WorldWideScience

Sample records for excluding non-variable cpg

  1. An excluded diagnosis

    Directory of Open Access Journals (Sweden)

    Paolo Ghiringhelli

    2007-12-01

    Full Text Available We describe a 50-years-old patient with septic fever of unidentifiable source, following resection for rectal adenocarcinoma. He has been in treatment for sepsi two months before. Blood coltures, an accurate amanestic analysis and a transesophageal echocardiography were the major tools for the diagnosis of this disease. After the diagnosis of infective endocarditis had been excluded, antibiotic treatment (with teicoplanin and rifampicine was given for the presence of Staphylococcus epidermidis. The previous pacemaker system was removed and a DDD pacemaker was implanted.

  2. Being Included and Excluded

    DEFF Research Database (Denmark)

    Korzenevica, Marina

    2016-01-01

    Following the civil war of 1996–2006, there was a dramatic increase in the labor mobility of young men and the inclusion of young women in formal education, which led to the transformation of the political landscape of rural Nepal. Mobility and schooling represent a level of prestige that rural...... politics. It analyzes how formal education and mobility either challenge or reinforce traditional gendered norms which dictate a lowly position for young married women in the household and their absence from community politics. The article concludes that women are simultaneously excluded and included from...... people regard as a prerequisite for participating in local community politics. Based on a fieldwork in two villages of Panchthar district in eastern Nepal, this article explores how these changes strengthen or weaken women’s political agency and how this is reflected in their participation in community...

  3. CpG island mapping by epigenome prediction.

    Directory of Open Access Journals (Sweden)

    Christoph Bock

    2007-06-01

    Full Text Available CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1 reliance on arbitrary threshold parameters that bear little biological justification, (2 failure to account for widespread heterogeneity among CpG islands, and (3 apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of "CpG island strength" that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted "bona fide" CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to

  4. Critique of the hyperthyroidism and hypothyroidism CPG.

    Science.gov (United States)

    Scatcherd, Julie A

    2004-10-01

    The clinical practice guideline (CPG) for the evaluation and treatment of hyperthyroidism and hypothyroidism was developed in 2002 to update the original American Association of Clinical Endocrinologists (AACE) thyroid guidelines, which were published in 1995 (AACE Thyroid Task Force). The mission of this guideline as stated by the authors was to provide a framework for managing the diagnosis and treatment of patients with hyperthyroidism and hypothyroidism. The guidelines are intended to improve outcomes and reduce costs while stressing the importance of routine continual care provided by one physician. The guidelines are also intended to enhance physicians' awareness of subclinical hyperthyroidism and subclinical hypothyroidism, which are frequently encountered in the clinical setting and often have detrimental health consequences when untreated. The organization of the guideline is clear and easy to follow. Hyperthyroidism and hypothyroidism are described in two separate sections, each of which covers clinical features, diagnosis, laboratory evaluation, differential diagnosis, treatment, and management. (See previous article in this column.).

  5. Liposomal SLA co-incorporated with PO CpG ODNs or PS CpG ODNs induce the same protection against the murine model of leishmaniasis.

    Science.gov (United States)

    Shargh, Vahid Heravi; Jaafari, Mahmoud Reza; Khamesipour, Ali; Jaafari, Iman; Jalali, Seyed Amir; Abbasi, Azam; Badiee, Ali

    2012-06-06

    First generation Leishmania vaccines consisting of whole killed parasites with or without adjuvants have reached phase 3 trial and failed to show enough efficacy mainly due to the lack of an appropriate adjuvant. In this study, the nuclease-resistant phosphorothioate CpG oligodeoxynucleotides (PS CpG) or nuclease-sensitive phosphodiester CpG ODNs (PO CpG) were used as adjuvants to enhance immunogenicity and rate of protection against leishmaniasis. Due to the susceptibility of PO CpG to nuclease degradation, an efficient liposomal delivery system was developed to protect them from degradation. 1, 2-dioleoyl-3-trimethylammonium-propane (DOTAP) as a cationic lipid was used because of its unique adjuvanticity and electrostatic interaction with negatively charged CpG ODNs. To evaluate the role of liposomal formulation in protection rate and enhanced immune response, BALB/c mice were immunized subcutaneously with liposomal soluble Leishmania antigens (SLA) co-incorporated with PO CpG (Lip-SLA-PO CpG), Lip-SLA-PS CpG, SLA+PO CpG, SLA+PS CpG, SLA or buffer. As criteria for protection, footpad swelling at the site of challenge, parasite loads, the levels of IFN-γ and IL-4, and the IgG subtypes were evaluated. The groups of mice receiving Lip-SLA-PO CpG or Lip-SLA-PS CpG showed a high protection rate compared with the control groups. In addition, there was no significant difference in immune response generation between mice immunized with PS CpG and the group receiving PO CpG when incorporated into the liposomes. The results suggested that liposomal form of PO CpG might be used instead of PS CpG in future vaccine formulations as an efficient adjuvant. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Excluding interlopers from asteroid families

    Science.gov (United States)

    Novakovic, B.; Radovic, V.

    2014-07-01

    from AstDys database. Next, all family members that do not meet adopted criteria (based on physical and spectral characteristics) are excluded from the initial catalogue. Finally, the HCM analysis is performed again using the improved catalogue. Results: We apply this approach to the Themis family. In the first step the HCM links 3061 asteroids to the family. Among them we identify 113 potential interlopers. After removing interlopers, in the second run of the HCM, the total number of members has decreased to 2847. Thus, 101 extra objects have been excluded from the membership list (see Figure).

  7. CpG traffic lights are markers of regulatory regions in humans

    KAUST Repository

    Khamis, Abdullah M.

    2016-12-29

    DNA methylation is involved in regulation of gene expression. Although modern methods profile DNA methylation at single CpG sites, methylation levels are usually averaged over genomic regions in the downstream analyses. In this study we demonstrate that single CpG methylation can serve as a more accurate predictor of gene expression compared to average promoter / gene body methylation. CpG positions with significant correlation between methylation and expression of a gene nearby (named CpG traffic lights) are evolutionary conserved and enriched for exact TSS positions and active enhancers. Among all promoter types, CpG traffic lights are especially enriched in poised promoters. Genes that harbor CpG traffic lights are associated with development and signal transduction. Methylation levels of individual CpG traffic lights vary between cell types dramatically with the increased frequency of intermediate methylation levels, indicating cell population heterogeneity in CpG methylation levels. Being in line with the concept of the inherited stochastic epigenetic variation, methylation of such CpG positions might contribute to transcriptional regulation. Alternatively, one can hypothesize that traffic lights are markers of absent gene expression resulting from inactivation of their regulatory elements. The CpG traffic lights provide a promising insight into mechanisms of enhancer activity and gene regulation linking methylation of single CpG to expression.

  8. Collaborations between CpG sites in DNA methylation

    Science.gov (United States)

    Song, You; Ren, Honglei; Lei, Jinzhi

    2017-08-01

    DNA methylation patterns have profound impacts on genome stability, gene expression and development. The molecular base of DNA methylation patterns has long been focused at single CpG sites level. Here, we construct a kinetic model of DNA methylation with collaborations between CpG sites, from which a correlation function was established based on experimental data. The function consists of three parts that suggest three possible sources of the correlation: movement of enzymes along DNA, collaboration between DNA methylation and nucleosome modification, and global enzyme concentrations within a cell. Moreover, the collaboration strength between DNA methylation and nucleosome modification is universal for mouse early embryo cells. The obtained correlation function provides insightful understanding for the mechanisms of inheritance of DNA methylation patterns.

  9. Electrophysiological Representation of Scratching CPG Activity in the Cerebellum

    Science.gov (United States)

    Martínez-Silva, Lourdes; Manjarrez, Elias; Gutiérrez-Ospina, Gabriel; Quevedo, Jorge N.

    2014-01-01

    We analyzed the electrical activity of neuronal populations in the cerebellum and the lumbar spinal cord during fictive scratching in adult decerebrate cats before and after selective sections of the Spino-Reticulo Cerebellar Pathway (SRCP) and the Ventral-Spino Cerebellar Tract (VSCT). During fictive scratching, we found a conspicuous sinusoidal electrical activity, called Sinusoidal Cerebellar Potentials (SCPs), in the cerebellar vermis, which exhibited smaller amplitude in the paravermal and hemisphere cortices. There was also a significant spino-cerebellar coherence between these SCPs and the lumbar sinusoidal cord dorsum potentials (SCDPs). However, during spontaneous activity such spino-cerebellar coherence between spontaneous potentials recorded in the same regions decreased. We found that the section of the SRCP and the VSCT did not abolish the amplitude of the SCPs, suggesting that there are additional pathways conveying information from the spinal CPG to the cerebellum. This is the first evidence that the sinusoidal activity associated to the spinal CPG circuitry for scratching has a broad representation in the cerebellum beyond the sensory representation from hindlimbs previously described. Furthermore, the SCPs represent the global electrical activity of the spinal CPG for scratching in the cerebellar cortex. PMID:25350378

  10. 7 CFR 58.137 - Excluded milk.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Excluded milk. 58.137 Section 58.137 Agriculture... Milk § 58.137 Excluded milk. A plant shall not accept milk from a producer if: (a) The milk has been in...) Three of the last five milk samples have exceeded the maximum bacterial estimate of 500,000 per ml...

  11. Consolidated Recovered Materials Advisory Notice (RMAN) for the Comprehensive Procurement Guideline (CPG)

    Data.gov (United States)

    U.S. Environmental Protection Agency — EPA's Comprehensive Procurement Guideline (CPG) designates recycled content products that government agencies should buy. EPA publishes purchasing guidance and...

  12. Robust control of CPG-based 3D neuromusculoskeletal walking model.

    Science.gov (United States)

    Kim, Youngwoo; Tagawa, Yusuke; Obinata, Goro; Hase, Kazunori

    2011-10-01

    This paper proposes a method for enhancing the robustness of the central pattern generator (CPG)-based three-dimensional (3D) neuromusculoskeletal walking controller. The CPG has been successfully applied to walking controllers and controllers for walking robots. However, the robustness of walking motion with the CPG-based controller is not sufficient, especially when subjected to external forces or environmental variations. To achieve a realistic and stable walking motion of the controller, we propose the use of an attracting controller in parallel with the CPG-based controller. The robustness of the proposed controller is confirmed through simulation results.

  13. Correlation between BPI Gene Upstream CpG Island Methylation and mRNA Expression in Piglets

    Directory of Open Access Journals (Sweden)

    Jing Wang

    2014-06-01

    Full Text Available Diarrhea and edematous disease are two major causes of mortality in postweaning piglets, and these conditions lead to huge economic losses in the swine industry. E. coli F18 is the primary causative agent of these two diseases. Bactericidal/permeability-increasing protein (BPI plays an important role in the natural defense of the host. The aim of this study was to determine the correlation between BPI gene upstream CpG island methylation and mRNA expression. In this study, bisulfite sequencing PCR (BSP was used to detect the methylation status of the BPI gene upstream CpG island and fluorescence quantitative PCR was used to detect BPI expression in the duodenum of piglets from birth to weaning age. BPI upstream CpG islands were shown to have many putative transcription factor binding sites, 10 CpG sites and every CpG site was methylated. The CpG island methylation level was lowest in 30-day piglets and was significantly lower than levels in 8-day piglets (p < 0.05. BPI mRNA expression was significantly higher in 30-day piglets than at any other age (p < 0.05. Pearson’s correlation analysis showed that the methylation status of the CpG island was negatively correlated with BPI mRNA expression. Statistical significances were found in CpG_1, CpG_3, CpG_4, CpG_7 and CpG_10 (p < 0.05. The data indicate that BPI expression is improved by demethylation of the BPI gene upstream CpG island. Furthermore, CpG_1, CpG_3, CpG_4, CpG_7 and CpG_10 may be critical sites in the regulation of BPI gene expression.

