. Visual Equivalence and Amodal Completion in Cuttlefish

    Science.gov (United States)

    Lin, I-Rong; Chiao, Chuan-Chin

    2017-01-01

    Modern cephalopods are notably the most intelligent invertebrates and this is accompanied by keen vision. Despite extensive studies investigating the visual systems of cephalopods, little is known about their visual perception and object recognition. In the present study, we investigated the visual processing of the cuttlefish Sepia pharaonis, including visual equivalence and amodal completion. Cuttlefish were trained to discriminate images of shrimp and fish using the operant conditioning paradigm. After cuttlefish reached the learning criteria, a series of discrimination tasks were conducted. In the visual equivalence experiment, several transformed versions of the training images, such as images reduced in size, images reduced in contrast, sketches of the images, the contours of the images, and silhouettes of the images, were used. In the amodal completion experiment, partially occluded views of the original images were used. The results showed that cuttlefish were able to treat the training images of reduced size and sketches as the visual equivalence. Cuttlefish were also capable of recognizing partially occluded versions of the training image. Furthermore, individual differences in performance suggest that some cuttlefish may be able to recognize objects when visual information was partly removed. These findings support the hypothesis that the visual perception of cuttlefish involves both visual equivalence and amodal completion. The results from this research also provide insights into the visual processing mechanisms used by cephalopods. PMID:28220075

  18. Angular Momentum Eigenstates for Equivalent Electrons.

    Science.gov (United States)

    Tuttle, E. R.; Calvert, J. B.

    1981-01-01

    Simple and efficient methods for adding angular momenta and for finding angular momentum eigenstates for systems of equivalent electrons are developed. Several different common representations are used in specific examples. The material is suitable for a graduate course in quantum mechanics. (SK)

  19. Fuel Cell Equivalent Electric Circuit Parameter Mapping

    DEFF Research Database (Denmark)

    Jeppesen, Christian; Zhou, Fan; Andreasen, Søren Juhl

    In this work a simple model for a fuel cell is investigated for diagnostic purpose. The fuel cell is characterized, with respect to the electrical impedance of the fuel cell at non-faulty conditions and under variations in load current. Based on this the equivalent electrical circuit parameters c...

  20. The equivalence principle in a quantum world

    DEFF Research Database (Denmark)

    Bjerrum-Bohr, N. Emil J.; Donoghue, John F.; El-Menoufi, Basem Kamal

    2015-01-01

    We show how modern methods can be applied to quantum gravity at low energy. We test how quantum corrections challenge the classical framework behind the equivalence principle (EP), for instance through introduction of nonlocality from quantum physics, embodied in the uncertainty principle. When t...... (EFT)....

  1. A quality index for equivalent uniform dose

    Science.gov (United States)

    Henríquez, Francisco Cutanda; Castrillón, Silvia Vargas

    2011-01-01

    Equivalent uniform dose (EUD) is the absorbed dose that, when homogeneously given to a tumor, yields the same mean surviving clonogen number as the given non-homogeneous irradiation. EUD is used as an evaluation tool under the assumption that two plans with the same value of EUD are equivalent, and their biological effect on the tumor (clonogen survival) would be the same as the one of a homogeneous irradiation of absorbed dose EUD. In this work, this assumption has been studied, and a figure of merit of its applicability has been obtained. Distributions of surviving clonogen number for homogeneous and non-homogeneous irradiations are found to be different even if their mean values are the same, the figure of merit being greater when there is a wider difference, and the equivalence assumption being less valid. Therefore, EUD can be closer to a uniform dose for some cases than for other ones (high α values, extreme heterogeneity), and the accuracy of the radiobiological indices obtained for evaluation, could be affected. Results show that the equivalence is very sensitive to the choice of radiobiological parameters, and this conclusion has been derived from mathematical properties of EUD. PMID:21897557

  2. The quantitative Morse theorem

    OpenAIRE

    Loi, Ta Le; Phien, Phan

    2013-01-01

    In this paper, we give a proof of the quantitative Morse theorem stated by {Y. Yomdin} in \\cite{Y1}. The proof is based on the quantitative Sard theorem, the quantitative inverse function theorem and the quantitative Morse lemma.

  3. Equivalent dynamic model of DEMES rotary joint

    Science.gov (United States)

    Zhao, Jianwen; Wang, Shu; Xing, Zhiguang; McCoul, David; Niu, Junyang; Huang, Bo; Liu, Liwu; Leng, Jinsong

    2016-07-01

    The dielectric elastomer minimum energy structure (DEMES) can realize large angular deformations by a small voltage-induced strain of the dielectric elastomer (DE), so it is a suitable candidate to make a rotary joint for a soft robot. Dynamic analysis is necessary for some applications, but the dynamic response of DEMESs is difficult to model because of the complicated morphology and viscoelasticity of the DE film. In this paper, a method composed of theoretical analysis and experimental measurement is presented to model the dynamic response of a DEMES rotary joint under an alternating voltage. Based on measurements of equivalent driving force and damping of the DEMES, the model can be derived. Some experiments were carried out to validate the equivalent dynamic model. The maximum angle error between model and experiment is greater than ten degrees, but it is acceptable to predict angular velocity of the DEMES, therefore, it can be applied in feedforward-feedback compound control.

  4. Developing equivalent circuits for radial distribution networks

    Energy Technology Data Exchange (ETDEWEB)

    Prada, Ricardo; Coelho, Agnelo; Rodrigues, Anselmo [Catholic University of Rio de Janeiro (PUC-Rio), RJ (Brazil). Dept. of Electrical Engineering], Emails: prada@ele.puc-rio.br, agnelo@ele.puc-rio.br, nebulok_99@yahoo.com; Silva, Maria da Guia da [Federal University of Maranhao, Sao Luiz, MA (Brazil). Dept. of Electrical Engineering

    2009-07-01

    This paper presents a method for evaluating External Equivalent in Electric Distribution Networks (EDN).The proposed method has as its main objectives the reduction of the computational costs in distribution network reconfiguration, investigation of the optimal allocation of banks of capacitors, investigation of the allocation of distributed generation, etc. In these sorts of problems a large number of alternative projects must be assessed in order to identify the optimal solution. The optimal solution comes up with the voltage level in the load points within specified limits. Consequently, the EDN must retain the external network load points but without major increasing in the dimension of the equivalent circuit. The proposed method has been tested and validated in a substation of the Electricity Utility of Maranhao - CEMAR, in Brazil. (author)

  5. On the equivalence of GPD representations

    Science.gov (United States)

    Müller, Dieter; Semenov-Tian-Shansky, Kirill

    2016-10-01

    Phenomenological representations of generalized parton distributions (GPDs) implementing the non-trivial field theoretical requirements are employed in the present day strategies for extracting of hadron structure information encoded in GPDs from the observables of hard exclusive reactions. Showing out the equivalence of various GPD representations can help to get more insight into GPD properties and allow to build up flexible GPD models capable of satisfactory description of the whole set of available experimental data. Below we review the mathematical aspects of establishing equivalence between the the double partial wave expansion of GPDs in the conformal partial waves and in the t-channel SO(3) partial waves and the double distribution representation of GPDs

  6. Testing the Equivalence of Regular Languages

    Directory of Open Access Journals (Sweden)

    Marco Almeida

    2009-07-01

    Full Text Available The minimal deterministic finite automaton is generally used to determine regular languages equality. Antimirov and Mosses proposed a rewrite system for deciding regular expressions equivalence of which Almeida et al. presented an improved variant. Hopcroft and Karp proposed an almost linear algorithm for testing the equivalence of two deterministic finite automata that avoids minimisation. In this paper we improve the best-case running time, present an extension of this algorithm to non-deterministic finite automata, and establish a relationship between this algorithm and the one proposed in Almeida et al. We also present some experimental comparative results. All these algorithms are closely related with the recent coalgebraic approach to automata proposed by Rutten.

  7. Galilean Equivalence for Galactic Dark Matter

    CERN Document Server

    Kesden, M; Kesden, Michael; Kamionkowski, Marc

    2006-01-01

    Satellite galaxies of the Milky Way experience a tidal disruption as they orbit in the Milky Way's dark halo. While the bound core of the satellite remains dominated by dark matter, the tidally disrupted stars behave like purely baryonic tracers of the Milky Way's potential well. If dark matter experiences a stronger self attraction than visible matter, stars will preferentially gain rather than lose energy during tidal disruption. This leads to a relative enhancement in the trailing as compared to the leading tidal stream. We show that the absence of a strong asymmetry in the surface brightness of the leading and trailing tidal streams already constrains the equivalence of acceleration of dark matter and baryons in a gravitational field to less than ten percent--thus ruling out a recently proposed mechanism to clear dwarf galaxies from voids. Future observations should be sensitive at the percent level to departures from the equivalence of dark matter and baryons.

  8. Underlining some aspects of the equivalence principle

    Science.gov (United States)

    Benedetto, E.; Feoli, A.

    2017-09-01

    We want to shed light on some discussed aspects of the principle of equivalence. We consider two different phases in the evolution of the principle. We pay attention to the fact that some textbooks do not dwell on the mathematical meaning of ‘locally flat spacetime’, which can confuse students and, occasionally, can also lead to misinterpretations. For example, the non-eliminability of tidal forces, not even locally, may suggest that the equivalence principle is wrong. By contrast, we want to show that this is in perfect agreement with the Einstein geometrical interpretation of spacetime. Finally, in order to check the approximations used in the Gedankenexperiment of an elevator, we estimate explicitly the magnitude of the deflection of light and the effects of tidal forces in a ‘real lift’.

  9. On the equivalence of GPD representations

    CERN Document Server

    Müller, Dieter

    2016-01-01

    Phenomenological representations of generalized parton distributions (GPDs) implementing the non-trivial field theoretical requirements are employed in the present day strategies for extracting of hadron structure information encoded in GPDs from the observables of hard exclusive reactions. Showing out the equivalence of various GPD representations can help to get more insight into GPD properties and allow to build up flexible GPD models capable of satisfactory description of the whole set of available experimental data. We review the mathematical aspects of establishing equivalence between the the double partial wave expansion of GPDs in the conformal partial waves and in the $t$-channel ${\\rm SO}(3)$ partial waves and the double distribution representation of GPDs.

  10. Probing Quantum Violations of the Equivalence Principle

    CERN Document Server

    Adunas, G Z; Ahluwalia, D V

    2001-01-01

    The joint realm of quantum mechanics and the general-relativistic description of gravitation is becoming increasingly accessible to terrestrial experiments and observations. In this essay we study the emerging indications of the violation of equivalence principle (VEP). While the solar neutrino anomaly may find its natural explanation in a VEP, the statistically significant discrepancy observed in the gravitationally induced phases of neutron interferometry seems to be the first indication of a VEP. However, such a view would seem immediately challenged by the atomic interferometry results. The latter experiments see no indications of VEP, in apparent contradiction to the neutron interferometry results. Here we present arguments that support the view that these, and related torsion pendulum experiments, probe different aspects of gravity; and that current experimental techniques, when coupled to the solar-neutrino data, may be able to explore quantum mechanically induced violations of the equivalence principl...

  11. Orientifold Planar Equivalence: The Quenched Meson Spectrum

    CERN Document Server

    Lucini, Biagio; Patella, Agostino; Rago, Antonio

    2010-01-01

    A numerical study of Orientifold Planar Equivalence is performed in SU(N) Yang-Mills theories for N=2,3,4,6. Quenched meson masses are extracted in the antisymmetric, symmetric and adjoint representations for the pseudoscalar and vector channels. An extrapolation of the vector mass as a function of the pseudoscalar mass to the large-N limit shows that the numerical results agree within errors for the three theories, as predicted by Orientifold Planar Equivalence. As a byproduct of the extrapolation, the size of the corrections up to O(1/N^3) are evaluated. A crucial prerequisite for the extrapolation is the determination of an analytical relationship between the corrections in the symmetric and in the antisymmetric representations, order by order in a 1/N expansion.

  12. Electromagnetic Boundaries with PEC/PMC Equivalence

    CERN Document Server

    Lindell, Ismo V

    2016-01-01

    The most general electromagnetic boundary, defined by linear and local boundary conditions, is defined in terms of conditions which can be called generalized impedance boundary conditions. Requiring that the boundary be equivalent to PEC and PMC boundaries for its two eigen-plane waves, which property is known to exist for many of its special cases, it is shown that the recently introduced Generalized Soft-and-Hard/DB (GSHDB) boundary is the most general boundary satisfying this property.

  13. Capacitors with low equivalent series resistance

    Science.gov (United States)

    Fleig, Patrick Franz (Inventor); Lakeman, Charles D. E. (Inventor); Fuge, Mark (Inventor)

    2011-01-01

    An electric double layer capacitor (EDLC) in a coin or button cell configuration having low equivalent series resistance (ESR). The capacitor comprises mesh or other porous metal that is attached via conducting adhesive to one or both the current collectors. The mesh is embedded into the surface of the adjacent electrode, thereby reducing the interfacial resistance between the electrode and the current collector, thus reducing the ESR of the capacitor.

  14. Quantum mechanics from an equivalence principle

    Energy Technology Data Exchange (ETDEWEB)

    Faraggi, A.E. [Univ. of Florida, Gainesville, FL (United States). Inst. for Fundamental Theory; Matone, M. [Univ. of Padova (Italy)

    1997-05-15

    The authors show that requiring diffeomorphic equivalence for one-dimensional stationary states implies that the reduced action S{sub 0} satisfies the quantum Hamilton-Jacobi equation with the Planck constant playing the role of a covariantizing parameter. The construction shows the existence of a fundamental initial condition which is strictly related to the Moebius symmetry of the Legendre transform and to its involutive character. The universal nature of the initial condition implies the Schroedinger equation in any dimension.

  15. Translation Theory and the Problem of Equivalence

    OpenAIRE

    García-Landa, Mariano

    2000-01-01

    El presente artículo se ocupa de estudiar el problema de la equivalencia desde la perspectiva de la teoría de la traducción, y las posibles soluciones que puede dársele a esta cuestión This article is devoted to the study of the problem of equivalence in translation theory, and to the different possibilities available to find a solution

  16. Residential Building Envelope Alternatives with Equivalent Cost

    OpenAIRE

    2011-01-01

    Selecting the optimum envelope alternative in buildings is one of the most important factors in ensuring thermal comfort. This study calculated the heating costs, construction and lifecycle costs for a residential building in Istanbul with different envelope alternatives created by changing the type and thickness of the body and insulation materials used in the walls and roof, which are the structural components forming the building envelope. Envelope alternatives with equivalent costs were d...