  14. Trials of electronet fencing to exclude coyotes

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report is on the trials of using electronet fencing to exclude coyotes for the protection of black-footed ferrets in Montana. Reintroduction of black-tailed...

  15. AFSC/ABL: 2009 Chinook Excluder Samples

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This project genetically analyzed 1,620 chinook salmon samples from the 2009 spring salmon excluder device test. These samples were collected over a short period of...

  16. Reproducibility of methylated CpG typing with the Illumina MiSeq

    DEFF Research Database (Denmark)

    Kampmann, Marie-Louise; Meyer, Olivia Strunge; Greby Schmidt, Suzanne

    2017-01-01

    DNA methylation patterns may be used for identification of body fluids and for age estimation of human individuals. We evaluated some of the challenges and pitfalls of studying methylated CpG sites. We compared the methylated CpG analysis of two different methods 1) massively parallel sequencing...

  17. Modulation of CpG oligodeoxynucleotide-mediated immune stimulation by locked nucleic acid (LNA)

    DEFF Research Database (Denmark)

    Vollmer, Jörg; Jepsen, Jan Stenvang; Uhlmann, Eugen

    2004-01-01

    Locked nucleic acid (LNA) is an RNA derivative that when introduced into oligodeoxynucleotides (ODN), mediates high efficacy and stability. CpG ODNs are potent immune stimulators and are recognized by toll-like receptor-9 (TLR9). Some phosphorothioate antisense ODNs bearing CpG dinucleotides have...

  18. Carbon Nanotubes Enhance CpG Uptake and Potentiate Anti-Glioma Immunity

    Science.gov (United States)

    Zhao, Dongchang; Alizadeh, Darya; Zhang, Leying; Liu, Wei; Farrukh, Omar; Manuel, Edwin; Diamond, Don J.; Badie, Behnam

    2010-01-01

    Purpose Stimulation of toll-like receptor-9 (TLR9) by CpG oligodeoxynucleotides (CpG) has been shown to counteract the immunosuppressive microenvironment and to inhibit tumor growth in glioma models. Since TLR9 is located intracellularly, we hypothesized that methods that enhance its internalization may also potentiate its immunostimulatory response. The goal of this study was to evaluate carbon nanotubes (CNTs) as a CpG delivery vehicle in brain tumor models. Experimental Design Functionalized single-walled CNTs were conjugated with CpG (CNT-CpG) and evaluated in vitro and in mice bearing intracranial GL261 gliomas. Flow cytometry was used to assess CNT-CpG uptake and anti-glioma immune response. Tumor growth was measured by bioluminescent imaging, histology, and animal survival. Results CNT-CpG was nontoxic and enhanced CpG uptake both in vitro and intracranial gliomas. CNT-mediated CpG delivery also potentiated pro-inflammatory cytokine production by primary monocytes. Interestingly, a single intracranial injection of low-dose CNT-CpG (but not free CpG or blank CNT) eradicated intracranial GL261 gliomas in half of tumor-bearing mice. Moreover, surviving animals exhibited durable tumor-free remission (> 3 months), and were protected from intracranial tumor rechallenge, demonstrating induction of long-term anti-tumor immunity. Conclusions These findings suggest that CNTs can potentiate CpG immunopotency by enhancing its delivery into tumor-associated inflammatory cells. PMID:21088258

  19. Carbon nanotubes enhance CpG uptake and potentiate antiglioma immunity.

    Science.gov (United States)

    Zhao, Dongchang; Alizadeh, Darya; Zhang, Leying; Liu, Wei; Farrukh, Omar; Manuel, Edwin; Diamond, Don J; Badie, Behnam

    2011-02-15

    Stimulation of toll-like receptor-9 (TLR9) by CpG oligodeoxynucleotides (CpG) has been shown to counteract the immunosuppressive microenvironment and to inhibit tumor growth in glioma models. Because TLR9 is located intracellularly, we hypothesized that methods that enhance its internalization may also potentiate its immunostimulatory response. The goal of this study was to evaluate carbon nanotubes (CNT) as a CpG delivery vehicle in brain tumor models. Functionalized single-walled CNTs were conjugated with CpG (CNT-CpG) and evaluated in vitro and in mice bearing intracranial GL261 gliomas. Flow cytometry was used to assess CNT-CpG uptake and antiglioma immune response. Tumor growth was measured by bioluminescent imaging, histology, and animal survival. CNT-CpG was nontoxic and enhanced CpG uptake both in vitro and intracranial gliomas. CNT-mediated CpG delivery also potentiated proinflammatory cytokine production by primary monocytes. Interestingly, a single intracranial injection of low-dose CNT-CpG (but not free CpG or blank CNT) eradicated intracranial GL261 gliomas in half of tumor-bearing mice. Moreover, surviving animals exhibited durable tumor-free remission (>3 months), and were protected from intracranial tumor rechallenge, demonstrating induction of long-term antitumor immunity. These findings suggest that CNTs can potentiate CpG immunopotency by enhancing its delivery into tumor-associated inflammatory cells. ©2010 AACR.

  20. CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

    DEFF Research Database (Denmark)

    Hobolth, Asger; Nielsen, Rasmus; Wang, Ying

    2006-01-01

    We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We...

  1. The CpG island methylator phenotype: What's in a name?

    NARCIS (Netherlands)

    L.A.E. Hughes (Laura A.); V. Melotte (Veerle); J.D. Schrijver (Joachim De); M.P.M. de Maat (Moniek); V.T.H.B.M. Smit (Vincent); J.V.M.G. Bovée (Judith); P.J. French (Pim); P.A. van den Brandt (Piet); L. Schouten (Leo); T. Meyer (Thorsten); W. van Criekinge (Wim); N. Ahuja (Nita); J.G. Herman (James); M.P. Weijenberg (Matty); M. van Engeland (Manon)

    2013-01-01

    textabstractAlthough the CpG island methylator phenotype (CIMP) was first identified and has been most extensively studied in colorectal cancer, the term "CIMP" has been repeatedly used over the past decade to describe CpG island promoter methylation in other tumor types, including bladder, breast,

  2. Efficacy of rSEB Vaccine and CpG ODN Administered by Inhalation in Monkeys

    Science.gov (United States)

    2003-11-19

    aerosol challenge using either rSEB alone, CpG ODN alone, or comixed administered either by injection, inhalation, or combination of routes thereof...using either rSEB alone, CpG ODN alone, or comixed administered either by injection, inhalation, or combination of routes thereof. P R O J E C

  3. Endogenous sunk costs and the geographic differences in the market structures of CPG Categories

    NARCIS (Netherlands)

    Bronnenberg, B.J.; Dhar, S.; Dube, J.P.

    2011-01-01

    We describe the industrial market structure of CPG categories. The analysis uses a unique database spanning 31 consumer package goods (CPG) categories, 39 months, and the 50 largest US metropolitan markets. We organize our description of market structure around the notion that firms can improve

  4. Impact of critical success factors on successful technology implementation in Consumer Packaged Goods (CPG supply chain

    Directory of Open Access Journals (Sweden)

    Ranjan Arora

    2017-05-01

    Full Text Available The purpose of this study is to identify and analyze the impact of critical success factors (CSFs impacting technology implementation in Consumer Packaged Goods (CPG supply chain. The study has used existing literature to identify CSFs and then questionnaire-based survey and Ex-ploratory Factor Analysis (EFA to group CSFs. The paper has revealed that “Inter-Organizational”, “Organizational”, “CPG Sector Specific”, “Human” and “Program Manage-ment” CSFs impact successful technology implementation in CPG supply chain. The paper fills the gap in existing literature by studying the impact of CSFs on successful technology imple-mentation in CPG supply chain and providing guidance to practitioners working in CPG sector.

  5. The counter regulatory response induced by CpG oligonucleotides prevents bleomycin induced pneumopathy

    Directory of Open Access Journals (Sweden)

    Kinjo Takeshi

    2012-06-01

    Full Text Available Abstract Bleomycin (BLM induces life-threatening pneumonitis and pulmonary fibrosis in 20% of patients, limiting its use as a chemotherapeutic agent. Oligonucleotides expressing immunostimulatory CpG motifs (CpG ODN stimulate cells that express Toll-like receptor 9 to initiate an inflammatory response. This short-lived inflammation is physiologically suppressed by a counter-regulatory process that peaks five days later. Using a murine model of BLM-induced lung injury, the effect of CpG ODN treatment on pulmonary inflammation, fibrosis and mortality was examined. Administering CpG ODN 5 days before BLM (so that the peak of the counter-regulatory process induced by CpG ODN coincided with BLM delivery resulted in a dose-dependent reduction in pulmonary toxicity (p 

  6. Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues.

    Science.gov (United States)

    Yan, Haidan; Guan, Qingzhou; He, Jun; Lin, Yunqing; Zhang, Juan; Li, Hongdong; Liu, Huaping; Gu, Yunyan; Guo, Zheng; He, Fei

    2017-02-08

    Due to the heterogeneity of cancer, identifying differentially methylated (DM) CpG sites between a set of cancer samples and a set of normal samples cannot tell us which patients have methylation aberrations in a particular DM CpG site. We firstly showed that the relative methylation-level orderings (RMOs) of CpG sites within individual normal lung tissues are highly stable but widely disrupted in lung adenocarcinoma tissues. This finding provides the basis of using the RankComp algorithm, previously developed for differential gene expression analysis at the individual level, to identify DM CpG sites in each cancer tissue compared with its own normal state. Briefly, through comparing with the highly stable normal RMOs predetermined in a large collection of samples for normal lung tissues, the algorithm finds those CpG sites whose hyper- or hypo-methylations may lead to the disrupted RMOs of CpG site pairs within a disease sample based on Fisher's exact test. Evaluated in 59 lung adenocarcinoma tissues with paired adjacent normal tissues, RankComp reached an average precision of 94.26% for individual-level DM CpG sites. Then, after identifying DM CpG sites in each of the 539 lung adenocarcinoma samples from TCGA, we found five and 44 CpG sites hypermethylated and hypomethylated in above 90% of the disease samples, respectively. These findings were validated in 140 publicly available and eight additionally measured paired cancer-normal samples. Gene expression analysis revealed that four of the five genes, HOXA9, TAL1, ATP8A2, ENG and SPARCL1, each harboring one of the five frequently hypermethylated CpG sites within its promoters, were also frequently down-regulated in lung adenocarcinoma. The common DNA methylation aberrations in lung adenocarcinoma tissues may be important for lung adenocarcinoma diagnosis and therapy.

  7. What is the Right to Exclude Immigrants?

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2010-01-01

    of states. The right to exclude claimed by states is analysed and it is shown to differ both conceptually and normatively from rights to impose political authority within a territory. The paper finally indicates how this analysis might broaden the focus of debates about immigration and suggest alternative......It is normally taken for granted that states have a right to control immigration into their territory. When immigration is raised as a normative issue two questions become salient, one about what the right to exclude is, and one about whether and how it might be justified. This paper considers...... the first question. The paper starts by noting that standard debates about immigration have not addressed what the right to exclude is. Standard debates about immigration furthermore tend to result either in fairly strong cases for open borders or in denials that considerations of justice apply...

  8. Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites.

    Science.gov (United States)

    Grandi, Fiorella C; Rosser, James M; Newkirk, Simon J; Yin, Jun; Jiang, Xiaoling; Xing, Zhuo; Whitmore, Leanne; Bashir, Sanum; Ivics, Zoltán; Izsvák, Zsuzsanna; Ye, Ping; Yu, Y Eugene; An, Wenfeng

    2015-08-01

    Long interspersed elements (LINEs), through both self-mobilization and trans-mobilization of short interspersed elements and processed pseudogenes, have made an indelible impact on the structure and function of the human genome. One consequence is the creation of new CpG islands (CGIs). In fact, more than half of all CGIs in the genome are associated with repetitive DNA, three-quarters of which are derived from retrotransposons. However, little is known about the epigenetic impact of newly inserted CGIs. We utilized a transgenic LINE-1 mouse model and tracked DNA methylation dynamics of individual germline insertions during mouse development. The retrotransposed GFP marker sequence, a strong CGI, is hypomethylated in male germ cells but hypermethylated in somatic tissues, regardless of genomic location. The GFP marker is similarly methylated when delivered into the genome via the Sleeping Beauty DNA transposon, suggesting that the observed methylation pattern may be independent of the mode of insertion. Comparative analyses between insertion- and non-insertion-containing alleles further reveal a graded influence of the retrotransposed CGI on flanking CpG sites, a phenomenon that we described as "sloping shores." Computational analyses of human and mouse methylomic data at single-base resolution confirm that sloping shores are universal for hypomethylated CGIs in sperm and somatic tissues. Additionally, the slope of a hypomethylated CGI can be affected by closely positioned CGI neighbors. Finally, by tracing sloping shore dynamics through embryonic and germ cell reprogramming, we found evidence of bookmarking, a mechanism that likely determines which CGIs will be eventually hyper- or hypomethylated. © 2015 Grandi et al.; Published by Cold Spring Harbor Laboratory Press.

  9. Polyelectrolyte solutions: Excluded-volume considerations

    Science.gov (United States)

    Mattoussi, Hedi; Karasz, Frank E.

    1993-12-01

    We provide experimental evidence for the electrostatically related excluded-volume effects on the colligative properties and the single chain behavior of polyelectrolyte solutions in the dilute regime. The data are compared to the theory developed by Fixman, Skolnick, Odijk, and Houwaart. Good agreement between these theoretical considerations and the experimental data is observed.

  10. 21 CFR 1308.22 - Excluded substances.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Excluded substances. 1308.22 Section 1308.22 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE SCHEDULES OF CONTROLLED SUBSTANCES... may, under the Federal Food, Drug, and Cosmetic Act (21 U.S.C. 301), be lawfully sold over the counter...

  11. CpG islands undermethylation in human genomic regions under selective pressure.

    Directory of Open Access Journals (Sweden)

    Sergio Cocozza

    Full Text Available DNA methylation at CpG islands (CGIs is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG islands methylation and signatures of selective pressure in Homo Sapiens, using a computational biology approach. By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. To define genomic regions under selective pressure, we used three different methods, each oriented to provide distinct information about selective events. Independently of the method and of the cell type used, we found evidences of undermethylation of CGIs in human genomic regions under selective pressure. Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. Our findings suggest that the CpG islands in regions under selective pressure seem to be somehow more "protected" from methylation when compared with other regions of the genome.

  12. CpG oligodeoxynucleotide nanomedicines for the prophylaxis or treatment of cancers, infectious diseases, and allergies.

    Science.gov (United States)

    Hanagata, Nobutaka

    2017-01-01

    Unmethylated cytosine-guanine dinucleotide-containing oligodeoxynucleotides (CpG ODNs), which are synthetic agonists of Toll-like receptor 9 (TLR9), activate humoral and cellular immunity and are being developed as vaccine adjuvants to prevent or treat cancers, infectious diseases, and allergies. Free CpG ODNs have been used in many clinical trials implemented to verify their effects. However, recent research has reported that self-assembled CpG ODNs, protein/peptide-CpG ODN conjugates, and nanomaterial-CpG ODN complexes demonstrate higher adjuvant effects than free CpG ODNs, owing to their improved uptake efficiency into cells expressing TLR9. Moreover, protein/peptide-CpG ODN conjugates and nanomaterial-CpG ODN complexes are able to deliver CpG ODNs and antigens (or allergens) to the same types of cells, which enables a higher degree of prophylaxis or therapeutic effect. In this review, the author describes recent trends in the research and development of CpG ODN nanomedicines containing self-assembled CpG ODNs, protein/peptide-CpG ODN conjugates, and nanomaterial-CpG ODN complexes, focusing mainly on the results of preclinical and clinical studies.

  13. Multi-layered multi-pattern CPG for adaptive locomotion of humanoid robots.

    Science.gov (United States)

    Nassour, John; Hénaff, Patrick; Benouezdou, Fethi; Cheng, Gordon

    2014-06-01

    In this paper, we present an extended mathematical model of the central pattern generator (CPG) in the spinal cord. The proposed CPG model is used as the underlying low-level controller of a humanoid robot to generate various walking patterns. Such biological mechanisms have been demonstrated to be robust in locomotion of animal. Our model is supported by two neurophysiological studies. The first study identified a neural circuitry consisting of a two-layered CPG, in which pattern formation and rhythm generation are produced at different levels. The second study focused on a specific neural model that can generate different patterns, including oscillation. This neural model was employed in the pattern generation layer of our CPG, which enables it to produce different motion patterns-rhythmic as well as non-rhythmic motions. Due to the pattern-formation layer, the CPG is able to produce behaviors related to the dominating rhythm (extension/flexion) and rhythm deletion without rhythm resetting. The proposed multi-layered multi-pattern CPG model (MLMP-CPG) has been deployed in a 3D humanoid robot (NAO) while it performs locomotion tasks. The effectiveness of our model is demonstrated in simulations and through experimental results.

  14. Clean Water Act (excluding Section 404)

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-15

    This Reference Book contains a current copy of the Clean Water Act (excluding Section 404) and those regulations that implement the statutes and appear to be most relevant to US Department of Energy (DOE) activities. The document is provided to DOE and contractor staff for informational purposes only and should not be interpreted as legal guidance. Updates that include important new requirements will be provided periodically. Questions concerning this Reference Book may be directed to Mark Petts, EH-231 (202/586-2609).

  15. Effect of amino groups of mesoporous silica nanoparticles on CpG oligodexynucleotide delivery

    OpenAIRE

    Xu, Yi; Claiden, Peter; Zhu, Yufang; Morita, Hiromi; Hanagata, Nobutaka

    2015-01-01

    In this study, we proposed to modify mesoporous silica nanoparticles (MSNs) with 3-aminopropyltriethoxysilane (NH2-TES), aminoethylaminopropyltriethoxysilane (2NH2-TES) and 3-[2-(2-aminoethylamino)ethylamino] propyl-trimethoxysilane (3NH2-TES) for binding of cytosine-phosphate-guanosine oligodexynucleotides (CpG ODN), and investigated the effect of different amino groups of MSNs on the CpG ODN delivery. Serum stability, in vitro cytotoxicity, and cytokine interleukin-6 (IL-6) induction by MSN...

  16. CpG methylated minichromosomes become inaccessible for V(D)J recombination after undergoing replication.

    OpenAIRE

    Hsieh, C L; Lieber, M R

    1992-01-01

    The physical parameters controlling the accessibility of antigen receptor loci to the V(D)J recombination activity are unknown. We have used minichromosome substrates to study the role that CpG methylation might play in controlling V(D)J recombination site accessibility. We find that CpG methylation decreases the V(D)J recombination of these substrates more than 100-fold. The decrease correlates with a considerable increase in resistance to endonuclease digestion of the methylated minichromos...

  17. CpG oligodeoxyribonucleotides protect mice from Burholderia pseudomallei but not Francisella tularensis Schu 54 aersols

    Science.gov (United States)

    2010-01-01

    including the biological warfare threat agents Burkholderia mallei [4] and Burkholderia pseudo- mallei [5]. Murine studies of the Francisella...PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 from Burkholderia mallei challenges [4]. Despite CpG ODN 10103’s...and B. mallei (unpublished data) suggest that, as with the CpG motifs used in other Burkholderia and F. tular- ensis murine studies [3-6], the

  18. Graphene oxide-chitosan nanocomposites for intracellular delivery of immunostimulatory CpG oligodeoxynucleotides.

    Science.gov (United States)

    Zhang, Huijie; Yan, Ting; Xu, Sha; Feng, Shini; Huang, Dandi; Fujita, Morihisa; Gao, Xiao-Dong

    2017-04-01

    CpG oligodeoxynucleotides (ODNs) activate innate and adaptive immune responses, and show strong potential as immunotherapeutic agents against various diseases. Benefiting from their unique physicochemical properties, graphene oxide (GO) has recently attracted great attention in nanomedicine. In this study, we developed a novel CpG ODNs delivery system based on GO-chitosan (GO-CS) nanocomposites. GO-CS nanocomposites were prepared by self-assembly of both components via electrostatic interactions. Compared with GO, GO-CS nanocomposites possessed smaller size, positive surface charge and lower cytotoxicity. CpG ODNs were loaded onto GO-CS nanocomposites via electrostatic interactions. GO-CS nanocomposites greatly improved the loading capacity and cellular uptake of CpG ODNs. GO-CS/CpG ODNs complexes further resulted in an enhanced interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) production compared with that of free CpG ODNs and GO/CpG ODNs complexes. Therefore, GO-CS nanocomposites can serve as efficient nanocarriers for enhancing the delivery efficiency of CpG ODNs. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. A species-generalized probabilistic model-based definition of CpG islands.

    Science.gov (United States)

    Irizarry, Rafael A; Wu, Hao; Feinberg, Andrew P

    2009-01-01

    The DNA of most vertebrates is depleted in CpG dinucleotides, the target for DNA methylation. The remaining CpGs tend to cluster in regions referred to as CpG islands (CGI). CGI have been useful as marking functionally relevant epigenetic loci for genome studies. For example, CGI are enriched in the promoters of vertebrate genes and thought to play an important role in regulation. Currently, CGI are defined algorithmically as an observed-to-expected ratio (O/E) of CpG greater than 0.6, G+C content greater than 0.5, and usually but not necessarily greater than a certain length. Here we find that the current definition leaves out important CpG clusters associated with epigenetic marks, relevant to development and disease, and does not apply at all to nonvertabrate genomes. We propose an alternative Hidden Markov model-based approach that solves these problems. We fit our model to genomes from 30 species, and the results support a new epigenomic view toward the development of DNA methylation in species diversity and evolution. The O/E of CpG in islands and nonislands segregated closely phylogenetically and showed substantial loss in both groups in animals of greater complexity, while maintaining a nearly constant difference in CpG O/E between islands and nonisland compartments. Lists of CGI for some species are available at http://www.rafalab.org .