  17. Equivalent Lagrangians: Generalization, Transformation Maps, and Applications

    Directory of Open Access Journals (Sweden)

    N. Wilson

    2012-01-01

    Full Text Available Equivalent Lagrangians are used to find, via transformations, solutions and conservation laws of a given differential equation by exploiting the possible existence of an isomorphic algebra of Lie point symmetries and, more particularly, an isomorphic Noether point symmetry algebra. Applications include ordinary differential equations such as the Kummer equation and the combined gravity-inertial-Rossbywave equation and certain classes of partial differential equations related to multidimensional wave equations.

  18. Adaptive passive equivalence of uncertain Lü system

    Institute of Scientific and Technical Information of China (English)

    Qi Dong-Lian

    2006-01-01

    An adaptive passive strategy for controlling uncertain Lü system is proposed. Since the uncertain Lü system is minimum phase and the uncertain parameters are from a bounded compact set, the essential conditions are studied by which uncertain Lü system could be equivalent to a passive system, and the adaptive control law is given. Using passive theory, the uncertain Lü system could be globally asymptotically stabilized at different equilibria by the smooth state feedback.

  19. On the equivalence theorem for integrable systems

    CERN Document Server

    Melikyan, A; Rivelles, V O

    2014-01-01

    We investigate the equivalence theorem for integrable systems using two formulations of the Alday-Arutyunov-Frolov model. We show that the S-matrix is invariant under the field transformation which reduces the non-linear Dirac brackets of one formulation into the standard commutation relations in the second formulation. We also explain how to perform the direct diagonalization of the transformed Hamiltonian by constructing the states corresponding to self-adjoint extensions.

  20. Cyclic and Inductive Calculi are equivalent

    CERN Document Server

    Voicu, Razvan

    2011-01-01

    Brotherston and Simpson [citation] have formalized and investigated cyclic reasoning, reaching the important conclusion that it is at least as powerful as inductive reasoning (specifically, they showed that each inductive proof can be translated into a cyclic proof). We add to their investigation by proving the converse of this result, namely that each inductive proof can be translated into an inductive one. This, in effect, establishes the equivalence between first order cyclic and inductive calculi.

  1. Cyclic and Inductive Calculi are equivalent

    OpenAIRE

    Razvan VOICU; Li, Mengran

    2011-01-01

    Brotherston and Simpson [citation] have formalized and investigated cyclic reasoning, reaching the important conclusion that it is at least as powerful as inductive reasoning (specifically, they showed that each inductive proof can be translated into a cyclic proof). We add to their investigation by proving the converse of this result, namely that each inductive proof can be translated into an inductive one. This, in effect, establishes the equivalence between first order cyclic and inductive...

  2. The Otto-engine-equivalent vehicle concept

    Science.gov (United States)

    Dowdy, M. W.; Couch, M. D.

    1978-01-01

    A vehicle comparison methodology based on the Otto-Engine Equivalent (OEE) vehicle concept is described. As an illustration of this methodology, the concept is used to make projections of the fuel economy potential of passenger cars using various alternative power systems. Sensitivities of OEE vehicle results to assumptions made in the calculational procedure are discussed. Factors considered include engine torque boundary, rear axle ratio, performance criteria, engine transient response, and transmission shift logic.

  3. Equivalency of two-dimensional algebras

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Gildemar Carneiro dos; Pomponet Filho, Balbino Jose S. [Universidade Federal da Bahia (UFBA), BA (Brazil). Inst. de Fisica

    2011-07-01

    Full text: Let us consider a vector z = xi + yj over the field of real numbers, whose basis (i,j) satisfy a given algebra. Any property of this algebra will be reflected in any function of z, so we can state that the knowledge of the properties of an algebra leads to more general conclusions than the knowledge of the properties of a function. However structural properties of an algebra do not change when this algebra suffers a linear transformation, though the structural constants defining this algebra do change. We say that two algebras are equivalent to each other whenever they are related by a linear transformation. In this case, we have found that some relations between the structural constants are sufficient to recognize whether or not an algebra is equivalent to another. In spite that the basis transform linearly, the structural constants change like a third order tensor, but some combinations of these tensors result in a linear transformation, allowing to write the entries of the transformation matrix as function of the structural constants. Eventually, a systematic way to find the transformation matrix between these equivalent algebras is obtained. In this sense, we have performed the thorough classification of associative commutative two-dimensional algebras, and find that even non-division algebra may be helpful in solving non-linear dynamic systems. The Mandelbrot set was used to have a pictorial view of each algebra, since equivalent algebras result in the same pattern. Presently we have succeeded in classifying some non-associative two-dimensional algebras, a task more difficult than for associative one. (author)

  4. TNT equivalency of M10 propellant

    Science.gov (United States)

    Mcintyre, F. L.; Price, P.

    1978-01-01

    Peak, side-on blast overpressure and scaled, positive impulse have been measured for M10 single-perforated propellant, web size 0.018 inches, using configurations that simulate the handling of bulk material during processing and shipment. Quantities of 11.34, 22.7, 45.4, and 65.8 kg were tested in orthorhombic shipping containers and fiberboard boxes. High explosive equivalency values for each test series were obtained as a function of scaled distance by comparison to known pressure, arrival time and impulse characteristics for hemispherical TNT surface bursts. The equivalencies were found to depend significantly on scaled distance, with higher values of 150-100 percent (pressure) and 350-125 percent (positive impulse) for the extremes within the range from 1.19 to 3.57 m/cube root of kg. Equivalencies as low as 60-140 percent (pressure) and 30-75 percent (positive impulse) were obtained in the range of 7.14 to 15.8 m/cube root of kg. Within experimental error, both peak pressure and positive impulse scaled as a function of charge weight for all quantities tested in the orthorhombic configuration.

  5. Measurement equivalence in mixed mode surveys

    Directory of Open Access Journals (Sweden)

    Joop J. Hox

    2015-02-01

    Full Text Available Surveys increasingly use mixed mode data collection (e.g., combining face-to-face and web because this controls costs and helps to maintain good response rates. However, a combination of different survey modes in one study, be it cross-sectional or longitudinal, can lead to different kinds of measurement errors. For example, respondents in a face-to-face survey or a web survey may interpret the same question differently, and might give a different answer, just because of the way the question is presented. This effect of survey mode on the question-answer process is called measurement mode effect. This study develops methodological and statistical tools to identify the existence and size of mode effects in a mixed mode survey. In addition, it assesses the size and importance of mode effects in measurement instruments using a specific mixed mode panel survey (Netherlands Kinship Panel Study. Most measurement instruments in the NKPS are multi-item scales, therefore confirmatory factor analysis (CFA will be used as the main analysis tool, using propensity score methods to correct for selection effects.The results show that the NKPS scales by and large have measurement equivalence, but in most cases only partial measurement equivalence. Controlling for respondent differences on demographic variables, and on scale scores from the previous uni-mode measurement occasion, tends to improve measurement equivalence, but not for all scales. The discussion ends with a review of the implications of our results for analyses employing these scales.

  6. Orientifold Planar Equivalence: The Chiral Condensate

    CERN Document Server

    Armoni, A; Patella, A; Pica, C

    2008-01-01

    The recently introduced orientifold planar equivalence is a promising tool for solving non-perturbative problems in QCD. One of the predictions of orientifold planar equivalence is that the chiral condensates of a theory with $N_f$ flavours of Dirac fermions in the symmetric (or antisymmetric) representation and $N_f$ flavours of Majorana fermions in the adjoint representation have the same large $N$ value for any value of the mass of the (degenerate) fermions. Assuming the invariance of the theory under charge conjugation, we prove this statement on the lattice for staggered quenched condensates in SU($N$) Yang-Mills in the large $N$ limit. Then, we compute numerically those quenched condensates for $N$ up to 8. After separating the even from the odd corrections in $1/N$, we are able to show that our data support the equivalence; however, unlike other quenched observables, subleading terms in $1/N$ are needed for describing the data for the symmetric and antisymmetric representation at $N$=3. Possible lesson...

  7. Homeomorphisms, homotopy equivalences and chain complexes

    CERN Document Server

    Adams-Florou, Spiros

    2012-01-01

    This thesis concerns the relationship between bounded and controlled topology and how these can be used to recognise which homotopy equivalences of reasonable topological spaces are homotopic to homeomorphisms. Let $f:X\\to Y$ be a simplicial map of finite-dimensional locally finite simplicial complexes. We prove that $f$ has contractible point inverses if and only if it is an $\\epsilon$-controlled homotopy equivalences for all $\\epsilon>0$, if and only if $f\\times\\mathrm{id}:X\\times\\mathbb{R} \\to Y\\times\\mathbb{R}$ is a homotopy equivalence bounded over the open cone $O(Y^+)$ of Pedersen and Weibel. This approach can be generalised to algebra using geometric categories: the $X$-controlled categories $\\mathbb{A}^*(X)$, $\\mathbb{A}_*(X)$ of Ranicki and Weiss together with the bounded categories $\\mathcal{C}_M(\\mathbb{A})$ of Pedersen and Weibel. Analogous to the barycentric subdivision of a simplicial complex, we define the algebraic subdivision of a chain complex over that simplicial complex. The main theorem ...

  8. Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires

    DEFF Research Database (Denmark)

    Bergseng, Elin; Dørum, Siri; Arntzen, Magnus Ø.

    2014-01-01

    . It was recently demonstrated that T cells of DQ2.5 and DQ2.2 patients recognize distinct sets of gluten epitopes, suggesting that these two DQ2 variants select different peptides for display. To explore whether this is the case, we performed a comprehensive comparison of the endogenous self-peptides bound to HLA......-DQ molecules of B-lymphoblastoid cell lines. Peptides were eluted from affinity-purified HLA molecules of nine cell lines and subjected to quadrupole orbitrap mass spectrometry and MaxQuant software analysis. Altogether, 12,712 endogenous peptides were identified at very different relative abundances...... at position P3. This study demonstrates that relative quantitative comparison of endogenous peptides sampled from our protein metabolism by HLA molecules provides clues to understand HLA association with disease....

  9. Approximate trace and singleton failures equivalences for transition systems

    Institute of Scientific and Technical Information of China (English)

    Chao Wang; Jinzhao Wu; Hongyan Tan

    2015-01-01

    Established system equivalences for transition systems, such as trace equivalence and failures equivalence, require the ob-servations to be exactly identical. However, an accurate measure-ment is impossible when interacting with the physical world, hence exact equivalence is restrictive and not robust. Using Baire met-ric, a generalized framework of transition system approximation is proposed by developing the notions of approximate language equivalence and approximate singleton failures (SF) equivalence. The framework takes the traditional exact equivalence as a special case. The approximate language equivalence is coarser than the approximate SF equivalence, just like the hierarchy of the exact ones. The main conclusion is that the two approximate equiva-lences satisfy the transitive property, consequently, they can be successively used in transition system approximation.

  10. In Quest of Sufficient Equivalence. Polish and English Insolvency Terminology in Translation. a Comparative Study

    Directory of Open Access Journals (Sweden)

    Matulewska Aleksandra

    2014-09-01

    Full Text Available The paper deals with the problem of translating selected insolvency terminology from Polish into English and from English into Polish. The re- search corpora encompassed the Insolvency Act 1986 (England and Wales as amended and Ustawa z dnia 28 lutego 2003. Prawo upadłościowe i naprawcze [the Act on Polish Insolvency and Rehabilitation Law of 28th February 2003 as amended]. The research methods included: (i the comparison of parallel texts, (ii the method of axiomatisation of the legal linguistic reality, (iii the termino- logical analysis of the corpus material, (iv the concept of adjusting the target text to the communicative needs and requirements of the community of recipients and (v the techniques of providing equivalents for non-equivalent terminology. The research hypothesis has been so formulated that the parametrisation of legal reality may assist in finding more adequate equivalents and determine differences in meaning of compared source and target language terms, which in turn facilitates the choice of a more adequate technique of providing equivalents for non-equivalent or partially equivalent legal terminology meeting the com- municative needs of translation recipients. The research results revealed that insolvency terminology is highly system-bound and available equivalents may often be misleading for the community of target text recipients

  11. Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: Protein synthesis, cell proliferation, and T-cell activation

    Energy Technology Data Exchange (ETDEWEB)

    Navare, Arti T.; Sova, Pavel; Purdy, David E.; Weiss, Jeffrey M. [Department of Microbiology, University of Washington, Seattle, WA (United States); Wolf-Yadlin, Alejandro [Department of Genome Sciences, University of Washington, Seattle, WA (United States); Korth, Marcus J.; Chang, Stewart T.; Proll, Sean C. [Department of Microbiology, University of Washington, Seattle, WA (United States); Jahan, Tahmina A. [Proteomics Resource, UW Medicine at South Lake Union, Seattle, WA (United States); Krasnoselsky, Alexei L.; Palermo, Robert E. [Department of Microbiology, University of Washington, Seattle, WA (United States); Katze, Michael G., E-mail: honey@uw.edu [Department of Microbiology, University of Washington, Seattle, WA (United States); Washington National Primate Research Center, University of Washington, Seattle, WA (United States)

    2012-07-20

    Human immunodeficiency virus (HIV-1) depends upon host-encoded proteins to facilitate its replication while at the same time inhibiting critical components of innate and/or intrinsic immune response pathways. To characterize the host cell response on protein levels in CD4+ lymphoblastoid SUP-T1 cells after infection with HIV-1 strain LAI, we used mass spectrometry (MS)-based global quantitation with iTRAQ (isobaric tag for relative and absolute quantification). We found 266, 60 and 22 proteins differentially expressed (DE) (P-value{<=}0.05) at 4, 8, and 20 hours post-infection (hpi), respectively, compared to time-matched mock-infected samples. The majority of changes in protein abundance occurred at an early stage of infection well before the de novo production of viral proteins. Functional analyses of these DE proteins showed enrichment in several biological pathways including protein synthesis, cell proliferation, and T-cell activation. Importantly, these early changes before the time of robust viral production have not been described before.

  12. Ambiguity Revealed

    OpenAIRE

    Subir Bose; Matthew Polisson; Ludovic Renou

    2012-01-01

    We derive necessary and suffcient conditions for data sets composed of state-contingent prices and consumption to be consistent with two prominent models of decision making under ambiguity: variational preferences and smooth ambiguity. The revealed preference conditions for the maxmin expected utility and subjective expected utility models are characterized as special cases.