  20. Nucleosome dynamics and maintenance of epigenetic states of CpG islands

    Science.gov (United States)

    Sneppen, Kim; Dodd, Ian B.

    2016-06-01

    Methylation of mammalian DNA occurs primarily at CG dinucleotides. These CpG sites are located nonrandomly in the genome, tending to occur within high density clusters of CpGs (islands) or within large regions of low CpG density. Cluster methylation tends to be bimodal, being dominantly unmethylated or mostly methylated. For CpG clusters near promoters, low methylation is associated with transcriptional activity, while high methylation is associated with gene silencing. Alternative CpG methylation states are thought to be stable and heritable, conferring localized epigenetic memory that allows transient signals to create long-lived gene expression states. Positive feedback where methylated CpG sites recruit enzymes that methylate nearby CpGs, can produce heritable bistability but does not easily explain that as clusters increase in size or density they change from being primarily methylated to primarily unmethylated. Here, we show that an interaction between the methylation state of a cluster and its occupancy by nucleosomes provides a mechanism to generate these features and explain genome wide systematics of CpG islands.

  1. CPG-based Locomotion Controller Design for a Boxfish-like Robot

    Directory of Open Access Journals (Sweden)

    Wei Wang

    2014-06-01

    Full Text Available This paper focuses on a Central Pattern Generator (CPG-based locomotion controller design for a boxfish-like robot. The bio-inspired controller is aimed at flexible switching in multiple 3D swimming patterns and exact attitude control of yaw and roll such that the robot will swim more like a real boxfish. The CPG network comprises two layers, the lower layer is the network of coupled linear oscillators and the upper is the transition layer where the lower-dimensional locomotion stimuli are transformed into the higher-dimensional control parameters serving for all the oscillators. Based on such a two-layer framework, flexible switching between multiple three-dimensional swimming patterns, such as swimming forwards/backwards, turning left/right, swimming upwards/downwards and rolling clockwise/counter-clockwise, can be simply realized by inputting different stimuli. Moreover, the stability of the CPG network is strictly proved to guarantee the intrinsic stability of the swimming patterns. As to exact attitude control, based on this open-loop CPG network and the sensory feedback from the Inertial Measurement Unit (IMU, a closed-loop CPG controller is advanced for yaw and roll control of the robotic fish for the first time. This CPG-based online attitude control for a robotic fish will greatly facilitate high-level practical underwater applications. A series of relevant experiments with the robotic fish are conducted systematically to validate the effectiveness and stability of the open-loop and closed-loop CPG controllers.

  2. The Genomic Impact of DNA CpG Methylation on Gene Expression; Relationships in Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Mark D. Long

    2017-02-01

    Full Text Available The process of DNA CpG methylation has been extensively investigated for over 50 years and revealed associations between changing methylation status of CpG islands and gene expression. As a result, DNA CpG methylation is implicated in the control of gene expression in developmental and homeostasis processes, as well as being a cancer-driver mechanism. The development of genome-wide technologies and sophisticated statistical analytical approaches has ushered in an era of widespread analyses, for example in the cancer arena, of the relationships between altered DNA CpG methylation, gene expression, and tumor status. The remarkable increase in the volume of such genomic data, for example, through investigators from the Cancer Genome Atlas (TCGA, has allowed dissection of the relationships between DNA CpG methylation density and distribution, gene expression, and tumor outcome. In this manner, it is now possible to test that the genome-wide correlations are measurable between changes in DNA CpG methylation and gene expression. Perhaps surprisingly is that these associations can only be detected for hundreds, but not thousands, of genes, and the direction of the correlations are both positive and negative. This, perhaps, suggests that CpG methylation events in cancer systems can act as disease drivers but the effects are possibly more restricted than suspected. Additionally, the positive and negative correlations suggest direct and indirect events and an incomplete understanding. Within the prostate cancer TCGA cohort, we examined the relationships between expression of genes that control DNA methylation, known targets of DNA methylation and tumor status. This revealed that genes that control the synthesis of S-adenosyl-l-methionine (SAM associate with altered expression of DNA methylation targets in a subset of aggressive tumors.

  3. Queueing process with excluded-volume effect.

    Science.gov (United States)

    Arita, Chikashi

    2009-11-01

    We introduce an extension of the M/M/1 queueing process with a spatial structure and excluded-volume effect. The rule of particle hopping is the same as for the totally asymmetric simple exclusion process (TASEP). A stationary-state solution is constructed in a slightly arranged matrix product form of the open TASEP. We obtain the critical line that separates the parameter space depending on whether the model has the stationary state. We calculate the average length of the model and the number of particles and show the monotonicity of the probability of the length in the stationary state. We also consider a generalization of the model with backward hopping of particles allowed and an alternate joined system of the M/M/1 queueing process and the open TASEP.

  4. 34 CFR 85.950 - Excluded Parties List System

    Science.gov (United States)

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Excluded Parties List System 85.950 Section 85.950... (NONPROCUREMENT) Definitions § 85.950 Excluded Parties List System Excluded Parties List System (EPLS) means the... entitled, “List of Parties Excluded or Disqualified from Federal Procurement and Nonprocurement Programs...

  5. CpG methylation increases the DNA binding of 9-aminoacridine carboxamide Pt analogues.

    Science.gov (United States)

    Kava, Hieronimus W; Murray, Vincent

    2016-10-01

    This study investigated the effect of CpG methylation on the DNA binding of cisplatin analogues with an attached aminoacridine intercalator. DNA-targeted 9-aminoacridine carboxamide Pt complexes are known to bind at 5'-CpG sequences. Their binding to methylated and non-methylated 5'-CpG sequences was determined and compared with cisplatin. The damage profiles of each platinum compound were quantified via a polymerase stop assay with fluorescently labelled primers and capillary electrophoresis. Methylation at 5'-CpG was shown to significantly increase the binding intensity for the 9-aminoacridine carboxamide compounds, whereas no significant increase was found for cisplatin. 5'-CpG methylation had the largest effect on the 9-ethanolamine-acridine carboxamide Pt complex, followed by the 9-aminoacridine carboxamide Pt complex and the 7-fluoro complex. The methylation state of a cell's genome is important in maintaining normal gene expression, and is often aberrantly altered in cancer cells. An analogue of cisplatin which differentially targets methylated DNA may be able to improve its therapeutic activity, or alter its range of targets and evade the chemoresistance which hampers cisplatin efficacy in clinical use. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. State-Dependent Rhythmogenesis and Frequency Control in a Half-Center Locomotor CPG.

    Science.gov (United States)

    Ausborn, Jessica; Snyder, Abigail C; Shevtsova, Natalia A; Rybak, Ilya A; Rubin, Jonathan E

    2017-10-04

    The spinal locomotor central pattern generator (CPG) generates rhythmic activity with alternating flexion and extension phases. This rhythmic pattern is likely to result from inhibitory interactions between neural populations representing flexor and extensor half-centers. However, it is unclear whether the flexor-extensor CPG has a quasi-symmetric organization with both half-centers critically involved in rhythm generation, features an asymmetric organization with flexor-driven rhythmogenesis, or comprises a pair of intrinsically rhythmic half-centers. There are experimental data that support each of the above concepts but appear to be inconsistent with the others. In this theoretical/modeling study, we present and analyze a CPG model architecture that can operate in different regimes consistent with the above three concepts depending on conditions, which are defined by external excitatory drives to CPG half-centers. We show that control of frequency and phase durations within each regime depends on network dynamics, defined by the regime-dependent expression of the half-centers' intrinsic rhythmic capabilities and the operating phase transition mechanisms (escape versus release). Our study suggests state-dependency in locomotor CPG operation and proposes explanations for seemingly contradictory experimental data. Copyright © 2017, Journal of Neurophysiology.

  7. [Treatment of adenomyosis (excluding pregnancy project)].

    Science.gov (United States)

    Pelage, L; Fenomanana, S; Brun, J-L; Levaillant, J-M; Fernandez, H

    2015-05-01

    In this review we aimed to update the possibilities of adenomyosis treatment in women excluding those with a desire for pregnancy. Adenomyosis is defined as the presence of endometrial tissue within the myometrium and frequently underestimated. Over the last decades, its pathophysiology has been better known. The diagnosis is essentially based on clinical symptoms like menorrhagia and dysmenorrhea. Transvaginal ultrasound and magnetic resonance imaging are the main tools of the radiologic diagnosis. However, the definitive diagnosis is histological. The most effective treatment remains hysterectomy; however it is expensive, radical and at risk of morbidity compared with medical or surgical conservative management. The literature has reported several series of patients undergoing various treatments, thus allowing different therapeutic options. The levonorgestrel-releasing intrauterine device showed its efficacy alone or in combination with hysteroscopic treatment. Oral progestins, GnRH agonists are useful at short term or in preoperative condition. Some conservative treatments like focused ultrasound therapies or uterus-sparing operative treatment stay under evaluation and seems to be effective. Embolization has been the subject of several studies and must be outlined. Furthermore, several molecules, such as modulators of progesterone receptors and the aromatase inhibitors have been recently studied and are perhaps future treatments. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  8. Neutron resonance data exclude random matrix theory

    Science.gov (United States)

    Koehler, P. E.; Bečvář, F.; Krtička, M.; Guber, K. H.; Ullmann, J. L.

    2013-02-01

    Almost since the time it was formulated, the overwhelming consensus has been that random matrix theory (RMT) is in excellent agreement with neutron resonance data. However, over the past few years, we have obtained new neutron-width data at Oak Ridge and Los Alamos National Laboratories that are in stark disagreement with this theory. We also have reanalyzed neutron widths in the most famous data set, the nuclear data ensemble (NDE), and found that it is seriously flawed, and, when analyzed carefully, excludes RMT with high confidence. More recently, we carefully examined energy spacings for these same resonances in the NDE using the $\\Delta_{3}$ statistic. We conclude that the data can be found to either confirm or refute the theory depending on which nuclides and whether known or suspected p-wave resonances are included in the analysis, in essence confirming results of our neutron-width analysis of the NDE. We also have examined radiation widths resulting from our Oak Ridge and Los Alamos measurements, and find that in some cases they do not agree with RMT. Although these disagreements presently are not understood, they could have broad impact on basic and applied nuclear physics, from nuclear astrophysics to nuclear criticality safety.

  9. Neutron resonance data exclude random matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Koehler, P.E. [Physics Division, Oak Ridge National Laboratory, MailStop 6356, Oak Ridge, Tennessee 37831 (United States); Becvar, F.; Krticka, M. [Charles University, Faculty of Mathematics and Physics, 180 00 Prague 8 (Czech Republic); Guber, K.H. [Reactor and Nuclear Systems Division, Oak Ridge National Laboratory, Mail Stop 6356, Oak Ridge, Tennessee 37831 (United States); Ullmann, J.L. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2013-02-15

    Almost since the time it was formulated, the overwhelming consensus has been that random matrix theory (RMT) is in excellent agreement with neutron resonance data. However, over the past few years, we have obtained new neutron-width data at Oak Ridge and Los Alamos National Laboratories that are in stark disagreement with this theory. We also have reanalyzed neutron widths in the most famous data set, the nuclear data ensemble (NDE), and found that it is seriously flawed, and, when analyzed carefully, excludes RMT with high confidence. More recently, we carefully examined energy spacings for these same resonances in the NDE using the {Delta}{sub 3} statistic. We conclude that the data can be found to either confirm or refute the theory depending on which nuclides and whether known or suspected p-wave resonances are included in the analysis, in essence confirming results of our neutron-width analysis of the NDE. We also have examined radiation widths resulting from our Oak Ridge and Los Alamos measurements, and find that in some cases they do not agree with RMT. Although these disagreements presently are not understood, they could have broad impact on basic and applied nuclear physics, from nuclear astrophysics to nuclear criticality safety. (Copyright copyright 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  10. CPG-inspired workspace trajectory generation and adaptive locomotion control for quadruped robots.