  13. Ambiguity revealed

    OpenAIRE

    Bayer, Ralph-C; Bose, Subir; Polisson, Matthew; Renou, Ludovic

    2013-01-01

    We derive necessary and sufficient conditions for data sets composed of state-contingent prices and consumption to be consistent with two prominent models of decision making under uncertainty: variational preferences and smooth ambiguity. The revealed preference conditions for subjective expected utility, maxmin expected utility, and multiplier preferences are characterised as special cases. We implement our tests on data from a portfolio choice experiment.

  14. An equivalent system of Einstein Equations

    Science.gov (United States)

    Ospino, J.; Hernández-Pastora, J. L.; Núñez, L. A.

    2017-03-01

    We provide the full set of equations governing the evolution of self-gravitating systems by using a tetrad formalism in General Relativity and the orthogonal splitting of the Riemann tensor. We apply this formalism to spherical case and found that: the only static solution with homogeneous energy density, under the physical reasonable considerations, is the Schwarzchild solution; the conditions under which a non-dissipative fluid is static and finally that shear-free and isotropic pressure conditions are equivalent, for non-dissipative fluids with homogeneous energy density.

  15. Equivalent Circuit Modeling of Hysteresis Motors

    Energy Technology Data Exchange (ETDEWEB)

    Nitao, J J; Scharlemann, E T; Kirkendall, B A

    2009-08-31

    We performed a literature review and found that many equivalent circuit models of hysteresis motors in use today are incorrect. The model by Miyairi and Kataoka (1965) is the correct one. We extended the model by transforming it to quadrature coordinates, amenable to circuit or digital simulation. 'Hunting' is an oscillatory phenomenon often observed in hysteresis motors. While several works have attempted to model the phenomenon with some partial success, we present a new complete model that predicts hunting from first principles.

  16. Development and Testing of Living Skin Equivalent.

    Science.gov (United States)

    1988-05-01

    Model a) The use of Isografts in an inbred strain of rats. In a preliminary series of experiments the potential use of Fischer strain rats has been...tested by preparing a series of isografts made by grafting skin equivalents with cells from female donors to male hosts. On the average, wound...Autograft--rat 4 1 4 3 5 17 Autograft--rabbit 6 3 1 1 11 Isograft --rat 37 13 13 1 64 Allo fib., iso ker--rat 15 12 3 30 Allo fib, iso ker--rab 8 6 14 Iso

  17. The equivalence principle in a quantum world

    DEFF Research Database (Denmark)

    Bjerrum-Bohr, N. Emil J.; Donoghue, John F.; El-Menoufi, Basem Kamal;

    2015-01-01

    the energy is small, we now have the tools to address this conflict explicitly. Despite the violation of some classical concepts, the EP continues to provide the core of the quantum gravity framework through the symmetry - general coordinate invariance - that is used to organize the effective field theory......We show how modern methods can be applied to quantum gravity at low energy. We test how quantum corrections challenge the classical framework behind the equivalence principle (EP), for instance through introduction of nonlocality from quantum physics, embodied in the uncertainty principle. When...

  18. European Equivalencies in Legal Interpreting and Translation

    DEFF Research Database (Denmark)

    Corsellis, Ann; Hertog, Erik; Martinsen, Bodil

    2002-01-01

    Within Europe there is increasing freedom of movement between countries and increasing inward migration. As a result, equivalent standards of legl interpreting and translation are required to allow reliable communication for judicial cooperation between member states, for criminal and civil matters...... which cross national borders and for the needs of multilingual populations. The European Convention of Human Rights (article 6, paragrph 3) is one of the main planks of relevant legislation. This international, two year project has been funded by the EU Grotius programme to set out what is required...

  19. The Search for a New Equivalence Principle

    CERN Document Server

    Ionescu, Lucian M

    2007-01-01

    The new emerging quantum physics - quantum computing conceptual bridge, mandates a ``grand unification'' of space-time-matter and quantum information (all quantized), with deep implications for science in general. The major physics revolutions in our understanding of the universe are briefly reviewed and a ``missing'' equivalence principle is identified and its nature explained. An implementation as an external super-symmetry $\\C{E}=ic\\C{P}$ is suggested, generalizing the Wick rotation ``trick''. Taking advantage of the interpretation of entropy as a measure of symmetry, it is naturally asimilated within the present Feynman Path Integral algebraic formalism.

  20. Gravitational leptogenesis, C, CP and strong equivalence

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, Jamie I.; Shore, Graham M. [Department of Physics, Swansea University,Swansea, SA2 8PP (United Kingdom)

    2015-02-12

    The origin of matter-antimatter asymmetry is one of the most important outstanding problems at the interface of particle physics and cosmology. Gravitational leptogenesis (baryogenesis) provides a possible mechanism through explicit couplings of spacetime curvature to appropriate lepton (or baryon) currents. In this paper, the idea that these strong equivalence principle violating interactions could be generated automatically through quantum loop effects in curved spacetime is explored, focusing on the realisation of the discrete symmetries C, CP and CPT which must be broken to induce matter-antimatter asymmetry. The related issue of quantum corrections to the dispersion relation for neutrino propagation in curved spacetime is considered within a fully covariant framework.

  1. Hysteretic damping in rotordynamics: An equivalent formulation

    Science.gov (United States)

    Genta, Giancarlo; Amati, Nicola

    2010-10-01

    The hysteretic damping model cannot be applied to time domain dynamic simulations: this is a well-known feature that has been discussed in the literature since the time when analog computers were widespread. The constant equivalent damping often introduced to overcome this problem is also discussed, and its limitations are stated, in particular those linked with its application in rotordynamics to simulate rotating damping. An alternative model based on the nonviscous damping (NVD) model, but with a limited number of additional degrees of freedom, is proposed, and the relevant equations are derived. Some examples show applications to the rotordynamics field.

  2. Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses.

    Science.gov (United States)

    Shen, Jianqiang; Xie, Kabin; Xiong, Lizhong

    2010-12-01

    MicroRNAs are a class of endogenous small RNA molecules (20-24 nucleotides) that have pivotal roles in regulating gene expression mostly at posttranscriptional levels in plants. Plant microRNAs have been implicated in the regulation of diverse biological processes including growth and stress responses. However, the information about microRNAs in regulating abiotic stress responses in rice is limited. We optimized a one-tube stem-loop reverse transcription quantitative PCR (ST-RT qPCR) for high-throughput expression profiling analysis of microRNAs in rice under normal and stress conditions. The optimized ST-RT qPCR method was as accurate as small RNA gel blotting and was more convenient and time-saving than other methods in quantifying microRNAs. With this method, 41 rice microRNAs were quantified for their relative expression levels after drought, salt, cold, and abscisic acid (ABA) treatments. Thirty-two microRNAs showed induced or suppressed expression after stress or ABA treatment. Further analysis suggested that stress-responsive cis-elements were enriched in the promoters of stress-responsive microRNA genes. The expressions of five and seven microRNAs were significantly affected in the rice plant with defects in stress tolerance regulatory genes OsSKIPa and OsbZIP23, respectively. Some of the predicted target genes of these microRNAs were also related to abiotic stresses. We conclude that ST-RT qPCR is an efficient and reliable method for expression profiling of microRNAs and a significant portion of rice microRNAs participate in abiotic stress response and regulation.

  3. Investigating Starburst Galaxy Emission Line Equivalent Widths

    Science.gov (United States)

    Meskhidze, Helen; Richardson, Chris T.

    2016-01-01

    Modeling star forming galaxies with spectral synthesis codes allows us to study the gas conditions and excitation mechanisms that are necessary to reproduce high ionization emission lines in both local and high-z galaxies. Our study uses the locally optimally-emitting clouds model to develop an atlas of starburst galaxy emission line equivalent widths. Specifically, we address the following question: What physical conditions are necessary to produce strong high ionization emission lines assuming photoionization via starlight? Here we present the results of our photoionization simulations: an atlas spanning 15 orders of magnitude in ionizing flux and 10 orders of magnitude in hydrogen density that tracks over 150 emission lines ranging from the UV to the near IR. Each simulation grid contains ~1.5x104 photoionization models calculated by supplying a spectral energy distribution, grain content, and chemical abundances. Specifically, we will be discussing the effects on the emission line equivalent widths of varying the metallicity of the cloud, Z = 0.2 Z⊙ to Z = 5.0 Z⊙, and varying the star-formation history, using the instantaneous and continuous evolution tracks and the newly released Starburst99 Geneva rotation tracks.

  4. Equivalent circuit analysis of terahertz metamaterial filters

    Institute of Scientific and Technical Information of China (English)

    Xueqian Zhang; Quan Li; Wei Cao; Weisheng Yue; Jianqiang Gu; Zhen Tian; Jiaguang Han; Weili Zhang

    2011-01-01

    Metamaterials have been demonstrated over a significant portion of the electromagnetic spectra from radio,microwave,and terahertz (THz) to the optical regimes.The unique properties of metamaterials are not attainable with naturally occurring materials[1].Thus,enormous applications in devices and techniques,such as superlens,cloaking antenna,and sub-wavelength photolithography are enabled[2-5].The capability of metamaterials has been broadly expanded because they allow precise control of the electromagnetic responses.The appreciation of electromagnetic response control through metamaterial structures provides unique benefits in the design of versatile devices,including filters,modulators,and switchable components.%An equivalent circuit model for the analysis and design of terahertz (THz) metamaterial filters is presented. The proposed model, derived based on LMC equivalent circuits, takes into account the detailed geometrical parameters and the presence of a dielectric substrate with the existing analytic expressions for self-inductance, mutual inductance, and capacitance. The model is in good agreement with the experimental measurements and full-wave simulations. Exploiting the circuit model has made it possible to predict accurately the resonance frequency of the proposed structures and thus, quick and accurate process of designing THz device from artificial metamaterials is offered.

  5. Equivalence of open/closed strings

    CERN Document Server

    Wang, Peng; Yang, Haitang

    2015-01-01

    In this paper, we prove that the open and closed strings are $O(D,D)$ equivalent. The equivalence requires an AdS geometry near the boundaries. The $O(D,D)$ invariance is introduced into the Polyakov action by the Tseytlin's action. Traditionally, there exist disconnected open-open or closed-closed configurations in the solution space of the Tseytlin's action. The open-closed configuration is ruled out by the mixed terms of the dual fields. We show that, under some very general guidances, the dual fields are consistently decoupled if and only if the near horizon geometry is $AdS_5$. We then have open-closed and closed-open configurations in different limits of the distances of the $D3$-brane pairs. Inherited from the definition of the theory, these four configurations are of course related to each other by $O(D,D)$ transformations. We therefore conclude that both the open/closed relation and open/closed duality can be derived from $O(D,D)$ symmetries. By analyzing the couplings of the configurations, the low ...

  6. Equivalent Relaxations of Optimal Power Flow

    Energy Technology Data Exchange (ETDEWEB)

    Bose, S; Low, SH; Teeraratkul, T; Hassibi, B

    2015-03-01

    Several convex relaxations of the optimal power flow (OPF) problem have recently been developed using both bus injection models and branch flow models. In this paper, we prove relations among three convex relaxations: a semidefinite relaxation that computes a full matrix, a chordal relaxation based on a chordal extension of the network graph, and a second-order cone relaxation that computes the smallest partial matrix. We prove a bijection between the feasible sets of the OPF in the bus injection model and the branch flow model, establishing the equivalence of these two models and their second-order cone relaxations. Our results imply that, for radial networks, all these relaxations are equivalent and one should always solve the second-order cone relaxation. For mesh networks, the semidefinite relaxation and the chordal relaxation are equally tight and both are strictly tighter than the second-order cone relaxation. Therefore, for mesh networks, one should either solve the chordal relaxation or the SOCP relaxation, trading off tightness and the required computational effort. Simulations are used to illustrate these results.

  7. TRI12 based quantitative real-time PCR assays reveal the distribution of trichothecene genotype of F. graminearum and F. culmorum isolates in Danish small grain cereals

    DEFF Research Database (Denmark)

    Nielsen, L. K.; Jensen, J. D.; Rodríguez, A.;

    2012-01-01

    species complex, Fusarium culmorum, Fusarium cerealis and Fusarium pseudograminearum. These assays were applied on a total of 378 field samples of cereal grain of wheat, barley, triticale, rye and oats collected from 2003 to 2007 to study the trichothecene genotype composition in Danish cereals. The three...... in wheat. The NIV genotype was found at low levels in most samples. Study of genotype composition within the Danish F. graminearum and F. culmorum population was based on principal component analysis (PCA). PCA revealed that the dominating genotype of F. graminearum in wheat is 15ADON. For barley, the PCA...... analysis indicated that the F. graminearum population consisted of all three genotypes, and in triticale, the F. graminearum population consisted mainly of 15ADON genotype. F. culmorum/F. cerealis showed correlation to the NIV genotype in wheat and triticale but not in barley. F. culmorum/F. cerealis also...

  8. Equivalent Relation between Normalized Spatial Entropy and Fractal Dimension

    CERN Document Server

    Chen, Yanguang

    2016-01-01

    Fractal dimension is defined on the base of entropy, including macro state entropy and information entropy. The generalized dimension of multifractals is based on Renyi entropy. However, the mathematical transform from entropy to fractal dimension is not yet clear in both theory and practice. This paper is devoted to revealing the equivalence relation between spatial entropy and fractal dimension using box-counting method. Based on varied regular fractals, the numerical relationship between spatial entropy and fractal dimension is examined. The results show that the ratio of actual entropy (Mq) to the maximum entropy (Mmax) equals the ratio of actual dimension (Dq) to the maximum dimension (Dmax), that is, Mq/Mmax=Dq/Dmax. For real systems, the spatial entropy and fractal dimension of complex spatial systems such as cities can be converted into one another by means of functional box-counting method. The theoretical inference is verified by observational data of urban form. A conclusion is that normalized spat...

  9. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  10. Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus).

    Science.gov (United States)

    Kim, Kwang-Hwan; Hwang, Ji-Hyun; Han, Dong-Yeup; Park, Minkyu; Kim, Seungill; Choi, Doil; Kim, Yongjae; Lee, Gung Pyo; Kim, Sun-Tae; Park, Young-Hoon

    2015-01-01

    An intraspecific genetic map for watermelon was constructed using an F2 population derived from 'Arka Manik' × 'TS34' and transcript sequence variants and quantitative trait loci (QTL) for resistance to powdery mildew (PMR), seed size (SS), and fruit shape (FS) were analyzed. The map consists of 14 linkage groups (LGs) defined by 174 cleaved amplified polymorphic sequences (CAPS), 2 derived-cleaved amplified polymorphic sequence markers, 20 sequence-characterized amplified regions, and 8 expressed sequence tag-simple sequence repeat markers spanning 1,404.3 cM, with a mean marker interval of 6.9 cM and an average of 14.6 markers per LG. Genetic inheritance and QTL analyses indicated that each of the PMR, SS, and FS traits is controlled by an incompletely dominant effect of major QTLs designated as pmr2.1, ss2.1, and fsi3.1, respectively. The pmr2.1, detected on chromosome 2 (Chr02), explained 80.0% of the phenotypic variation (LOD = 30.76). This QTL was flanked by two CAPS markers, wsb2-24 (4.00 cM) and wsb2-39 (13.97 cM). The ss2.1, located close to pmr2.1 and CAPS marker wsb2-13 (1.00 cM) on Chr02, explained 92.3% of the phenotypic variation (LOD = 68.78). The fsi3.1, detected on Chr03, explained 79.7% of the phenotypic variation (LOD = 31.37) and was flanked by two CAPS, wsb3-24 (1.91 cM) and wsb3-9 (7.00 cM). Candidate gene-based CAPS markers were developed from the disease resistance and fruit shape gene homologs located on Chr.02 and Chr03 and were mapped on the intraspecific map. Colocalization of these markers with the major QTLs indicated that watermelon orthologs of a nucleotide-binding site-leucine-rich repeat class gene containing an RPW8 domain and a member of SUN containing the IQ67 domain are candidate genes for pmr2.1 and fsi3.1, respectively. The results presented herein provide useful information for marker-assisted breeding and gene cloning for PMR and fruit-related traits.

  11. The quantitative analysis by stem-loop real-time PCR revealed the microRNA-34a, microRNA-155 and microRNA-200c overexpression in human colorectal cancer.

    Science.gov (United States)

    Wang, Mojin; Zhang, Peng; Li, Yuan; Liu, Guanghui; Zhou, Bin; Zhan, Lan; Zhou, Zongguang; Sun, Xiaofeng

    2012-12-01

    The recently identified class of microRNAs (miRNAs) provided a new insight in cancer research. As the member of miRNAs family, miR-34a, miR-155 and miR-200c abnormalities have been found in various types of cancer. However, the relationship between these three miRNAs (miR-34a, miR-155 and miR-200c) and colorectal cancer is unclear. In this study, we applied stem-loop real-time PCR to quantitatively detect miR-34a, miR-155 and miR-200c expression in 109 pair-matched human colorectal cancers and the corresponding normal mucosa. MiR-34a (2.2-fold), miR-155 (2.3-fold) and miR-200c (3.1-fold) were all expressed at higher levels in colorectal cancer (P = 0.001, 0.005 and 0.001, respectively). In rectum, miR-34a and miR-200c were significantly upregulated (P = 0.006 and 0.007), while the miR-155 overexpression was not statistically significant (P = 0.083). In colon, the higher expression of three miRNAs was seen, however, without significant difference (P > 0.05). We also found that the miR-34a expression was higher in rectal cancer having more advanced TNM stage (III + IV, P = 0.03). Then miR-200c expression was positively correlated with and sera CEA level of rectal cancer patients (P = 0.04). In conclusion, our results thus suggest that the overexpression of miR-34a, miR-155 and miR-200c be associated with the development of colorectal cancer, meanwhile miR-34a may be involved in the development and progression of rectal cancer. The more deeply and larger scale research are required to prove the correlation.

  12. REVEALED ALTRUISM

    OpenAIRE

    Cox, James C; Friedman, Daniel; Sadiraj, Vjollca

    2009-01-01

    This pap er develops a theory of revealed preferences over oneís own and othersímonetary payo§s. We intro duce ìmore altruistic thanî(MAT), a partial ordering over preferences, and interpret it with known parametric mo dels. We also intro duce and illustrate ìmore generous thanî (MGT), a partial ordering over opp ortunity sets. Several recent discussions of altruism fo cus on two player extensive form games of complete information in which the Örst mover (FM) cho oses a more or less gen...

  13. Equivalent Resistance in Pulse Electric Current Sintering

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The sintering resistance for conductive TiB2 and non-conductive Al2O3 as well as empty die during pulse current sintering were investigated in this paper.Equivalent resistances were measured by current and valtage during sintering the conductive and non-conductive materials in the same conditions.It is found that the current paths for conductive are different from those for non-conductive materials.For non-conductive materials,sintering resistances are influenced by powder sizes and heating rates,which indicates that pulse current has some interaction with non-conductive powders.For conductive TiB2,sintering resistances are influenced by heating rates and ball-milling time,which indicates the effect of powders activated by spark.

  14. FUZZY ORDER EQUIVALENT CLASS WITH UNCERTAINTY

    Institute of Scientific and Technical Information of China (English)

    Wei ZHOU; Mingzhe WANG

    2005-01-01

    It is a new research topic to create a rational judgment matrix using the cognition theory because of the construction of judgment matrix in AHP involving the decision-maker's cognitive activities.Owing to the presence of uncertain information in the decision procedure, the improper use of the uncertain information will doubtless cause weight changes. In this paper, we add a feedforward process prior to constructing the judgment matrix so that the decision maker can use both the certain and uncertain information to get the initial uncertain rough judgment matrix, and then convert it into a fuzzy matrix. Consequently, it will be better for decision maker to obtain the rough set of order equivalent classes through the decision graph. According to the qualitative analysis, the decision maker can easily construct the final judgment matrix instructed by the rough set created earlier.

  15. Expressivism, Relativism and the analytic equivalence test

    Directory of Open Access Journals (Sweden)

    Maria J. Frapolli

    2015-11-01

    Full Text Available The purpose of this paper is to show that, pace (Field 2009, 252, MacFarlane’s assessment relativism and expressivism should be sharply distinguished. We do so by arguing that relativism and expressivism exemplify two very different approaches to context-dependence. Relativism, on the one hand, shares with other contemporary approaches a bottom-up, building block, model, while expressivism is part of a different tradition, one that might include Lewis’ epistemic contextualism and Frege’s content individuation, with which it shares an organic model to deal with context-dependence. The building-block model and the organic model, and thus relativism and expressivism, are set apart with the aid of a particular test: only the building-block model is compatible with the idea that there might be analytically equivalent, and yet different, propositions.

  16. Expressivism, Relativism, and the Analytic Equivalence Test.

    Science.gov (United States)

    Frápolli, Maria J; Villanueva, Neftalí

    2015-01-01

    The purpose of this paper is to show that, pace (Field, 2009), MacFarlane's assessment relativism and expressivism should be sharply distinguished. We do so by arguing that relativism and expressivism exemplify two very different approaches to context-dependence. Relativism, on the one hand, shares with other contemporary approaches a bottom-up, building block, model, while expressivism is part of a different tradition, one that might include Lewis' epistemic contextualism and Frege's content individuation, with which it shares an organic model to deal with context-dependence. The building-block model and the organic model, and thus relativism and expressivism, are set apart with the aid of a particular test: only the building-block model is compatible with the idea that there might be analytically equivalent, and yet different, propositions.

  17. [The false equivalent Galeazzi in children].

    Science.gov (United States)

    Marzouki, A; Elibrahimi, A; Elmrini, A; Boutayeb, F

    2009-02-01

    We report the case of a false Galeazzi equivalent in children. This injury is characterised by an epiphyseal detachment of the distal extremity of the ulna rather than a distal radio-ulnar dislocation. A 16-year-old patient was injured in a fall from a bike. Radiographs showed a fracture of the radial shaft with anterior angulation, together with a type II Salter-Harris epiphyseal injury at the level of the distal ulna. We were unable to perform a closed reduction under general anesthesia due to interposition of periosteum at the fracture site. Thus surgical management was the only option, which consisted of removing the offending periosteum and performing osteosynthesis of the radial shaft fracture with a plate, and the epiphyseal detachment with pins. After 10 months, we noted no bone growth disturbance, or any reduced mobility of the wrist. We will continue the follow-up to monitor bone growth disturbance of the distal extremity of the ulna.

  18. Equivalence Bimodule between Spherical Noncommutative Tori

    Institute of Scientific and Technical Information of China (English)

    Chun Gil PARK

    2003-01-01

    Let ni,mj > 1. In [5], the spherical noncommutative torus Sppd was defined by twisting Tr+2 × Zl in Tpd C*(Zl) by a totally skew multiplier p on Tr+2 × Zl for Tpd a pd-homogeneous C*-algebra over Пs4i=1 S2n+I ×Пs2 S2 ×Пs3j=1 S2mj-1 ×Пs1 S1 × Tr+2. It is shown that Sppd is strongly Morita equivalent to C(Пs4i=1 S2ni ×Пs2S2×Пs3j=1 S2mj-1 ×Пs1 S1) C*(Tr+3× Zl, p).

  19. Characterization of Destrins with Different Dextrose Equivalents

    Directory of Open Access Journals (Sweden)

    Guanglei Li

    2010-07-01

    Full Text Available Dextrins are widely used for their functional properties and prepared by partial hydrolysis of starch using acid, enzymes, or combinations of both. The physiochemical properties of dextrins are dependent on their molecular distribution and oligosaccharide profiles. In this study, scanning electron microscopy (SEM, X-ray diffractometry (XRD, rapid viscoanalysis (RVA, high-performance Liquid Chromatography (HPLC and gel permeation chromatography (GPC were used to characterize dextrins prepared by common neutral and thermostable α-amylase hydrolysis. The dextrin granules displayed irregular surfaces and were badly damaged by the enzyme treatment. They displayed A-type X-ray diffraction patterns with a decrease of intensity of the characteristic diffraction peaks. The RVA profiles showed that the viscosity of dextrin decreased with the increase of its Dextrose Equivalent (DE value. According to HPLC analysis, the molecular weight, degree of polymerization and the composition of oligosaccharides in dextrins were different.

  20. Equivalent damage validation by variable cluster analysis

    Science.gov (United States)

    Drago, Carlo; Ferlito, Rachele; Zucconi, Maria

    2016-06-01

    The main aim of this work is to perform a clustering analysis on the damage relieved in the old center of L'Aquila after the earthquake occurred on April 6, 2009 and to validate an Indicator of Equivalent Damage ED that summarizes the information reported on the AeDES card regarding the level of damage and their extension on the surface of the buildings. In particular we used a sample of 13442 masonry buildings located in an area characterized by a Macroseismic Intensity equal to 8 [1]. The aim is to ensure the coherence between the clusters and its hierarchy identified in the data of damage detected and in the data of the ED elaborated.

  1. Premetric equivalent of general relativity: Teleparallelism

    Science.gov (United States)

    Itin, Yakov; Hehl, Friedrich W.; Obukhov, Yuri N.

    2017-04-01

    In general relativity (GR), the metric tensor of spacetime is essential since it represents the gravitational potential. In other gauge theories (such as electromagnetism), the so-called premetric approach succeeds in separating the purely topological field equation from the metric-dependent constitutive law. We show here that GR allows for a premetric formulation, too. For this purpose, we apply the teleparallel approach of gravity, which represents GR as a gauge theory based on the translation group. We formulate the metric-free topological field equation and a general linear constitutive law between the basic field variables. The requirement of local Lorentz invariance turns the model into a full equivalent of GR. Our approach opens a way for a natural extension of GR to diverse geometrical structures of spacetime.

  2. Equivalency and unbiasedness of grey prediction models

    Institute of Scientific and Technical Information of China (English)

    Bo Zeng; Chuan Li; Guo Chen; Xianjun Long

    2015-01-01

    In order to deeply research the structure discrepancy and modeling mechanism among different grey prediction mo-dels, the equivalence and unbiasedness of grey prediction mo-dels are analyzed and verified. The results show that al the grey prediction models that are strictly derived from x(0)(k) +az(1)(k) = b have the identical model structure and simulation precision. Moreover, the unbiased simulation for the homoge-neous exponential sequence can be accomplished. However, the models derived from dx(1)/dt+ax(1) =b are only close to those derived from x(0)(k)+az(1)(k)=b provided that|a|has to satisfy|a| < 0.1; neither could the unbiased simulation for the homoge-neous exponential sequence be achieved. The above conclusions are proved and verified through some theorems and examples.

  3. Isomorphism and Morita equivalence of graph algebras

    CERN Document Server

    Abrams, Gene

    2008-01-01

    For any countable graph $E$, we investigate the relationship between the Leavitt path algebra $L_{\\C}(E)$ and the graph C*-algebra $C^*(E)$. For graphs $E$ and $F$, we examine ring homomorphisms, ring *-homomorphisms, algebra homomorphisms, and algebra *-homomorphisms between $L_{\\C}(E)$ and $L_{\\C}(F)$. We prove that in certain situations isomorphisms between $L_{\\C}(E)$ and $L_{\\C}(F)$ yield *-isomorphisms between the corresponding C*-algebras $C^*(E)$ and $C^*(F)$. Conversely, we show that *-isomorphisms between $C^*(E)$ and $C^*(F)$ produce isomorphisms between $L_{\\C}(E)$ and $L_{\\C}(F)$ in specific cases. The relationship between Leavitt path algebras and graph C*-algebras is also explored in the context of Morita equivalence.

  4. Correlation Measure Equivalence in Dynamic Causal Structures

    CERN Document Server

    Gyongyosi, Laszlo

    2016-01-01

    We prove an equivalence transformation between the correlation measure functions of the causally-unbiased quantum gravity space and the causally-biased standard space. The theory of quantum gravity fuses the dynamic (nonfixed) causal structure of general relativity and the quantum uncertainty of quantum mechanics. In a quantum gravity space, the events are causally nonseparable and all time bias vanishes, which makes it no possible to use the standard causally-biased entropy and the correlation measure functions. Since a corrected causally-unbiased entropy function leads to an undefined, obscure mathematical structure, in our approach the correction is made in the data representation of the causally-unbiased space. We prove that the standard causally-biased entropy function with a data correction can be used to identify correlations in dynamic causal structures. As a corollary, all mathematical properties of the causally-biased correlation measure functions are preserved in the causally-unbiased space. The eq...