    Science.gov (United States)

    Liu, Chengju; Chen, Qijun; Wang, Danwei

    2011-06-01

    This paper deals with the locomotion control of quadruped robots inspired by the biological concept of central pattern generator (CPG). A control architecture is proposed with a 3-D workspace trajectory generator and a motion engine. The workspace trajectory generator generates adaptive workspace trajectories based on CPGs, and the motion engine realizes joint motion imputes. The proposed architecture is able to generate adaptive workspace trajectories online by tuning the parameters of the CPG network to adapt to various terrains. With feedback information, a quadruped robot can walk through various terrains with adaptive joint control signals. A quadruped platform AIBO is used to validate the proposed locomotion control system. The experimental results confirm the effectiveness of the proposed control architecture. A comparison by experiments shows the superiority of the proposed method against the traditional CPG-joint-space control method.

  11. CpG oligodeoxynucleotides with crude parasite antigens reduce worm recovery in Opisthorchis viverrini infected hamsters.

    Science.gov (United States)

    Kaewraemruaen, Chamraj; Sermswan, Rasana W; Wongratanacheewin, Surasakdi

    2016-12-01

    Opisthorchis viverrini, a human liver fluke, is still an endemic parasitic infection in Thailand and nearly all countries in Southeast Asia. O. viverrini induces a chronic stage of infection in hamsters. During the first 2 weeks of infection, Th1 inducing cytokine, IL-12, increased but was down regulated in chronic infection. In this study it was found that unmethylated-CpG ODN (oligodeoxynucleotides) 1826 increased hamster mononuclear cell proliferation and stimulated IFN-γ production in vitro. The IFN-γ levels in hamster sera were significantly increased in hamsters injected with CpG ODN 1826 alone or plus crude somatic antigens (CSAg). Further investigation using the flow cytometer found that CD4(+)T cells and IFN-γ(+) CD4(+)T cells (Th1-like cells) in the hamster blood were significantly increased. The role of these cells in the protective responses in hamsters was evaluated by challenging with 25 metacercaria and observation for 3 months. The number of worms recovered was significantly reduced in the hamsters injected with CpG ODN 1826 with CSAg, but not in CpG ODN 1826 alone groups when compared to PBS control. The percent of reduction in hamsters against this parasite were 32.95% and 21.49% in the CpG ODN 1826 with CSAg and CpG ODN 1826 alone. This study indicates that CpG ODN 1826 plus parasite antigens elicit a Th1-like response that leads to the enhancement of worm reduction. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

    Directory of Open Access Journals (Sweden)

    Keightley Peter D

    2008-09-01

    Full Text Available Abstract Background Molecular evolutionary studies in mammals often estimate nucleotide substitution rates within and outside CpG dinucleotides separately. Frequently, in alignments of two sequences, the division of sites into CpG and non-CpG classes is based simply on the presence or absence of a CpG dinucleotide in either sequence, a procedure that we refer to as CpG/non-CpG assignment. Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related. Results Using simulations of DNA sequence evolution we show that assignment of the ancestral CpG state based on the simple presence/absence of the CpG dinucleotide can seriously bias estimates of the substitution rate, because many true non-CpG changes are misassigned as CpG. Paradoxically, this bias is most severe between closely related species, because a minimum of two substitutions are required to misassign a true ancestral CpG site as non-CpG whereas only a single substitution is required to misassign a true ancestral non-CpG site as CpG in a two branch tree. We also show that CpG misassignment bias differentially affects fourfold degenerate and noncoding sites due to differences in base composition such that fourfold degenerate sites can appear to be evolving more slowly than noncoding sites. We demonstrate that the effects predicted by our simulations occur in a real evolutionary setting by comparing substitution rates estimated from human-chimp coding and intronic sequence using CpG/non-CpG assignment with estimates derived from a method that is largely free from bias. Conclusion Our study demonstrates that a common method of assigning sites into CpG and non CpG classes in pairwise alignments is seriously biased and recommends against the adoption of ad hoc methods of ancestral state assignment.

  13. Protective immunity against Megalocytivirus infection in rock bream (Oplegnathus fasciatus) following CpG ODN administration.

    Science.gov (United States)

    Jung, Myung-Hwa; Lee, Jehee; Ortega-Villaizan, M; Perez, Luis; Jung, Sung-Ju

    2017-06-27

    Rock bream iridovirus (RBIV) disease in rock bream (Oplegnathus fasciatus) remains an unsolved problem in Korea aquaculture farms. CpG ODNs are known as immunostimulant, can improve the innate immune system of fish providing resistance to diseases. In this study, we evaluated the potential of CpG ODNs to induce anti-viral status protecting rock bream from different RBIV infection conditions. We found that, when administered into rock bream, CpG ODN 1668 induces better antiviral immune responses compared to other 5 CpG ODNs (2216, 1826, 2133, 2395 and 1720). All CpG ODN 1668 administered fish (1/5µg) at 2days before infection (1.1×10 7 ) held at 26°C died even though mortality was delayed from 8days (1µg) and 4days (5µg). Similarly, CpG ODN 1668 administered (5µg) at 2days before infection (1.2×10 6 ) held at 23/20°C had 100% mortality; the mortality was delayed from 9days (23°C) and 11days (20°C). Moreover, when CpG ODN 1668 administered (1/5/10µg) at 2/4/7days before infection or virus concentration was decreased to 1.1×10 4 and held at 20°C had mortality rates of 20/60/30% (2days), 30/40/60% (4days) and 60/60/20% (7days), respectively, for the respective administration dose, through 100 dpi. To investigate the development of a protective immune response, survivors were re-infected with RBIV (1.1×10 7 ) at 100 and 400 dpi, respectively. While 100% of the previously unexposed fish died, 100% of the previously infected fish survived. The high survival rate of fish following re-challenge with RBIV indicates that protective immunity was established in the surviving rock bream. Our results showed the possibility of developing preventive measures against RBIV using CpG ODN 1668 by reducing RBIV replication speed (i.e. water temperature of 20°C and infection dose of 1.1×10 4 ). Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Excluding the Excluded : New Labour’s Penchant for Punishment

    OpenAIRE

    Bell, Emma

    2011-01-01

    New Labour’s emphasis on personal responsibility leads it to shun any definition of the socially excluded as the passive victims of socio-economic circumstances. It encourages them to act positively to re-integrate themselves into “mainstream” society by participating in welfare-to-work schemes etc. Importantly, this involves an acceptance of a certain value system as promoted by the government. Refusal to accept these values - often taken to denote membership of an underclass (increasingly u...

  15. 48 CFR 9.404 - Excluded Parties List System.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Excluded Parties List... ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Debarment, Suspension, and Ineligibility 9.404 Excluded Parties List System. (a) The General Services Administration (GSA)— (1) Operates the web-based Excluded Parties...

  16. 29 CFR 1471.950 - Excluded Parties List System

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 4 2010-07-01 2010-07-01 false Excluded Parties List System 1471.950 Section 1471.950... GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) Definitions § 1471.950 Excluded Parties List System Excluded Parties List System (EPLS) means the list maintained and disseminated by the General Services...

  17. 26 CFR 1.1563-2 - Excluded stock.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 13 2010-04-01 2010-04-01 false Excluded stock. 1.1563-2 Section 1.1563-2...) INCOME TAXES Certain Controlled Corporations § 1.1563-2 Excluded stock. (a) Certain stock excluded. For purposes of sections 1561 through 1563 and the regulations thereunder, the term “stock” does not include...

  18. AtMBD6, a methyl CpG binding domain protein, maintains gene ...

    Indian Academy of Sciences (India)

    2017-01-13

    Jan 13, 2017 ... Arabidopsis thaliana; Argonoute 4; DNA methylation; histone deacetylase; methyl CpG binding domain protein; nuclear ..... involved in the process of RNA-directed DNA methylation. Sequence analysis of NTF2 protein revealed several impor- tant features. The protein is made of 460 amino acids with a.

  19. Clinical Practice Guidelines: AAO-HNSF Process for CPG Development and Topic Selection.

    Science.gov (United States)

    Choi, Sukgi; Nnacheta, Lorraine

    2017-10-01

    The American Academy of Otolaryngology-Head and Neck Surgery has been developing clinical practice guidelines (CPGs) for use by its members and the public. The process of CPG development and the selection of topics for CPGs can be confusing. This commentary attempts to clarify this process and delineate the issues that are considered in topic selection.

  20. High CpG island methylation of p16 gene and loss of p16 protein ...

    Indian Academy of Sciences (India)

    ... in p16 promoters in ToF patients was negatively correlated with p16 protein and gene expression (both P < 0.05). Our study reports that high CpG island methylation of p16 gene and loss of p16 protein expression associate with the development and progression of ToF, which may have significant therapeutic applications ...

  1. High CpG island methylation ofp16 gene and loss of p16 protein ...

    Indian Academy of Sciences (India)

    Navya

    in heart failure, and HFC senescence is associated with up-regulation of p16expression. (Golubnitschaja et al., 2003; Ball and Levine, 2005). Although the involvement of CpG island methylation in suppression ofp16 gene expression has been discussed in cancer settings, the status of p16 gene methylation and its effects ...

  2. YAC contig organization and CpG island analysis in Xq28

    Energy Technology Data Exchange (ETDEWEB)

    Palmieri, G.; Romano, G.; Ciccodicola, A. [International Institute of Genetics and Biophysics, Naples (Italy)] [and others

    1994-11-01

    One hundred nineteen YACs were assembled into 6 contigs spanning about 7.1 Mb of Xq28. The contigs were formatted with 65 STSs and 136 hybridization probes and were extensive enough to be aligned and oriented by published genetic linkage and somatic cell hybrid panel data. Selected YACs from the entire region were mapped with five rare-cutter restriction enzymes to infer the position of putative CpG islands indicative of gene locations; 48 such sites were identified by the near coincidence of at least three rare-cutter sites. The analysis defined three subregions of Xq28: 4 Mb of moderate GC and CpG island content from the Xq27 border through the GABRA locus; 1.5 to 2 Mb, extending to the G6PD gene, that is variably and poorly cloned, but contains a high concentration of CpG islands and GC; and about 1.5 Mb between G6PD and the telomere, which is generally low in CpG and GC levels, including a subtelomeric DNA region that shows extensive homology to Yq DNA. 53 refs., 2 figs., 3 tabs.