  5. The premetric equivalent of general relativity: teleparallelism

    CERN Document Server

    Itin, Yakov; Obukhov, Yuri N

    2016-01-01

    In general relativity (GR), the metric tensor of spacetime is essential since it represents the gravitational potential. In other gauge theories (such as electromagnetism), the so-called premetric approach succeeds in separating the purely topological field equation from the metric-dependent constitutive law. We show here that GR allows for a premetric formulation, too. For this purpose, we apply the teleparallel approach of gravity, which represents GR as a gauge theory based on the translation group. We formulate the metric-free topological field equation and a general linear constitutive law between the basic field variables. The requirement of local Lorentz invariance turns the model into a full equivalent of GR. Our approach opens a way for a natural extension of GR to diverse geometrical structures of spacetime.

  6. Snow water equivalent mapping in Norway

    Science.gov (United States)

    Tveito, O. E.; Udnæs, H.-C.; Engeset, R.; Førland, E. J.; Isaksen, K.; Mengistu, Z.

    2003-04-01

    In high latitude area snow covers the ground large parts of the year. Information about the water volume as snow is of major importance in many respects. Flood forecasters at NVE need it in order to assess possible flood risks. Hydropower producers need it to plan the most efficient production of the water in their reservoirs, traders to estimate the potential energy available for the market. Meteorologists on their side use the information as boundary conditions in weather forecasting models. The Norwegian meteorological institute has provided snow accumulation maps for Norway for more than 50 years. These maps are now produced twice a month in the winter season. They show the accumulated precipitation in the winter season from the day the permanent snow cover is established. They do however not take melting into account, and do therefore not give a good description of the actual snow amounts during and after periods with snowmelt. Due to an increased need for a direct measure of water volumes as snow cover, met.no and NVE initialized a joint project in order to establish maps of the actual snow cover expressed in water equivalents. The project utilizes recent developments in the use of GIS in spatial modeling. Daily precipitation and temperature are distributed in space by using objective spatial interpolation methods. The interpolation considers topographical and other geographical parameters as well as weather type information. A degree-day model is used at each modeling point to calculate snow-accumulation and snowmelt. The maps represent a spatial scale of 1x1 km2. The modeled snow reservoir is validated by snow pillow values as well traditional snow depth observations. Preliminary results show that the new snow modeling approach reproduces the snow water equivalent well. The spatial approach also opens for a wide use in the terms of areal analysis.

  7. A Solid State Tissue Equivalent Detector for Microdosimetry Project

    Data.gov (United States)

    National Aeronautics and Space Administration — QEL proposes to construct a tissue equivalent microdosimeter using a solid state tissue equivalent detector (SSTED). The Phase I study will produce the working...

  8. Proposed New Test of Equivalence Principle from Rotating Bodies

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yuan-Zhong; LUO Jun; NIE Yu-Xin

    2000-01-01

    We study a new kind of equivalence principle for rotating bodies and propose a test of the equivalence principle by comparing free-fall gravitational accelerations of two gyroscopes or a rotating and a non-rotating extended bodies.

  9. On Eugene A. Nida's Functional Equivalence%On Eugene A.Nida's Functional Equivalence

    Institute of Scientific and Technical Information of China (English)

    赵玲

    2016-01-01

    Eugene A. Nida's Functional Equivalence is a very useful theory in translation. This theory considers that translation is transference of the source language into the meaning of the target language in the way the author intended the text. It has a deep influence on translation.

  10. On the $c$ equivalence principle and its relation to the weak equivalence principle of general relativity

    CERN Document Server

    Choy, T C

    2011-01-01

    We clarify the status of the $c$ equivalence principle ($c_u=c$) recently proposed by Heras et al \\cite{JoseAJP2010,JoseEJP2010} and show that its proposal leads to an extension of the current framework of classical relativistic electrodynamics (CRE). This is because in the MLT (mass, length and time) system of units, CRE theory can contain only one fundamental constant of nature and special relativity dictates that this must be $c$, the standard speed of light in vacuum, a point not sufficiently emphasized in most textbooks with the exception of a few such as Panofsky and Phillips \\cite{PanofskyPhillips}. The $c$ equivalence principle Heras \\cite{JoseAJP2010,JoseEJP2010} can be shown to be linked to the second postulate of special relativity which extends the constancy of the unique velocity of light to all of physics (especially to mechanics) other than electromagnetism. An interesting corollary is that both the weak equivalence principle of general relativity and the $c$ equivalence principle are in fact o...

  11. Equivalence above Word Level in English——Chinese Translation

    Institute of Scientific and Technical Information of China (English)

    王奕君

    2008-01-01

    Translation is not accomplished by merely substituting words in a word-for-word equivalence.A word-for-word replacement is of little use,because it is only a form of words equivalent,and does not convey the force of meaning(the dynamic equivalence).The aim of this paper is to study equivalence above word level(collocation、idiom and fixed expression)in relation to English--Chinese translation process,using different approaches.

  12. Equivalent layers: another way to look at them

    Science.gov (United States)

    van der Laan, C. J.; Frankena, H. J.

    1995-02-01

    We describe the behavior of the equivalent refractive index (or Herpin index) and equivalent phase thickness in relation to the phase thicknesses of the layers in a dielectric stack. This relation is visualized by a diagram that provides insight into the existing solutions for given combinations of the Herpin index and the equivalent phase thickness. Furthermore, it can be used for the explanation of the occurrence of stop bands and of the dispersion of equivalent layer stacks.

  13. Equivalent Circuits For AC-Impedance Analysis Of Corrosion

    Science.gov (United States)

    Danford, M. D.

    1992-01-01

    Report presents investigation of equivalent circuits for ac-impedance analysis of corrosion. Impedance between specimen and electrolyte measured as function of frequency. Data used to characterize corrosion electrochemical system in terms of equivalent circuit. Eleven resistor/capacitor equivalent-circuit models were analyzed.

  14. 46 CFR Appendix A to Part 154 - Equivalent Stress

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 5 2010-10-01 2010-10-01 false Equivalent Stress A Appendix A to Part 154 Shipping... FOR SELF-PROPELLED VESSELS CARRYING BULK LIQUEFIED GASES Pt. 154, App. A Appendix A to Part 154—Equivalent Stress I. Equivalent stress (σ c) is calculated by the following formula or another formula...

  15. On the equivalence classes of linear non-autonomous systems *

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper, the equivalence classification of the linear non-autonomous dynamic systems near singularities is given. Under some conditions their equivalence classes are the same as the autonomous ones. Using a series of linear and nonlinear transforms, the equivalence classification is proved.

  16. Tests of the weak equivalence principle

    Science.gov (United States)

    Speake, C. C.; Will, C. M.

    2012-09-01

    The Einstein equivalence principle is the foundation for general relativity and all metric theories of gravity. Of its three tenets—the equality of acceleration of test bodies, or weak equivalence principle; the validity of Lorentz invariance in local freely falling frames; and the position invariance of local physical laws—the weak equivalence principle has played the most important role historically, and continues to be a focus of intense theoretical and experimental investigation. From the probably apocryphal 16th century demonstrations by Galileo at Pisa's leaning tower to the sensitive torsion-balance measurements of today (both pictured on the cover of this issue), this principle, dubbed WEP, has been crucial to the development of gravitation theory. The universality of the rate of acceleration of all types of matter in a gravitational field can be taken as evidence that gravitation is fundamentally determined by the geometry, or metric, of spacetime. Newton began his magnum opus 'The Principia' with a discussion of WEP and his experiments to verify it, while Einstein took WEP for granted in his construction of general relativity, never once referring to the epochal experiments by Baron Eötvös. The classic 1964 experiment of Roll, Krotkov and Dicke ushered in the modern era of high-precision tests, and the search for a 'fifth force' during the late 1980s (instigated, ironically, by purported anomalies in Eötvös's old data) caused the enterprise to pivot from pure tests of the foundation of GR to searches for new physics beyond the standard model of the non-gravitational interactions. Today, the next generation of experimental tests of WEP are being prepared for launch or are being developed, with the goal of reaching unprecedented levels of sensitivity, in search of signatures of interactions inspired by string theory, extra dimensions and other concepts from the world of high-energy physics. At the same time observations continue using lunar laser

  17. Prediction analysis of dose equivalent responses of neutron dosemeters used at a MOX fuel facility.

    Science.gov (United States)

    Tsujimura, N; Yoshida, T; Takada, C

    2011-07-01

    To predict how accurately neutron dosemeters can measure the neutron dose equivalent (rate) in MOX fuel fabrication facility work environments, the dose equivalent responses of neutron dosemeters were calculated by the spectral folding method. The dosemeters selected included two types of personal dosemeter, namely a thermoluminescent albedo neutron dosemeter and an electronic neutron dosemeter, three moderator-based neutron survey meters, and one special instrument called an H(p)(10) monitor. The calculations revealed the energy dependences of the responses expected within the entire range of neutron spectral variations observed in neutron fields at workplaces.

  18. Researching measurement equivalence in cross-cultural studies

    Directory of Open Access Journals (Sweden)

    Miloš Kankaraš

    2010-06-01

    Full Text Available In cross-cultural comparative studies it is essential to establish equivalent measurement of relevant constructs across cultures. If this equivalence is not confirmed it is difficult if not impossible to make meaningful comparison of results across countries. This work presents concept of measurement equivalence, its relationship with other related concepts, different equivalence levels and causes of inequivalence in cross-cultural research. It also reviews three main approaches to the analysis of measurement equivalence – multigroup confirmatory factor analysis, differential item functioning, and multigroup latent class analysis – with special emphasis on their similarities and differences, as well as comparative advantages.

  19. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  20. Equivalence Principle and the Baryon Acoustic Peak

    CERN Document Server

    Baldauf, Tobias; Simonović, Marko; Zaldarriaga, Matias

    2015-01-01

    We study the dominant effect of a long wavelength density perturbation $\\delta(\\lambda_L)$ on short distance physics. In the non-relativistic limit, the result is a uniform acceleration, fixed by the equivalence principle, and typically has no effect on statistical averages due to translational invariance. This same reasoning has been formalized to obtain a "consistency condition" on the cosmological correlation functions. In the presence of a feature, such as the acoustic peak at $l_{\\rm BAO}$, this naive expectation breaks down for $\\lambda_L

  1. Topological equivalence for multiple saddle connections

    Directory of Open Access Journals (Sweden)

    CLEMENTA ALONSO

    2002-12-01

    Full Text Available We study the topological equivalence between two vector fields defined in the neighborhood of the skeleton of a normal crossings divisor in an ambient space of dimension three. We deal with singularities obtained from local ones by ambient blowing-ups: we impose thus the non-degeneracy condition that they are all hyperbolic without certain algebraic resonances in the set of eigenvalues. Once we cut-out the attractors, we get the result if the corresponding graph has no cycles. The case of cycles is of another nature, as the Dulac Problem in dimension three.Estudamos a equivalência topológica entre dois campos de vetores na vizinhança do esqueleto de um divisor com cruzamento normal, num ambiente de dimensão três. Consideramos singularidades obtidas por explosões a partir de uma singularidade local: isto justifica a condição de hiperbolicidade e não ressonância no conjunto dos autovalores. O resultado principal se obtém quando, depois de retirar os atratores, o grafo resultante não tem ciclos. O caso dos ciclos é de natureza semelhante ao problema de Dulac em dimensão três.

  2. Mathematical Equivalence of Evolution and Design

    Directory of Open Access Journals (Sweden)

    Leonid Perlovsky

    2010-12-01

    Full Text Available "Every one who is seriously involved in the pursuit of science becomes convinced that a spirit is manifest in the laws of the Universe." This Einsteinian statement remains outside of science. Our current understanding of the mind mechanisms have come close to explaining spirituality from the scientific point of view. In this paper a theory is presented which is a mathematical breakthrough, overcoming decades of limitations in AI, pattern recognition, neural networks, and other attempts to model the brain-mind. Solutions to engineering problems are presented that have overcome previous difficulties in terms of computational complexity. These solutions result in orders of magnitude improvement in detection, prediction, tracking, fusion, and learning situations. The theory is also extended to higher cognitive functions. It models the knowledge instinct operating in the hierarchy of the human brain-mind. At the top are concepts unifying our entire knowledge; we perceive them as concepts of the meaning and purpose of our existence. This theory is formulated mathematically as dynamic and equivalently as teleological. Experimental results supporting the theory are discussed. The theory overcomes various difficulties, including reductionism, which, in the past, interfered with the acceptance of scientific explanations of the spiritual.

  3. Equivalency of Artificial and Natural Icing

    Institute of Scientific and Technical Information of China (English)

    wgI Xiao-xing; XU Zhi-hai; LI Zhi-ning; SU Hua-feng; JIA Zhi-dong; GUAN Zhi-cheng

    2011-01-01

    Climate room is an important instrument to study the icing problems in power networks, and the accuracy of the data from the climate room is under debate. There are many climate rooms in the world, but no standards about the parameters of the climate room such as the room's temperature, the velocity of the wind, and the particle diameters of the water droplets etc. These parameters will influence the icing processes on the lines and insulators. This paper gave a summary of the process and the feature of atmospheric icing of power networks. The speed of the icing on a cylinder rod as a new characteristic quantity was proposed to study the de-icing problems in this paper. For the purpose to analyze the equivalence between atmospheric icing and icing in climate room, a finite element model was made based on a small climate room located in the Graduate School at Shenzhen, Tsinghua University. Through the simulation analysis for the heat transfer and flow issues, the result showed that precooling droplets were cooled into supercooled ones soon after they came into the climate room. Based on the most serious icing-speed in Hengshan, Hunan and a series of experiments, the values of some parameters in studying icing problems were proposed to better simulate the atmospheric icing in climate room.

  4. Macrostate equivalence of two general ensembles and specific relative entropies

    Science.gov (United States)

    Mori, Takashi

    2016-08-01

    The two criteria of ensemble equivalence, i.e., macrostate equivalence and measure equivalence, are investigated for a general pair of states. Macrostate equivalence implies the two ensembles are indistinguishable by the measurement of macroscopic quantities obeying the large-deviation principle, and measure equivalence means that the specific relative entropy of these two states vanishes in the thermodynamic limit. It is shown that measure equivalence implies a macrostate equivalence for a general pair of states by deriving an inequality connecting the large-deviation rate functions to the specific relative Renyi entropies. The result is applicable to both quantum and classical systems. As applications, a sufficient condition for thermalization, the time scale of quantum dynamics of macrovariables, and the second law with strict irreversibility in a quantum quench are discussed.