  3. Preexposure to CpG protects against the delayed effects of neonatal respiratory syncytial virus infection.

    Science.gov (United States)

    Yamaguchi, Yuko; Harker, James A; Wang, Belinda; Openshaw, Peter J; Tregoning, John S; Culley, Fiona J

    2012-10-01

    Severe respiratory viral infection in early life is associated with recurrent wheeze and asthma in later childhood. Neonatal immune responses tend to be skewed toward T helper 2 (Th2) responses, which may contribute to the development of a pathogenic recall response to respiratory infection. Since neonatal Th2 skewing can be modified by stimulation with Toll-like receptor (TLR) ligands, we investigated the effect of exposure to CpG oligodeoxynucleotides (TLR9 ligands) prior to neonatal respiratory syncytial virus (RSV) infection in mice. CpG preexposure was protective against enhanced disease during secondary adult RSV challenge, with a reduction in viral load and an increase in Th1 responses. A similar Th1 switch and reduction in disease were observed if CpG was administered in the interval between neonatal infection and challenge. In neonates, CpG pretreatment led to a transient increase in expression of major histocompatibility complex class II (MHCII) and CD80 on CD11c-positive cells and gamma interferon (IFN-γ) production by NK cells after RSV infection, suggesting that the protective effects may be mediated by antigen-presenting cells (APC) and NK cells. We conclude that the adverse effects of early-life respiratory viral infection on later lung health might be mitigated by conditions that promote TLR activation in the infant lung.

  4. Promoter CpG island hypermethylation in the development of cutaneous melanoma

    NARCIS (Netherlands)

    Gao, Linda

    2015-01-01

    Epigenetic mechanisms such as promoter methylation affect gene expression by inducing changes in organizational structure of chromatin rather than in the DNA sequence. Increased methylation of cytosine within cystosine-guanine (CpG) dinucleotides that are located at higher density in gene promoter

  5. Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

    DEFF Research Database (Denmark)

    Riising, Eva Madi; Vacher-Comet, Itys; Leblanc, Benjamin Olivier

    2014-01-01

    -wide ectopic PRC2 recruitment to endogenous PcG target genes found in other tissues. PRC2 binding analysis shows that it is restricted to nucleosome-free CpG islands (CGIs) of untranscribed genes. Our results show that it is the transcriptional state that governs PRC2 binding, and we propose that it binds...

  6. On the role of sensory feedbacks in Rowat-Selverston CPG to improve robot legged locomotion

    Directory of Open Access Journals (Sweden)

    Elmira eAmrollah

    2010-12-01

    Full Text Available This paper presents the use of Rowat and Selverston-type of CPG to control locomotion. It focuses on the role of afferent exteroceptive and proprioceptive signals in the dynamic phase synchronization in CPG legged robots. The sensori-motor neural network architecture is evaluated to control a two-joint planar robot leg that slips on a rail. Then, the closed loop between the CPG and the mechanical system allows to study the modulation of rhythmic patterns and the effect of the sensing loop via sensory neurons during the locomotion task. Firstly simulations show that the proposed architecture easily allows to modulate rhythmic patterns of the leg, and therefore the velocity of the robot. Secondly, simulations show that sensori-feedbacks from foot/ground contact of the leg make the hip velocity smoother and larger. The results show that the Rowat-Selverston-type CPG with sensory feedbacks is an effective choice for building adaptive Neural Central Pattern Generators for legged robots.

  7. AtMBD6, a methyl CpG binding domain protein, maintains gene ...

    Indian Academy of Sciences (India)

    DNA methylation, mediated by double-stranded RNA, is a conserved epigenetic phenomenon that protects a genome fromtransposons, silences unwanted genes and has a paramount function in plant or animal development. Methyl CpG bindingdomain proteins are members of a class of proteins that bind tomethylated ...

  8. High CpG island methylation of p16 gene and loss of p16 protein ...

    Indian Academy of Sciences (India)

    SI-JU GAO

    examined owning to the limitation of biopsies. Accordingly, future studies on the association of p16 methylation and ToF incidence are required. In conclusion, we detected a novel loss of p16 expression in ToF patients and showed that p16 loss correlates with CpG island methylation of p16 gene. For the first time, our study.

  9. Effect of CpG dinucleotides within IgH switch region repeats on immunoglobulin class switch recombination.

    Science.gov (United States)

    Zhang, Zheng Z; Hsieh, Chih-Lin; Okitsu, Cindy Yen; Han, Li; Yu, Kefei; Lieber, Michael R

    2015-08-01

    Immunoglobulin (Ig) heavy chains undergo class switch recombination (CSR) to change the heavy chain isotype from IgM to IgG, A or E. The switch regions are several kilobases long, repetitive, and G-rich on the nontemplate strand. They are also relatively depleted of CpG (also called CG) sites for unknown reasons. Here we use synthetic switch regions at the IgH switch alpha (Sα) locus to test the effect of CpG sites and to try to understand why the IgH switch sequences evolved to be relatively depleted of CpG. We find that even just two CpG sites within an 80 bp synthetic switch repeat iterated 15 times (total switch region length of 1200 bp containing 30 CpG sites) are sufficient to dramatically reduce both Ig CSR and transcription through the switch region from the upstream Iα sterile transcript promoter, which is the promoter that directs transcripts through the Sα region. De novo DNA methylation occurs at the four CpG sites in and around the Iα promoter when each 80 bp Iα switch repeat contains the two CpG sites. Thus, a relatively low density of CpG sites within the switch repeats can induce upstream CpG methylation at the IgH alpha locus, and cause a substantial decrease in transcription from the sterile transcript promoter. This effect is likely the reason that switch regions evolved to contain very few CpG sites. We discuss these findings as they relate to DNA methylation and to Ig CSR. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Polycomb-like proteins link the PRC2 complex to CpG islands

    Energy Technology Data Exchange (ETDEWEB)

    Li, Haojie; Liefke, Robert; Jiang, Junyi; Kurland, Jesse Vigoda; Tian, Wei; Deng, Pujuan; Zhang, Weidi; He, Qian; Patel, Dinshaw J.; Bulyk, Martha L.; Shi, Yang; Wang, Zhanxin

    2017-09-06

    The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression1,2 and has essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like (PCL) proteins, such as PHF1, MTF2 and PHF19, are PRC2-associated factors that form sub-complexes with PRC2 core components3, and have been proposed to modulate the enzymatic activity of PRC2 or the recruitment of PRC2 to specific genomic loci4,5,6,7,8,9,10,11,12,13. Mammalian PRC2-binding sites are enriched in CG content, which correlates with CpG islands that display a low level of DNA methylation14. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. Here we solve the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We show that the extended homologous regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a completely different manner from the canonical winged-helix DNA recognition motif. We also show that the PCL extended homologous domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic stem cells. Our research provides the first, to our knowledge, direct evidence to demonstrate that PCL proteins are crucial for PRC2 recruitment to CpG islands, and further clarifies the roles of these proteins in transcriptional regulation in vivo.

  11. In Ovo Delivery of CpG DNA Reduces Avian Infectious Laryngotracheitis Virus Induced Mortality and Morbidity

    Directory of Open Access Journals (Sweden)

    Simrika Thapa

    2015-04-01

    Full Text Available Endosomal toll-like receptor-21 and -9 sense CpG DNA activating production of pro-inflammatory mediators with antimicrobial effects. Here, we investigated the induction of antiviral response of in ovo delivered CpG DNA against infectious laryngotracheitis virus (ILTV infection. We found that in ovo delivered CpG DNA significantly reduces ILTV infection pre-hatch correlating with the expression of IL-1β and increase of macrophages in lungs. As assessed in vitro, CpG DNA stimulated avian macrophages could be a potential source of IL-1β and other pro-inflammatory mediators. Since we also found that in ovo CpG DNA delivery maintains increased macrophages in the lungs post-hatch, we infected the chickens on the day of hatch with ILTV. We found that in ovo delivered CpG DNA significantly reduces mortality and morbidity resulting from ILTV infection encountered post-hatch. Thus, CpG DNA can be a candidate innate immune stimulant worthy of further investigation for the control of ILTV infection in chickens.

  12. GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences.

    Science.gov (United States)

    Yu, Ning; Guo, Xuan; Zelikovsky, Alexander; Pan, Yi

    2017-05-24

    As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+C content is ≥ 50%, (b) the ratio of the observed CpG content and the expected CpG content is ≥ 0.6, and (c) the general length of CGI is greater than 200 nucleotides. Most existing computational methods for the prediction of CpG island are programmed on these rules. However, many experimentally verified CpG islands deviate from these artificial criteria. Experiments indicate that in many cases %G+C is thousand of nucleotides. It implies that CGI detection is not just a straightly statistical task and some unrevealed rules probably are hidden. A novel Gaussian model, GaussianCpG, is developed for detection of CpG islands on human genome. We analyze the energy distribution over genomic primary structure for each CpG site and adopt the parameters from statistics of Human genome. The evaluation results show that the new model can predict CpG islands efficiently by balancing both sensitivity and specificity over known human CGI data sets. Compared with other models, GaussianCpG can achieve better performance in CGI detection. Our Gaussian model aims to simplify the complex interaction between nucleotides. The model is computed not by the linear statistical method but by the Gaussian energy distribution and accumulation. The parameters of Gaussian function are not arbitrarily designated but deliberately chosen by optimizing the biological statistics. By using the pseudopotential analysis on CpG islands, the novel model is validated on both the real and artificial data sets.

  13. Expression of metastasis suppressor gene AES driven by a Yin Yang (YY) element in a CpG island promoter and transcription factor YY2.

    Science.gov (United States)

    Kakizaki, Fumihiko; Sonoshita, Masahiro; Miyoshi, Hiroyuki; Itatani, Yoshiro; Ito, Shinji; Kawada, Kenji; Sakai, Yoshiharu; Taketo, M Mark

    2016-11-01

    We recently found that the product of the AES gene functions as a metastasis suppressor of colorectal cancer (CRC) in both humans and mice. Expression of amino-terminal enhancer of split (AES) protein is significantly decreased in liver metastatic lesions compared with primary colon tumors. To investigate its downregulation mechanism in metastases, we searched for transcriptional regulators of AES in human CRC and found that its expression is reduced mainly by transcriptional dysregulation and, in some cases, by additional haploidization of its coding gene. The AES promoter-enhancer is in a typical CpG island, and contains a Yin-Yang transcription factor recognition sequence (YY element). In human epithelial cells of normal colon and primary tumors, transcription factor YY2, a member of the YY family, binds directly to the YY element, and stimulates expression of AES. In a transplantation mouse model of liver metastases, however, expression of Yy2 (and therefore of Aes) is downregulated. In human CRC metastases to the liver, the levels of AES protein are correlated with those of YY2. In addition, we noticed copy-number reduction for the AES coding gene in chromosome 19p13.3 in 12% (5/42) of human CRC cell lines. We excluded other mechanisms such as point or indel mutations in the coding or regulatory regions of the AES gene, CpG methylation in the AES promoter enhancer, expression of microRNAs, and chromatin histone modifications. These results indicate that Aes may belong to a novel family of metastasis suppressors with a CpG-island promoter enhancer, and it is regulated transcriptionally. © 2016 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  14. Intratracheal synthetic CpG oligodeoxynucleotide causes acute lung injury with systemic inflammatory response

    Directory of Open Access Journals (Sweden)

    Hasegawa Naoki

    2009-09-01

    Full Text Available Abstract Bacterial genome is characterized by frequent unmethylated cytosine-phosphate-guanine (CpG motifs. Deleterious effects can occur when synthetic oligodeoxynucleotides (ODN with unmethylated CpG dinucleotides (CpG-ODN are administered in a systemic fashion. We aimed to evaluate the effect of intratracheal CpG-ODN on lung inflammation and systemic inflammatory response. C57BL/6J mice received intratracheal administration of CpG-ODN (0.01, 0.1, 1.0, 10, or 100 μM or control ODN without CpG motif. Bronchoalveolar lavage (BAL fluid was obtained 3 or 6 h or 1, 2, 7, or 14 days after the instillation and subjected to a differential cell count and cytokine measurement. Lung permeability was evaluated as the BAL fluid-to-plasma ratio of the concentration of human serum albumin that was injected 1 h before euthanasia. Nuclear factor (NF-κB DNA binding activity was also evaluated in lung homogenates. Intratracheal administration of 10 μM or higher concentration of CpG-ODN induced significant inflammatory cell accumulation into the airspace. The peak accumulation of neutrophils and lymphocytes occurred 1 and 2 days after the CpG-ODN administration, respectively. Lung permeability was increased 1 day after the 10 μM CpG-ODN challenge. CpG-ODN also induced nuclear translocation of NF-κB and upregulation of various inflammatory cytokines in BAL fluid and plasma. Histopathology of the lungs and liver revealed acute lung injury and liver damage with necrosis, respectively. Control ODN without CpG motif did not induce any inflammatory change. Since intratracheal CpG-ODN induced acute lung injury as well as systemic inflammatory response, therapeutic strategies to neutralize bacterial DNA that is released after administration of bactericidal agents should be considered.

  15. Methylation Linear Discriminant Analysis (MLDA for identifying differentially methylated CpG islands

    Directory of Open Access Journals (Sweden)

    Vass J Keith

    2008-08-01

    Full Text Available Abstract Background Hypermethylation of promoter CpG islands is strongly correlated to transcriptional gene silencing and epigenetic maintenance of the silenced state. As well as its role in tumor development, CpG island methylation contributes to the acquisition of resistance to chemotherapy. Differential Methylation Hybridisation (DMH is one technique used for genome-wide DNA methylation analysis. The study of such microarray data sets should ideally account for the specific biological features of DNA methylation and the non-symmetrical distribution of the ratios of unmethylated and methylated sequences hybridised on the array. We have therefore developed a novel algorithm tailored to this type of data, Methylation Linear Discriminant Analysis (MLDA. Results MLDA was programmed in R (version 2.7.0 and the package is available at CRAN 1. This approach utilizes linear regression models of non-normalised hybridisation data to define methylation status. Log-transformed signal intensities of unmethylated controls on the microarray are used as a reference. The signal intensities of DNA samples digested with methylation sensitive restriction enzymes and mock digested are then transformed to the likelihood of a locus being methylated using this reference. We tested the ability of MLDA to identify loci differentially methylated as analysed by DMH between cisplatin sensitive and resistant ovarian cancer cell lines. MLDA identified 115 differentially methylated loci and 23 out of 26 of these loci have been independently validated by Methylation Specific PCR and/or bisulphite pyrosequencing. Conclusion MLDA has advantages for analyzing methylation data from CpG island microarrays, since there is a clear rational for the definition of methylation status, it uses DMH data without between-group normalisation and is less influenced by cross-hybridisation of loci. The MLDA algorithm successfully identified differentially methylated loci between two classes of

  16. 48 CFR 609.404 - Excluded parties list system.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Excluded parties list system. 609.404 Section 609.404 Federal Acquisition Regulations System DEPARTMENT OF STATE COMPETITION... Excluded parties list system. A/OPE shall accomplish the agency responsibilities prescribed in FAR 9.404(c...

  17. 20 CFR 404.1313 - World War II service excluded.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false World War II service excluded. 404.1313... DISABILITY INSURANCE (1950- ) Wage Credits for Veterans and Members of the Uniformed Services World War II Veterans § 404.1313 World War II service excluded. Your service was not in the active service of the United...

  18. 8 CFR 1241.20 - Aliens ordered excluded.

    Science.gov (United States)

    2010-01-01

    ... 8 Aliens and Nationality 1 2010-01-01 2010-01-01 false Aliens ordered excluded. 1241.20 Section 1241.20 Aliens and Nationality EXECUTIVE OFFICE FOR IMMIGRATION REVIEW, DEPARTMENT OF JUSTICE IMMIGRATION REGULATIONS APPREHENSION AND DETENTION OF ALIENS ORDERED REMOVED Deportation of Excluded Aliens...

  19. The Value of the Right to Exclude: An Empirical Assessment

    NARCIS (Netherlands)

    J.M. Klick (Jonathan); G. Parchomovsky (Gideon)

    2016-01-01

    markdownabstractProperty theorists have long deemed the right to exclude fundamental and essential for the efficient use and allocation of property. Recently, however, proponents of the progressive property movement have called into question the centrality of the right to exclude, suggesting that it

  20. Dynamic Modelling of a CPG-Controlled Amphibious Biomimetic Swimming Robot

    Directory of Open Access Journals (Sweden)

    Rui Ding

    2013-04-01

    Full Text Available This paper focuses on the modelling and control problems of a self-propelled, multimodal amphibious robot. Inspired by the undulatory body motions of fish and dolphins, the amphibious robot propels itself underwater by oscillations of several modular fish-like propelling units coupled with a pair of pectoral fins capable of non-continuous 360 degree rotation. In order to mimic fish-like undulating propulsion, a control architecture based on Central Pattern Generator (CPG is applied to the amphibious robot for robust swimming gaits, including forward and backward swimming and turning, etc. With the simplification of the robot as a multi-link serial mechanism, a Lagrangian function is employed to establish the hydrodynamic model for steady swimming. The CPG motion control law is then imported into the Lagrangian-based dynamic model, where an associated system of kinematics and dynamics is formed to solve real-time movements and, further, to guide the exploration of the CPG parameters and steady locomotion gaits. Finally, comparative results between the simulations and experiments are provided to show the effectiveness of the built control models.

  1. Genome-wide DNA Methylation Profiling of CpG Islands in Hypospadias

    Science.gov (United States)

    Choudhry, Shweta; Deshpande, Archana; Qiao, Liang; Beckman, Kenneth; Sen, Saunak; Baskin, Laurence S.

    2013-01-01

    Purpose Hypospadias is one of the most frequent genital malformations in the male newborn, and results from abnormal penile and urethral development. The etiology of hypospadias remains largely unknown despite intensive investigations. Fetal androgens have a crucial role in genital differentiation. Recent studies have suggested that molecular mechanisms that underlie the effects of androgens on the fetus may involve disruption of epigenetic programming of gene expression during development. We assessed whether epigenetic modification of DNA methylation is associated with hypospadias in a case-control study of 12 hypospadias and 8 control subjects. Materials and Methods Genome-wide DNA methylation profiling was performed on the study subjects using the Illumina Infinium® HumanMethylation450 Bead-Chip, which enables the direct investigation of methylation status of more than 485,000 individual CpG sites throughout the genome. The methylation level at each CpG site was compared between cases and controls using the t test and logistic regression. Results We identified 14 CpG sites that were associated with hypospadias with p hypospadias using a unique and novel epigenetic approach. Our findings suggest DNA methylation patterns are useful in identifying new genes such as SCARB1 and MYBPH that may be involved in the etiology of hypospadias. PMID:22906644

  2. CpG DNA: A pathogenic factor in systemic lupus erythematosus?

    Energy Technology Data Exchange (ETDEWEB)

    Krieg, A.M. [Univ. of Iowa College of Medicine, Iowa City, IA (United States)

    1995-11-01

    Systemic lupus erythematosus (SLE) is a multifactorial disease of unknown etiology. Characteristic features of SLE include (1) polyclonal B cell activation, (2) overexpression of the immune stimulatory cytokine interleukin-6 (IL-6), (3) defective tolerance to self antigens, and (4) production of anti-DNA antibodies (Ab). Bacterial infection has been suspected as a triggering factor for lupus. Bacterial DNA differs from vertebrate DNA in the frequency and methylation of CpG dinucleotides. These CpG motifs in bacterial DNA induce a variety of immune effects, including (1) polyclonal activation of murine and human B cells, (2) IL-6 secretion, and (3) resistance to apoptosis, thereby potentially allowing the survival of autoreactive cells. These results suggest that microbial DNA could therefore be a pathogenic factor in SLE. SLE patients have elevated levels of circulating plasma DNA which is reportedly enriched in hypomethylated CpGs. Genomic DNA is also hypomethylated in SLE. The purpose of this review is to summarize the immune effects of CpG motifs and to present the evidence for their possible involvement in the pathogenesis of SLE. 77 refs.

  3. A novel CpG island set identifies tissue-specific methylation at developmental gene loci.

    Directory of Open Access Journals (Sweden)

    Robert Illingworth

    2008-01-01

    Full Text Available CpG islands (CGIs are dense clusters of CpG sequences that punctuate the CpG-deficient human genome and associate with many gene promoters. As CGIs also differ from bulk chromosomal DNA by their frequent lack of cytosine methylation, we devised a CGI enrichment method based on nonmethylated CpG affinity chromatography. The resulting library was sequenced to define a novel human blood CGI set that includes many that are not detected by current algorithms. Approximately half of CGIs were associated with annotated gene transcription start sites, the remainder being intra- or intergenic. Using an array representing over 17,000 CGIs, we established that 6%-8% of CGIs are methylated in genomic DNA of human blood, brain, muscle, and spleen. Inter- and intragenic CGIs are preferentially susceptible to methylation. CGIs showing tissue-specific methylation were overrepresented at numerous genetic loci that are essential for development, including HOX and PAX family members. The findings enable a comprehensive analysis of the roles played by CGI methylation in normal and diseased human tissues.

  4. Electrophysiological representation of scratching CpG activity in the cerebellum.

    Directory of Open Access Journals (Sweden)

    Lourdes Martínez-Silva

    Full Text Available We analyzed the electrical activity of neuronal populations in the cerebellum and the lumbar spinal cord during fictive scratching in adult decerebrate cats before and after selective sections of the Spino-Reticulo Cerebellar Pathway (SRCP and the Ventral-Spino Cerebellar Tract (VSCT. During fictive scratching, we found a conspicuous sinusoidal electrical activity, called Sinusoidal Cerebellar Potentials (SCPs, in the cerebellar vermis, which exhibited smaller amplitude in the paravermal and hemisphere cortices. There was also a significant spino-cerebellar coherence between these SCPs and the lumbar sinusoidal cord dorsum potentials (SCDPs. However, during spontaneous activity such spino-cerebellar coherence between spontaneous potentials recorded in the same regions decreased. We found that the section of the SRCP and the VSCT did not abolish the amplitude of the SCPs, suggesting that there are additional pathways conveying information from the spinal CPG to the cerebellum. This is the first evidence that the sinusoidal activity associated to the spinal CPG circuitry for scratching has a broad representation in the cerebellum beyond the sensory representation from hindlimbs previously described. Furthermore, the SCPs represent the global electrical activity of the spinal CPG for scratching in the cerebellar cortex.