  5. Equivalent probability density moments determine equivalent epidemics in an SIRS model with temporary immunity.

    Science.gov (United States)

    Carr, Thomas W

    2017-02-01

    In an SIRS compartment model for a disease we consider the effect of different probability distributions for remaining immune. We show that to first approximation the first three moments of the corresponding probability densities are sufficient to well describe oscillatory solutions corresponding to recurrent epidemics. Specifically, increasing the fraction who lose immunity, increasing the mean immunity time, and decreasing the heterogeneity of the population all favor the onset of epidemics and increase their severity. We consider six different distributions, some symmetric about their mean and some asymmetric, and show that by tuning their parameters such that they have equivalent moments that they all exhibit equivalent dynamical behavior. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Construct equivalence of the OPQ32n for Black and White people in South Africa

    Directory of Open Access Journals (Sweden)

    Deléne Visser

    2010-03-01

    Full Text Available Orientation: The construct equivalence of the Occupational Personality Questionnaire (OPQ32n for black and white groups was investigated.Research purpose: The objective was to investigate the structural invariance of the OPQ32n for two South African population groups.Motivation for the study: The OPQ32n is often used for making a variety of personnel decisions in South Africa. Evidence regarding the suitability of personality questionnaires for use across South Africa’s various population groups is required by practitioners for selecting appropriate psychometric instruments.Research design, approach and method: Data were collected by means of a questionnaire and the results were analysed using quantitative statistical methods. The sample consisted of 248 Black and 476 White people from the SHL (South Africa database. Structural equation modelling was used to examine the structural equivalence of the OPQ32n scale scores for these two groups.Main findings: A good fit regarding factor correlations and covariances on the 32 scales was obtained, partially supporting the structural equivalence of the questionnaire for the two groups. The analyses furthermore indicated that there was structural invariance, with the effect of the Social Desirability scale partialled out.Practical/managerial implications: The present study focused on aspects of structural equivalence only. The OPQ32n therefore passed the first hurdle in this particular context, but further investigation is necessary to provide evidence that the questionnaire is suitable for use in personnel decisions comparing the population groups.Contribution: Despite the positive findings with regard to structural equivalence and social desirability response style, it should be borne in mind that no assumptions regarding full scale equivalence can be made on the basis of the present findings.

  7. Equivalence of online and clinician administration of a patellar tendinopathy risk factor and severity questionnaire

    DEFF Research Database (Denmark)

    Morton, S; Morrissey, D; Valle, X;

    2015-01-01

    The VISA-P is a questionnaire for assessing the severity of patellar tendinopathy (PT). Our study aim was to evaluate the equivalence of self-administration of the VISA-P online with the addition of risk factor questions to develop a tool suitable for high-volume remote use. A crossover study...... design with 107 subjects was used to determine equivalence between online and clinician administration. Three population groups were used to ensure construct validity. Online vs clinician administration revealed an intraclass correlation (ICC) of 0.79 [confidence interval (CI): 0.68-0.86] for the VISA...... for risk factor questions was excellent at 0.89 (CI: 0.84-0.93) with no mean difference (P = 1.00). The online questionnaire enables equivalent collection of VISA-P data and risk factor information and may well improve further with the suggested modifications to the instructions for questions 7 and 8...

  8. Measurement of neutron dose equivalent to proton therapy patients outside of the proton radiation field

    CERN Document Server

    Yan, X; Köhler, A; Newhauser, W D

    2002-01-01

    Measurements of neutron dose equivalent values and neutron spectral fluences close to but outside of the therapeutic proton radiation field are presented. The neutron spectral fluences were determined at five locations with Bonner sphere measurements and established by unfolding techniques. More than 50 additional neutron dose equivalent values were measured with LiI and BF sub 3 thermal neutron detectors surrounded by a 25 cm polyethylene moderating sphere. For a large-field treatment, typical values of neutron dose equivalent per therapeutic proton absorbed dose, H/D, at 50 cm distance from isocenter, range from 1 mSv/Gy (at 0 deg.with respect to the proton beam axis) to 5 mSv/Gy (at 90 deg.). Experiments reveal that H/D varies significantly with the treatment technique, e.g., patient orientation, proton beam energy, and range-modulation. The relative uncertainty in H/D values is approximately 40% (one standard deviation).

  9. Kinetic simulation of hydrodynamic equivalent capsule implosions

    Science.gov (United States)

    Kwan, Thomas; Le, Ari; Schmitt, Mark; Herrmann, Hans

    2016-10-01

    We have carried out simulations of direct-drive hydrodynamic equivalent capsule implosion experiments conducted on Omega laser facility at the Laboratory of Laser Energetics of the University of Rochester. The capsules had a glass shell (SiO2) 4.87 μm with an inner diameter of 1086 μm. One was filled with deuterium (D) and tritium (T) at 6.635 and 2.475 atmospheric pressure respectively. The other capsule with D, T, and He-3 at 2.475, 2.475, and 5.55 atmospheric pressure respectively. The capsules were imploded with 60 laser beams with a square pulse length of 0.6ns of total energy of 15.6 kJ. One-dimensional radiation hydrodynamic calculations with HYDRA and kinetic particle/hybrid simulations with LSP are carried out for the post-shot analysis. HYDRA outputs at 0.6ns are linked to LSP, in which the electrons are treated as a fluid while all the ion dynamics is simulated by the standard particle-in-cell technique. Additionally, simulations with the new photon package in LSP are initiated at the beginning of the implosion to include the implosion phase of the capsule. The simulation results of density, temperature, and velocity profiles of the electrons, D, T, He-3, and SiO2species are compared with HYDRA. Detail comparisons among the kinetic simulations, rad-hydro simulations, and experimental results of neutron yield, yield ratio, fusion burn histories, and shell convergence will be presented to assess plasma kinetic effects. Work performed under the auspices of the US DOE by the Los Alamos National Laboratory under Contract No. W7405-ENG-36.

  10. Principle of Spacetime and Black Hole Equivalence

    Science.gov (United States)

    Zhang, Tianxi

    2016-06-01

    Modelling the universe without relying on a set of hypothetical entities (HEs) to explain observations and overcome problems and difficulties is essential to developing a physical cosmology. The well-known big bang cosmology, widely accepted as the standard model, stands on two fundamentals, which are Einstein’s general relativity (GR) that describes the effect of matter on spacetime and the cosmological principle (CP) of spacetime isotropy and homogeneity. The field equation of GR along with the Friedmann-Lemaitre-Robertson-Walker (FLRW) metric of spacetime derived from CP generates the Friedmann equation (FE) that governs the development and dynamics of the universe. The big bang theory has made impressive successes in explaining the universe, but still has problems and solutions of them rely on an increasing number of HEs such as inflation, dark matter, dark energy, and so on. Recently, the author has developed a new cosmological model called black hole universe, which, instead of making many those hypotheses, only includes a new single postulate (or a new principle) to the cosmology - Principle of Spacetime and Black Hole Equivalence (SBHEP) - to explain all the existing observations of the universe and overcome all the existing problems in conventional cosmologies. This study thoroughly demonstrates how this newly developed black hole universe model, which therefore stands on the three fundamentals (GR, CP, and SBHEP), can fully explain the universe as well as easily conquer the difficulties according to the well-developed physics, thus, neither needing any other hypotheses nor existing any unsolved difficulties. This work was supported by NSF/REU (Grant #: PHY-1263253) at Alabama A & M University.

  11. Assessing linguistic and cultural equivalency of two Chinese-version sexual health instruments among Chinese immigrant youth.

    Science.gov (United States)

    Chen, Angela Chia-Chen; Morrison-Beedy, Dianne; Han, Chong-Suk

    2010-06-01

    This study aimed to evaluate the linguistic and cultural equivalency of two Chinese-version instruments measuring sexual knowledge, attitudes, and behaviors among 10 bilingual and 2 monolingual Chinese immigrant youth aged 13-19 years. We used a rigorous design to translate, back-translate, and pilot test the instruments. Kappa coefficient, percentage agreement, and qualitative feedback from participants were used to examine reliability and validity of the instruments. Telephone interviews revealed that answer discrepancies in different language versions were due to external factors rather than lack of linguistic and cultural equivalency. This study offers preliminary evidence supporting the cultural and linguistic equivalence of two Chinese-version sexual scales.

  12. Flight Test of a Head-Worn Display as an Equivalent-HUD for Terminal Operations

    Science.gov (United States)

    Shelton, K. J.; Arthur, J. J., III; Prinzel, L. J., III; Nicholas, S. N.; Williams, S. P.; Bailey, R. E.

    2015-01-01

    Research, development, test, and evaluation of flight deck interface technologies is being conducted by NASA to proactively identify, develop, and mature tools, methods, and technologies for improving overall aircraft safety of new and legacy vehicles operating in the Next Generation Air Transportation System (NextGen). Under NASA's Aviation Safety Program, one specific area of research is the use of small Head-Worn Displays (HWDs) as a potential equivalent display to a Head-up Display (HUD). Title 14 of the US CFR 91.175 describes a possible operational credit which can be obtained with airplane equipage of a HUD or an "equivalent"' display combined with Enhanced Vision (EV). A successful HWD implementation may provide the same safety and operational benefits as current HUD-equipped aircraft but for significantly more aircraft in which HUD installation is neither practical nor possible. A flight test was conducted to evaluate if the HWD, coupled with a head-tracker, can provide an equivalent display to a HUD. Approach and taxi testing was performed on-board NASA's experimental King Air aircraft in various visual conditions. Preliminary quantitative results indicate the HWD tested provided equivalent HUD performance, however operational issues were uncovered. The HWD showed significant potential as all of the pilots liked the increased situation awareness attributable to the HWD's unique capability of unlimited field-of-regard.

  13. General Dynamic Equivalent Modeling of Microgrid Based on Physical Background

    Directory of Open Access Journals (Sweden)

    Changchun Cai

    2015-11-01

    Full Text Available Microgrid is a new power system concept consisting of small-scale distributed energy resources; storage devices and loads. It is necessary to employ a simplified model of microgrid in the simulation of a distribution network integrating large-scale microgrids. Based on the detailed model of the components, an equivalent model of microgrid is proposed in this paper. The equivalent model comprises two parts: namely, equivalent machine component and equivalent static component. Equivalent machine component describes the dynamics of synchronous generator, asynchronous wind turbine and induction motor, equivalent static component describes the dynamics of photovoltaic, storage and static load. The trajectory sensitivities of the equivalent model parameters with respect to the output variables are analyzed. The key parameters that play important roles in the dynamics of the output variables of the equivalent model are identified and included in further parameter estimation. Particle Swarm Optimization (PSO is improved for the parameter estimation of the equivalent model. Simulations are performed in different microgrid operation conditions to evaluate the effectiveness of the equivalent model of microgrid.

  14. Equivalent Circuit for Cavity Discharges Including Controlled Current Source and Controlled Switch

    Institute of Scientific and Technical Information of China (English)

    CHEN Weigen; CHEN Xi; XIE Bo; LIU Jun

    2013-01-01

    Numerous equivalent circuits for cavity discharges have been developed,yet most of these models cannot provide simulated signals that precisely reveal the variability of the discharge's characteristic parameters,such as repetition rate,magnitude and phase of discharges,which makes them not suitable for intensive studies of discharge process.Therefore,using Simulink code,we theoretically analyzed and studied the classical equivalent circuits of cavity discharges,as well as the influence of circuit components on simulation results,and then proposed a novel equivalent circuit,the key parameters of which were determined according to the physical behavior of cavity discharges.In the novel equivalent circuit,the repetition rate can be changed by discharge resistance,inception and residual voltages;meanwhile the phase of discharge can be controlled by adjusting the parameters of shunt resistance.Furthermore,a controlled current source as a function of space charge is introduced in the equivalent circuit.Compared with the former ones,the simulated signals obtained by this novel model are better approximation of real signals.This work could be referred by latter studies of the characteristics and the mechanisms of cavity discharge in oil-paper insulation.

  15. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Brunak, Søren; Olsen, JV

    2010-01-01

    ) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells....

  16. Quantitative flaw characterization with ultrasonic phased arrays

    Science.gov (United States)

    Engle, Brady John

    Ultrasonic nondestructive evaluation (NDE) is a critical diagnostic tool in many industries. It is used to characterize potentially dangerous flaws in critical components for aerospace, automotive, and energy applications. The use of phased array transducers allows for the extension of traditional techniques and the introduction of new methods for quantitative flaw characterization. An equivalent flaw sizing technique for use in time-of-flight diffraction setups is presented that provides an estimate of the size and orientation of isolated cracks, surface-breaking cracks, and volumetric flaws such as voids and inclusions. Experimental validation is provided for the isolated crack case. A quantitative imaging algorithm is developed that corrects for system effects and wave propagation, making the images formed directly related to the properties of the scatterer present. Simulated data is used to form images of cylindrical and spherical inclusions. The contributions of different signals to the image formation process are discussed and examples of the quantitative nature of the images are shown.

  17. A Novel Equivalent Agglomeration Model for Heat Conduction Enhancement in Nanofluids

    Science.gov (United States)

    Sui, Jize; Zheng, Liancun; Zhang, Xinxin; Chen, Ying; Cheng, Zhengdong

    2016-01-01

    We propose a multilevel equivalent agglomeration (MEA) model in which all particles in an irregular cluster are treated as a new particle with equivalent volume, the liquid molecules wrapping the cluster and in the gaps are considered to assemble on the surface of new particle as mixing nanolayer (MNL), the thermal conductivity in MNL is assumed to satisfy exponential distribution. Theoretical predictions for thermal conductivity enhancement are highly in agreement with the classical experimental data. Also, we first try to employ TEM information quantitatively to offer probable reference agglomeration ratio (not necessary a very precise value) to just test rational estimations range by present model. The comparison results indicate the satisfactory priori agglomeration ratio estimations range from renovated model. PMID:26777389

  18. Quantitative Convergence of Concepts in Physical Cosmology and Theology

    Science.gov (United States)

    Persinger, Michael A.; Burke, Ryan C.; Carniello, Trevor N.

    2012-09-01

    Physical cosmology and theology both explore the maximum boundary conditions of space and time. The possibility of consciousness and information involving the largest and smallest spaces and times within the universe is supported quantitatively by the physical properties of matter and the organization of the human brain. There are important roles for both approaches as required contrasts to discern the neurocognitive and quantitative equivalents that could facilitate discovery.

  19. Qualitative vs. quantitative software process simulation modelling: conversion and comparison

    OpenAIRE

    Zhang, He; Kitchenham, Barbara; Jeffery, Ross

    2009-01-01

    peer-reviewed Software Process Simulation Modeling (SPSM) research has increased in the past two decades. However, most of these models are quantitative, which require detailed understanding and accurate measurement. As the continuous work to our previous studies in qualitative modeling of software process, this paper aims to investigate the structure equivalence and model conversion between quantitative and qualitative process modeling, and to compare the characteristics and performance o...

  20. Quantitative lithofacies palaeogeography

    Institute of Scientific and Technical Information of China (English)

    Zeng-Zhao; Feng; Xiu-Juan; Zheng; Zhi-Dong; Bao; Zhen-Kui; Jin; Sheng-He; Wu; You-Bin; He; Yong-Min; Peng; Yu-Qing; Yang; Jia-Qiang; Zhang; Yong-Sheng; Zhang

    2014-01-01

    Quantitative lithofacies palaeogeography is an important discipline of palaeogeography.It is developed on the foundation of traditional lithofacies palaeogeography and palaeogeography,the core of which is the quantitative lithofacies palaeogeographic map.Quantity means that in the palaeogeographic map,the division and identification of each palaeogeographic unit are supported by quantitative data and quantitative fundamental maps.Our lithofacies palaeogeographic maps are quantitative or mainly quantitative.A great number of quantitative lithofacies palaeogeographic maps have been published,and articles and monographs of quantitative lithofacies palaeogeography have been published successively,thus the quantitative lithofacies palaeogeography was formed and established.It is an important development in lithofacies palaeogeography.In composing quantitative lithofacies palaeogeographic maps,the key measure is the single factor analysis and multifactor comprehensive mapping method—methodology of quantitative lithofacies palaeogeography.In this paper,the authors utilize two case studies,one from the Early Ordovician of South China and the other from the Early Ordovician of Ordos,North China,to explain how to use this methodology to compose the quantitative lithofacies palaeogeographic maps,and to discuss the palaeogeographic units in these maps.Finally,three characteristics,i.e.,quantification,multiple orders and multiple types,of quantitative lithofacies palaeogeographic maps are conclusively discussed.

  1. A new formulation of equivalent effective stratospheric chlorine (EESC

    Directory of Open Access Journals (Sweden)

    P. A. Newman

    2007-09-01

    Full Text Available Equivalent effective stratospheric chlorine (EESC is a convenient parameter to quantify the effects of halogens (chlorine and bromine on ozone depletion in the stratosphere. We show, discuss, and analyze a new formulation of EESC that now includes the effects of age-of-air dependent fractional release values and an age-of-air spectrum. This EESC can be more appropriately applied to various parts of the stratosphere because of this dependence on mean age-of-air. This new formulation provides quantitative estimates of EESC that can be directly related to inorganic chlorine and bromine throughout the stratosphere. In this paper, we first provide a detailed description of the EESC calculation. We then use this EESC formulation to estimate that human-produced ozone depleting substances will recover to 1980 levels in 2041 in the midlatitudes, and 2067 over Antarctica. These recovery dates are based upon the assumption that the international agreements for regulating ozone-depleting substances are adhered to. In addition to recovery dates, we also estimate the uncertainties and possible problems in the estimated times of recovery. The midlatitude recovery of 2041 has a 95% confidence uncertainty from 2028 to 2049, while the 2067 Antarctic recovery has a 95% confidence uncertainty from 2056 to 2078. The principal uncertainties are from the estimated mean age-of-air and fractional release values, and the assumption that these quantities are time independent. Using other model estimates of age decrease due to climate change, we estimate that midlatitude recovery may be significantly accelerated.

  2. Stress Response of Offshore Structures by Equivalent Polynomial Expansion Techniques

    DEFF Research Database (Denmark)

    Sigurdsson, Gudfinnur; Nielsen, Søren R.K.

    This paper concerns an investigation of the effects of nonlinearity of drag loading on offshore structures excited by 2D wave fields, where the nonlinear term in the Morison equation is replaced by an equivalent cubic expansion. The equivalent cubic expansion coefficients for the equivalent drag...... model are obtained using the least mean square procedure. Numerical results are given. The displacement response and stress response processes obtained using the above loading model are compared with simulation results and those obtained from equivalent linearization of the drag term....

  3. An improved model of Robinson equivalent circuit analytical model

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The Robinson equivalent circuit analytical model can be used only in calculating shielding effectiveness of enclosure with the same multi-holes in one wall, but cannot be used in different multi-holes in two walls. According to the practical requirement, this article uses Konefal’s and Farhana’s characteristic impedance of apertures to improve the equivalent circuit analytical model in different multi-holes in two walls. The improved equivalent circuit analytical model is more useful than Robinson equivalent circuit analytical model. In the article, all kinds of enclosures are simulated by TLM (Transmission-Line Matrix method) to prove that this improved model is feasible in multimode.

  4. Estimating Equivalency of Explosives Through A Thermochemical Approach

    Energy Technology Data Exchange (ETDEWEB)

    Maienschein, J L

    2002-07-08

    The Cheetah thermochemical computer code provides an accurate method for estimating the TNT equivalency of any explosive, evaluated either with respect to peak pressure or the quasi-static pressure at long time in a confined volume. Cheetah calculates the detonation energy and heat of combustion for virtually any explosive (pure or formulation). Comparing the detonation energy for an explosive with that of TNT allows estimation of the TNT equivalency with respect to peak pressure, while comparison of the heat of combustion allows estimation of TNT equivalency with respect to quasi-static pressure. We discuss the methodology, present results for many explosives, and show comparisons with equivalency data from other sources.

  5. Reconsidering the Equivalence in Translation From Cultural Differences Perspective

    Institute of Scientific and Technical Information of China (English)

    LI Yinling

    2009-01-01

    Translation involves language as well as culture. Cultural similarities exist in languages; however cultural differences have an essential bearing upon translation. Even approximate equivalent and loan words have different implications and usages in English and Chinese. So, this challenges the traditional concept of equivalence as a constitutive feature of translation. To an author, there is no such thing as absolute equivalence in the context of E-C translation for the simple reason that Chinese and English belong to two entirely different cultural traditions. However, through careful comparative studies, relative equivalents can be achieved.

  6. Quantitative investment analysis

    CERN Document Server

    DeFusco, Richard

    2007-01-01

    In the "Second Edition" of "Quantitative Investment Analysis," financial experts Richard DeFusco, Dennis McLeavey, Jerald Pinto, and David Runkle outline the tools and techniques needed to understand and apply quantitative methods to today's investment process.

  7. Rigour in quantitative research.

    Science.gov (United States)

    Claydon, Leica Sarah

    2015-07-22

    This article which forms part of the research series addresses scientific rigour in quantitative research. It explores the basis and use of quantitative research and the nature of scientific rigour. It examines how the reader may determine whether quantitative research results are accurate, the questions that should be asked to determine accuracy and the checklists that may be used in this process. Quantitative research has advantages in nursing, since it can provide numerical data to help answer questions encountered in everyday practice.

  8. Equivalent Sensor Radiance Generation and Remote Sensing from Model Parameters. Part 1; Equivalent Sensor Radiance Formulation

    Science.gov (United States)

    Wind, Galina; DaSilva, Arlindo M.; Norris, Peter M.; Platnick, Steven E.

    2013-01-01

    In this paper we describe a general procedure for calculating equivalent sensor radiances from variables output from a global atmospheric forecast model. In order to take proper account of the discrepancies between model resolution and sensor footprint the algorithm takes explicit account of the model subgrid variability, in particular its description of the probably density function of total water (vapor and cloud condensate.) The equivalent sensor radiances are then substituted into an operational remote sensing algorithm processing chain to produce a variety of remote sensing products that would normally be produced from actual sensor output. This output can then be used for a wide variety of purposes such as model parameter verification, remote sensing algorithm validation, testing of new retrieval methods and future sensor studies. We show a specific implementation using the GEOS-5 model, the MODIS instrument and the MODIS Adaptive Processing System (MODAPS) Data Collection 5.1 operational remote sensing cloud algorithm processing chain (including the cloud mask, cloud top properties and cloud optical and microphysical properties products.) We focus on clouds and cloud/aerosol interactions, because they are very important to model development and improvement.

  9. Does the Equivalence between Gravitational Mass and Energy Survive for a Composite Quantum Body?

    CERN Document Server

    Lebed, Andrei G

    2014-01-01

    We define passive and active gravitational mass operators of the simplest composite quantum body - a hydrogen atom. Although they do not commute with its energy operator, the equivalence between the expectation values of passive and active gravitational masses and energy is shown to survive for stationary quantum states. In our calculations of passive gravitational mass operator, we take into account not only kinetic and Coulomb potential energies but also the so-called relativistic corrections to electron motion in a hydrogen atom. Inequivalence between passive and active gravitational masses and energy at a macroscopic level is demonstrated to reveal itself as time dependent oscillations of the expectation values of the gravitational masses for superpositions of stationary quantum states. Breakdown of the equivalence between passive gravitational mass and energy at a microscopic level reveals itself as unusual electromagnetic radiation, emitted by macroscopic ensemble of hydrogen atoms, moved by small space...

  10. Analyzing the effects of post couplers in DTL tuning by the equivalent circuit model

    OpenAIRE

    Jia, Xiaoyu; Zheng, Shuxin

    2013-01-01

    Stabilization of the accelerating field in Drift Tube Linac(DTL) is obtained by inserting Post Couplers(PCs).On the basis of the circuit model equivalent for the DTL with and without asymmetrical PCs, stabilization is deduced quantitatively: let $\\delta \\omega/\\omega_0$ be the relative frequency error, then we discover that the sensitivity of field to perturbation is proportional to $\\sqrt{\\delta \\omega / \\omega_0}$ without PCs and to $\\delta \\omega/\\omega_0$ with PCs. Then we adapt the circu...

  11. Revealing alteration of membrane structures during ischema using impedance spectroscopy

    Directory of Open Access Journals (Sweden)

    Mihaela Gheorghiu

    2002-11-01

    Full Text Available Alterations of membrane structure and function are essential characteristics of cells undergoing ischemia. Noninvasive monitoring of tissue alterations during ischemia and the estimation of the reversibility domain (corresponding to organ capability to fully recover its functions after shifting back to normal blood perfusion are important for biomedical applications allowing better time management during surgical interventions, especially in organ transplantation. Due to it’s capability to reveal inhomogeneities, as well as it’s noninvasive character, impedance spectroscopy was used for continuous monitoring of the progression of excised tissue samples during ischemia. We have developed a fast, noninvasive, automated method for quantitative analysis of impedance spectra of tissue samples, capable of revealing, through characteristic parameters (dispersion amplitudes, time constants and distribution parameters membrane based microscopic processes like the closure ofgap-junctions (a characteristic of the early alterations of ischemic tissues in the reversibility phase. Microscopic and equivalent circuit modeling was used to probe the effect of closure of cell connections and of changes in electrical properties of cell constituents on impedance spectra. We have developed a normalizing procedure emphasizing the pattern of ischemic alterations and enabling the comparison of different data sets.

  12. Unpredictable elbow joint perturbation during reaching results in multijoint motor equivalence.

    Science.gov (United States)

    Mattos, D J S; Latash, M L; Park, E; Kuhl, J; Scholz, J P

    2011-09-01

    Motor equivalence expresses the idea that movement components reorganize in the face of perturbations to preserve the value of important performance variables, such as the hand's position in reaching. A formal method is introduced to evaluate this concept quantitatively: changes in joint configuration due to unpredictable elbow perturbation lead to a smaller change in performance variables than expected given the magnitude of joint configuration change. This study investigated whether motor equivalence was present during the entire movement trajectory and how magnitude of motor equivalence was affected by constraints imposed by two different target types. Subjects pointed to spherical and cylindrical targets both with and without an elbow joint perturbation produced by a low- or high-stiffness elastic band. Subjects' view of their arm was blocked in the initial position, and the perturbation condition was randomized to avoid prediction of the perturbation or its magnitude. A modification of the uncontrolled manifold method variance analysis was used to investigate how changes in joint configuration on perturbed vs. nonperturbed trials (joint deviation vector) affected the hand's position or orientation. Evidence for motor equivalence induced by the perturbation was present from the reach onset and increased with the strength of the perturbation after 40% of the reach, becoming more prominent as the reach progressed. Hand orientation was stabilized more strongly by motor equivalent changes in joint configuration than was three-dimensional position regardless of the target condition. Results are consistent with a recent model of neural control that allows for flexible patterns of joint coordination while resisting joint configuration deviations in directions that affect salient performance variables. The observations also fit a general scheme of synergic control with referent configurations defined across different levels of the motor hierarchy.

  13. Effect of Asymmetrical Edge Disconnection on Equivalent Series Resistance of Metalized Polypropylene Capacitors

    OpenAIRE

    J Sivakumar; S. Usa; M.A. Panneerselvam

    2014-01-01

    In order to investigate the effect of asymmetrical partial edge disconnection on the Equivalent Series Resistance (ESR) of Metalized polypropylene capacitors an experimental study has been made. Theoretical analysis made using PSPICE simulation package reveals that electrode resistance of individual turn rises from 10 to 30% depending on the location of the turn. This rise is not measureable at all the frequencies as ESR is frequency dependent and it includes resistance due to electrodes and ...

  14. A Group-Period Phase Comparison Method Based on Equivalent Phase Comparison Frequency

    Institute of Scientific and Technical Information of China (English)

    DU Bao-Qiang; ZHOU Wei; DONG Shao-Feng; ZHOU Hai-Niu

    2009-01-01

    Based on the principle of equivalent phase comparison frequency, we propose a group-period phase comparison method. This method can be used to reveal the inherent relations between periodic signals and the change laws of the phase difference. If these laws are applied in the processing of the mutual relations between frequency signals, phase comparison can be accomplished without frequency normalization. Experimental results show that the method can enhance the measurement resolution to 10-13/s in the time domain.

  15. 43 CFR 426.11 - Class 1 equivalency.

    Science.gov (United States)

    2010-10-01

    .... Equivalency determinations can be made only on a district-wide basis. (c) Definition of Class 1 land. Class 1... measured in terms of net income per acre (reflecting both productivity and costs of production). The... farm income will be the measure of productivity to establish equivalency factors reflecting the...

  16. Perverse equivalences, BB-tilting, mutations and applications

    CERN Document Server

    Ladkani, Sefi

    2010-01-01

    We relate the notions of BB-tilting and perverse derived equivalence at a vertex. Based on these notions, we define mutations of algebras, leading to derived equivalent ones. We present applications to endomorphism algebras of cluster-tilting objects in 2-Calabi-Yau categories and to algebras of global dimension at most 2.

  17. 40 CFR 63.469 - Equivalent methods of control.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 9 2010-07-01 2010-07-01 false Equivalent methods of control. 63.469 Section 63.469 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... Standards for Halogenated Solvent Cleaning § 63.469 Equivalent methods of control. Upon written application...

  18. Inter Digital Transducer Modelling through Mason Equivalent Circuit Model

    DEFF Research Database (Denmark)

    Mishra, Dipti; Singh, Abhishek; Hussain, Dil muhammed Akbar

    2016-01-01

    The frequency reliance of inter-digital transducer is analyzed with the help of MASON’s Equivalent circuit which is based on Smith’s Equivalent circuit which is further based on Foster’sNetwork. An inter-digital transducer has been demonstratedas a RLC network. The circuit is simulated by Simulat...

  19. Inter digital transducer modelling through Mason equivalent circuit model

    DEFF Research Database (Denmark)

    Mishra, Dipti; Singh, Abhishek; Hussain, Dil muhammed Akbar

    2016-01-01

    The frequency reliance of inter-digital transducer is analyzed with the help of MASON's Equivalent circuit which is based on Smith's Equivalent circuit which is further based on Foster's Network. An inter-digital transducer has been demonstrated as a RLC network. The circuit is simulated by Simul...

  20. On the equivalence of brushlet and wavelet bases

    DEFF Research Database (Denmark)

    Nielsen, Morten; Borup, Lasse

    2005-01-01

    We prove that the Meyer wavelet basis and a class of brushlet systems associated with exponential type partitions of the frequency axis form a family of equivalent (unconditional) bases for the Besov and Triebel-Lizorkin function spaces. This equivalence is then used to obtain new results on nonl...

  1. 40 CFR 133.105 - Treatment equivalent to secondary treatment.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 21 2010-07-01 2010-07-01 false Treatment equivalent to secondary treatment. 133.105 Section 133.105 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS SECONDARY TREATMENT REGULATION § 133.105 Treatment equivalent to secondary...

  2. Assessment Battery for Communication: Development of Two Equivalent Forms

    Science.gov (United States)

    Bosco, Francesca M.; Angeleri, Romina; Zuffranieri, Marco; Bara, Bruno G.; Sacco, Katiuscia

    2012-01-01

    The aim of this paper was to develop and test two equivalent forms of the Assessment Battery for Communication (ABaCo), a tool for evaluating pragmatic abilities in patients with neuropsychological and psychiatric disorders. The equivalent forms were created using the data from a sample of 390 children, then tested in a sample of 30 patients with…

  3. Stimulus Equivalence, Generalization, and Contextual Stimulus Control in Verbal Classes

    Science.gov (United States)

    Sigurdardottir, Zuilma Gabriela; Mackay, Harry A.; Green, Gina

    2012-01-01

    Stimulus generalization and contextual control affect the development of equivalence classes. Experiment 1 demonstrated primary stimulus generalization from the members of trained equivalence classes. Adults were taught to match six spoken Icelandic nouns and corresponding printed words and pictures to one another in computerized three-choice…

  4. Theory of Covariance Equivalent ARMAV Models of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Andersen, P.; Brincker, Rune; Kirkegaard, Poul Henning

    1996-01-01

    In this paper the theoretical background for using covariance equivalent ARMAV models in modal analysis is discussed. It is shown how to obtain a covariance equivalent ARMA model for a univariate linear second order continous-time system excited by Gaussian white noise. This result is generalized...

  5. Equivalent Widths of 15 Extrasolar-Planet Host Stars

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    We present the equivalent widths of 15 extrasolar-planet host stars.These data were based on the high-resolution, high signal-to-noise ratio spectra obtained with the 2.16 m telescope at Xinglong station. The error in the Xinglong equivalent width is estimated by a comparison of these data with those given in previous studies of common stars.

  6. IMPROVED RANDOMIZED ALGORITHM FOR THE EQUIVALENT 2-CATALOG SEGMENTATION PROBLEM

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    An improved randomized algorithm of the equivalent 2-catalog segmentation problem is presented. The result obtained in this paper makes some progress to answer the open problem by analyze this algorithm with performance guarantee. A 0.6378-approximation for the equivalent 2-catalog segmentation problem is obtained.

  7. - Synonymy in the Translation Equivalent Paradigms of a Standard ...

    African Journals Online (AJOL)

    given is truly a functional translation equivalent for the lemma and make sure that the ... a whole, with the concept of partial synonymy as the point of focus. ..... order in which these equivalents are listed, is based on intuitive frequency and.

  8. Theory of Covariance Equivalent ARMAV Models of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Andersen, P.; Brincker, Rune; Kirkegaard, Poul Henning

    In this paper the theoretical background for using covariance equivalent ARMAV models in modal analysis is discussed. It is shown how to obtain a covariance equivalent ARMA model for a univariate linear second order continuous-time system excited by Gaussian white noise. This result is generalize...

  9. Theory of Covariance Equivalent ARMAV Models of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Andersen, P.; Brincker, Rune; Kirkegaard, Poul Henning

    1996-01-01

    In this paper the theoretical background for using covariance equivalent ARMAV models in modal analysis is discussed. It is shown how to obtain a covariance equivalent ARMA model for a univariate linear second order continous-time system excited by Gaussian white noise. This result is generalized...

  10. On the equivalence of brushlet and wavelet bases

    DEFF Research Database (Denmark)

    Borup, Lasse; Nielsen, Morten

    We prove that the Meyer wavelet basis and a class of brushlet systems associated with exponential type partitions of the frequency axis form a family of equivalent (unconditional) bases for the Besov and Triebel-Lizorkin function spaces. This equivalence is then used to obtain new results...

  11. ROUTING AND WAVELENGTH ASSIGNMENT ALGORITHMS BASED ON EQUIVALENT NETWORKS

    Institute of Scientific and Technical Information of China (English)

    Qi Xiaogang; Liu Lifang; Lin Sanyang

    2006-01-01

    In this paper, a Wavelength Division Multiplexing (WDM) network model based on the equivalent networks is described, and wavelength-dependent equivalent arc, equivalent networks, equivalent multicast tree and some other terms are presented. Based on this model and relevant Routing and Wavelength Assignment (RWA) strategy, a unicast RWA algorithm and a multicast RWA algorithm are presented. The wavelength-dependent equivalent arc expresses the schedule of local RWA and the equivalent network expresses the whole topology of WDM optical networks, so the two algorithms are of the flexibility in RWA and the optimization of the whole problem. The theoretic analysis and simulation results show the two algorithms are of the stronger capability and the lower complexity than the other existing algorithms for RWA problem, and the complexity of the two algorithms are only related to the scale of the equivalent networks. Finally, we prove the two algorithms' feasibility and the one-by-one corresponding relation between the equivalent multicast tree and original multicast tree, and point out the superiorities and drawbacks of the two algorithms respectively.

  12. Equivalence of dynamical ensembles and Navier-Stokes equations

    CERN Document Server

    Gallavotti, G

    1996-01-01

    A reversible version of the Navier Stokes equation is studied. A conjecture emerges stating the equivalence between the reversible equation and the usual Navier Stokes equation. The latter appears as a statement of ensembles equivalence in the limit of infinite Reynolds number, which plays the role of the thermodynamic limit.

  13. Assessment Battery for Communication: development of two equivalent forms.

    Science.gov (United States)

    Bosco, Francesca M; Angeleri, Romina; Zuffranieri, Marco; Bara, Bruno G; Sacco, Katiuscia

    2012-01-01

    The aim of this paper was to develop and test two equivalent forms of the Assessment Battery for Communication (ABaCo), a tool for evaluating pragmatic abilities in patients with neuropsychological and psychiatric disorders. The equivalent forms were created using the data from a sample of 390 children, then tested in a sample of 30 patients with traumatic brain injury. Equivalent forms of the same test are useful in clinical practice and intervention research, when performance needs to be tested on two separate occasions, for example before and after a rehabilitation program. The present results provide additional evidence on the psychometric functioning of the equivalent forms of the ABaCo and their usability in a clinical context. The reader will be able to discuss the evidence of the psychometric propriety of the equivalent forms of the ABaCo and describe its potential usefulness. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. On identifying name equivalences in digital libraries. Name equivalence, Surname matching, Author identification, Databases

    Directory of Open Access Journals (Sweden)

    Dror G. Feitelson

    2004-01-01

    Full Text Available The services provided by digital libraries can be much improved by correctly identifying variants of the same name. For example, this will allow for better retrieval of all the works by a certain author. We focus on variants caused by abbreviations of first names, and show that significant achievements are possible by simple lexical analysis and comparison of names. This is done in two steps: first a pairwise matching of names is performed, and then these are used to find cliques of equivalent names. However, these steps can each be performed in a variety of ways. We therefore conduct an experimental analysis using two real datasets to find which approaches actually work well in practice. Interestingly, this depends on the size of the repository, as larger repositories may have many more similar names.

  15. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

    Science.gov (United States)

    Fowlkes, Charless C; Eckenrode, Kelly B; Bragdon, Meghan D; Meyer, Miriah; Wunderlich, Zeba; Simirenko, Lisa; Luengo Hendriks, Cris L; Keränen, Soile V E; Henriquez, Clara; Knowles, David W; Biggin, Mark D; Eisen, Michael B; DePace, Angela H

    2011-10-01

    Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3-4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of

  16. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

    Directory of Open Access Journals (Sweden)

    Charless C Fowlkes

    2011-10-01

    Full Text Available Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3-4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and

  17. Quantitative Safety: Linking Proof-Based Verification with Model Checking for Probabilistic Systems

    CERN Document Server

    Ndukwu, Ukachukwu

    2009-01-01

    This paper presents a novel approach for augmenting proof-based verification with performance-style analysis of the kind employed in state-of-the-art model checking tools for probabilistic systems. Quantitative safety properties usually specified as probabilistic system invariants and modeled in proof-based environments are evaluated using bounded model checking techniques. Our specific contributions include the statement of a theorem that is central to model checking safety properties of proof-based systems, the establishment of a procedure; and its full implementation in a prototype system (YAGA) which readily transforms a probabilistic model specified in a proof-based environment to its equivalent verifiable PRISM model equipped with reward structures. The reward structures capture the exact interpretation of the probabilistic invariants and can reveal succinct information about the model during experimental investigations. Finally, we demonstrate the novelty of the technique on a probabilistic library cas...

  18. Methodological issues in examining measurement equivalence in patient reported outcomes measures: Methods overview to the two-part series, “Measurement equivalence of the Patient Reported Outcomes Measurement Information System® (PROMIS® short forms”

    Directory of Open Access Journals (Sweden)

    Jeanne A. Teresi

    2016-03-01

    Full Text Available The purpose of this article is to introduce the methods used and challenges confronted by the authors of this two-part series of articles describing the results of analyses of measurement equivalence of the short form scales from the Patient Reported Outcomes Measurement Information System® (PROMIS®. Qualitative and quantitative approaches used to examine differential item functioning (DIF are reviewed briefly. Qualitative methods focused on generation of DIF hypotheses. The basic quantitative approaches used all rely on a latent variable model, and examine parameters either derived directly from item response theory (IRT or from structural equation models (SEM. A key methods focus of these articles is to describe state-of-the art approaches to examination of measurement equivalence in eight domains: physical health, pain, fatigue, sleep, depression, anxiety, cognition, and social function. These articles represent the first time that DIF has been examined systematically in the PROMIS short form measures, particularly among ethnically diverse groups. This is also the first set of analyses to examine the performance of PROMIS short forms in patients with cancer. Latent variable model state-of-the-art methods for examining measurement equivalence are introduced briefly in this paper to orient readers to the approaches adopted in this set of papers. Several methodological challenges underlying (DIF-free anchor item selection and model assumption violations are presented as a backdrop for the articles in this two-part series on measurement equivalence of PROMIS measures.

  19. Bulk Density Adjustment of Resin-Based Equivalent Material for Geomechanical Model Test

    Directory of Open Access Journals (Sweden)

    Pengxian Fan

    2015-01-01

    Full Text Available An equivalent material is of significance to the simulation of prototype rock in geomechanical model test. Researchers attempt to ensure that the bulk density of equivalent material is equal to that of prototype rock. In this work, barite sand was used to increase the bulk density of a resin-based equivalent material. The variation law of the bulk density was revealed in the simulation of a prototype rock of a different bulk density. Over 300 specimens were made for uniaxial compression test. Test results indicated that the substitution of quartz sand by barite sand had no apparent influence on the uniaxial compressive strength and elastic modulus of the specimens but can increase the bulk density, according to the proportional coarse aggregate content. An ideal linearity was found in the relationship between the barite sand substitution ratio and the bulk density. The relationship between the bulk density and the usage of coarse aggregate and barite sand was also presented. The test results provided an insight into the bulk density adjustment of resin-based equivalent materials.

  20. A first vascularized skin equivalent for as an alternative to animal experimentation.

    Science.gov (United States)

    Groeber, Florian; Engelhardt, Lisa; Lange, Julia; Kurdyn, Szymon; Schmid, Freia F; Rücker, Christoph; Mielke, Stephan; Walles, Heike; Hansmann, Jan

    2016-01-01

    Tissue-engineered skin equivalents mimic key aspects of the human skin, and can thus be employed as wound coverage for large skin defects or as in vitro test systems as an alternative to animal models. However, current skin equivalents lack a functional vasculature limiting clinical and research applications. This study demonstrates the generation of a vascularized skin equivalent with a perfused vascular network by combining a biological vascularized scaffold (BioVaSc) based on a decellularized segment of a porcine jejunum and a tailored bioreactor system. Briefly, the BioVaSc was seeded with human fibroblasts, keratinocytes, and human microvascular endothelial cells. After 14 days at the air-liquid interface, hematoxylin & eosin and immunohistological staining revealed a specific histological architecture representative of the human dermis and epidermis including a papillary-like architecture at the dermal-epidermal-junction. The formation of the skin barrier was measured non-destructively using impedance spectroscopy. Additionally, endothelial cells lined the walls of the formed vessels that could be perfused with a physiological volume flow. Due to the presence of a complex in-vivo-like vasculature, the here shown skin equivalent has the potential for skin grafting and represents a sophisticated in vitro model for dermatological research.