  5. Humanoids Learning to Walk: a Natural CPG-Actor-Critic Architecture

    Directory of Open Access Journals (Sweden)

    CAI eLI

    2013-04-01

    Full Text Available The identification of learning mechanisms for locomotion has been the subject of much researchfor some time but many challenges remain. Dynamic systems theory (DST offers a novel approach to humanoid learning through environmental interaction. Reinforcement learning (RL has offered a promising method to adaptively link the dynamic system to the environment it interacts with via a reward-based value system.In this paper, we propose a model that integrates the above perspectives and applies it to the case of a humanoid (NAO robot learning to walk the ability of which emerges from its value-based interaction with the environment. In the model,a simplified central pattern generator (CPG architecture inspired by neuroscientific research and DST is integrated with an actor-critic approach to RL (cpg-actor-critic. In the cpg-actor-critic architecture, least-square-temporal-difference (LSTD based learning converges to the optimal solution quickly by using natural gradient and balancing exploration and exploitation. Futhermore, rather than using a traditional (designer-specified reward it uses a dynamic value function as a stability indicator (SI that adapts to the environment.The results obtained are analyzed and explained by using a novel DST embodied cognition approach. Learning to walk, from this perspective, is a process of integrating sensorimotor levels and value.

  6. Humanoids Learning to Walk: A Natural CPG-Actor-Critic Architecture.

    Science.gov (United States)

    Li, Cai; Lowe, Robert; Ziemke, Tom

    2013-01-01

    The identification of learning mechanisms for locomotion has been the subject of much research for some time but many challenges remain. Dynamic systems theory (DST) offers a novel approach to humanoid learning through environmental interaction. Reinforcement learning (RL) has offered a promising method to adaptively link the dynamic system to the environment it interacts with via a reward-based value system. In this paper, we propose a model that integrates the above perspectives and applies it to the case of a humanoid (NAO) robot learning to walk the ability of which emerges from its value-based interaction with the environment. In the model, a simplified central pattern generator (CPG) architecture inspired by neuroscientific research and DST is integrated with an actor-critic approach to RL (cpg-actor-critic). In the cpg-actor-critic architecture, least-square-temporal-difference based learning converges to the optimal solution quickly by using natural gradient learning and balancing exploration and exploitation. Futhermore, rather than using a traditional (designer-specified) reward it uses a dynamic value function as a stability indicator that adapts to the environment. The results obtained are analyzed using a novel DST-based embodied cognition approach. Learning to walk, from this perspective, is a process of integrating levels of sensorimotor activity and value.

  7. Activation of foal neutrophils at different ages by CpG oligodeoxynucleotides and Rhodococcus equi.

    Science.gov (United States)

    Liu, Mei; Liu, Tong; Bordin, Angela; Nerren, Jessica; Cohen, Noah

    2009-12-01

    Toll-like receptor 9 (TLR9) activation stimulates protective immune responses against intracellular pathogens by phagocytes, including neutrophils. This study examined TLR9-mediated neutrophil activation in neonatal foals. Unmethylated CpGs, ligands for TLR9, were used to stimulate equine neutrophils, either purified or in contact with other peripheral blood leukocytes. Rhodococcus equi was used as another stimulus in parallel. TLR9 mRNA was constitutively expressed at a similar level in purified equine neutrophils across different ages from birth to adulthood, and expression was not affected by either CpG or R. equi. Purified foal neutrophils were directly sensitive to CpG stimulation, reflected by enhanced reactive oxygen species generation following fMLP stimulation, and by expressing significantly (Pfoal neutrophils stimulated by R. equi showed significantly (Pfoal neutrophils were significantly (Pfoal neutrophils at birth, R. equi significantly (Pfoal neutrophils were sensitive to CpG or R. equi activation as early as at birth, and that B-class CpGs enhanced foal neutrophil functions in vitro.

  8. Orphan CpG islands define a novel class of highly active enhancers.

    Science.gov (United States)

    Bell, Joshua S K; Vertino, Paula M

    2017-06-03

    CpG islands (CGI) are critical genomic regulatory elements that support transcriptional initiation and are associated with the promoters of most human genes. CGI are distinguished from the bulk genome by their high CpG density, lack of DNA methylation, and euchromatic features. While CGI are canonically known as strong promoters, thousands of 'orphan' CGI lie far from any known transcript, leaving their function an open question. We undertook a comprehensive analysis of the epigenetic state of orphan CGI across over 100 cell types. Here we show that most orphan CGI display the chromatin features of active enhancers (H3K4me1, H3K27Ac) in at least one cell type. Relative to classical enhancers, these enhancer CGI (ECGI) are stronger, as gauged by chromatin state and in functional assays, are more broadly expressed, and are more highly conserved. Likewise, ECGI engage in more genomic contacts and are enriched for transcription factor binding relative to classical enhancers. In human cancers, these epigenetic differences between ECGI vs. classical enhancers manifest in distinct alterations in DNA methylation. Thus, ECGI define a class of highly active enhancers, strengthened by the broad transcriptional activity, CpG density, hypomethylation, and chromatin features they share with promoter CGI. In addition to indicating a role for thousands of orphan CGI, these findings suggests that enhancer activity may be an intrinsic function of CGI in general and provides new insights into the evolution of enhancers and their epigenetic regulation during development and tumorigenesis.

  9. Gene silencing of Nox4 by CpG island methylation during hepatocarcinogenesis in rats

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    Guadalupe S. López-Álvarez

    2017-01-01

    Full Text Available The association between the downregulation of genes and DNA methylation in their CpG islands has been extensively studied as a mechanism that favors carcinogenesis. The objective of this study was to analyze the methylation of a set of genes selected based on their microarray expression profiles during the process of hepatocarcinogenesis. Rats were euthanized at: 24 h, 7, 11, 16 and 30 days and 5, 9, 12 and 18 months post-treatment. We evaluated the methylation status in the CpG islands of four deregulated genes (Casp3, Cldn1, Pex11a and Nox4 using methylation-sensitive high-resolution melting technology for the samples obtained from different stages of hepatocarcinogenesis. We did not observe methylation in Casp3, Cldn1 or Pex11a. However, Nox4 exhibited altered methylation patterns, reaching a maximum of 10%, even during the early stages of hepatocarcinogenesis. We observed downregulation of mRNA and protein of Nox4 (97.5% and 40%, respectively after the first carcinogenic stimulus relative to the untreated samples. Our results suggest that Nox4 downregulation is associated with DNA methylation of the CpG island in its promoter. We propose that methylation is a mechanism that can silence the expression of Nox4, which could contribute to the acquisition of neoplastic characteristics during hepatocarcinogenesis in rats.

  10. The Effect of TLR9 Agonist CpG Oligodeoxynucleotides on the Intestinal Immune Response of Cobia (Rachycentron canadum

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    Omkar Byadgi

    2014-01-01

    Full Text Available Cytosine-guanine oligodeoxynucleotide (CpG ODN motifs of bacterial DNA are recognized through toll-like receptor 9 (TLR9 and are potent activators of innate immunity. However, the interaction between TLR9 and CpG ODN in aquatic species has not been well characterized. Hence, cobia TLR9 isoform B (RCTLR9B was cloned and its expression and induction in intestine were investigated. RCTLR9B cDNA consists of 3113bp encoding 1009 amino acids containing three regions, leucine rich repeats, transmembrane domain, and toll/interleukin-1 receptor (TIR domain. Intraperitoneal injection of CpG ODN 2395 upregulated RCTLR9 A and B and MyD88 and also induced the expressions of Mx, chemokine CC, and interleukin IL-1β. Cobia intraperitoneally injected with CpG ODN 1668 and 2395 had increased survival rates after challenge with Photobacterium damselae subsp. piscicida. In addition, formulation of CpG ODN with formalin-killed bacteria (FKB and aluminum hydroxide gel significantly increased expressions of RCTLR9 A (50 folds and B (30 folds isoforms at 10 dpi (CpG ODN 1668 and MyD88 (21 folds at 6 dpv (CpG ODN 2395. Subsequently, IL-1β increased at 6 dpv in 1668 group. No histopathological damage and inflammatory responses were observed in the injected cobia. Altogether, these results facilitate CpG ODNs as an adjuvant to increase bacterial disease resistance and efficacy of vaccines in cobia.

  11. Single CpG site methylation controls estrogen receptor gene transcription and correlates with hormone therapy resistance.

    Science.gov (United States)

    Tsuboi, Kouki; Nagatomo, Takamasa; Gohno, Tatsuyuki; Higuchi, Toru; Sasaki, Shunta; Fujiki, Natsu; Kurosumi, Masafumi; Takei, Hiroyuki; Yamaguchi, Yuri; Niwa, Toshifumi; Hayashi, Shin-Ichi

    2017-07-01

    Hormone therapy is the most effective treatment for patients with estrogen receptor α-positive breast cancers. However, although resistance occurs during treatment in some cases and often reflects changed estrogen receptor α status, the relationship between changes in estrogen receptor α expression and resistance to therapy are poorly understood. In this study, we identified a mechanism for altered estrogen receptor α expression during disease progression and acquired hormone therapy resistance in aromatase inhibitor-resistant breast cancer cell lines. Subsequently, we investigated promoter switching and DNA methylation status of the estrogen receptor α promoter, and found marked changes of methylation at a single CpG site (CpG4) in resistant cells. In addition, luciferase reporter assays showed reduced transcriptional activity from this methylated CpG site. This CpG region was also completely conserved among species, suggesting that it acts as a methylation-sensitive Ets-2 transcription factor binding site, as confirmed using chromatin immunoprecipitation assays. In estrogen receptor α-positive tumors, CpG4 methylation levels were inversely correlated with estrogen receptor α expression status, suggesting that single CpG site plays an important role in the regulation of estrogen receptor α transcription. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Evaluation of infection course in mice induced by L. major in presence of positively charged liposomes containing CpG ODN

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    Hesamoddin Hoseinjani

    2013-01-01

    Full Text Available Abstract An inoculation of virulent Leishmania major is known as leishmanization (LZ which is proven to be the most effective control measure against Cutaneous Leishmaniasis (CL. However, using LZ is restricted due to various side effects such as uncontrolled lesion development. In the present research, the efficacy of cationic nanoliposomes containing CpG oligodeoxynucleotides (CpG ODN as an improved adjuvant delivery system was studied to diminish the lesion development and infection course of L. major after inoculation into the mice. BALB/c mice were inoculated subcutaneously (SC with L. major plus empty DSPC, DSPC (CpG ODN, DSPC (Non CpG ODN, empty DMPC, DMPC (CpG ODN, DMPC (Non CpG ODN or HEPES buffer. The results showed that group of mice received DMPC (CpG ODN nanoliposomes developed a significantly smaller lesion and showed minimum number of L. major in the spleen and draining lymph nodes. In addition, using DMPC (CpG ODN liposomes resulted in a Th1 type of immune response with a preponderance of IgG2a isotype which is concurrent with the production of DMPC (CpG induced IFN-γ in the spleen of the mice. Taken together, the results suggested that immune modulation using DMPC (CpG ODN nanoliposomes might be a practical approach to improve the safety of LZ

  13. Office of Inspector General List of Excluded Individuals and Entities

    Data.gov (United States)

    U.S. Department of Health & Human Services — The objective is to ensure that providers who bill Federal health care programs do not submit claims for services furnished, ordered or prescribed by an excluded...

  14. Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin.

    Science.gov (United States)

    Bina, Minou; Wyss, Phillip; Novorolsky, Elise; Zulkelfi, Noorfatin; Xue, Jing; Price, Randi; Fay, Matthew; Gutmann, Zach; Fogler, Brian; Wang, Daidong

    2013-12-28

    Mixed Lineage Leukemia 1 (MLL1) is a mammalian ortholog of the Drosophila Trithorax. In Drosophila, Trithorax complexes transmit the memory of active genes to daughter cells through interactions with Trithorax Response Elements (TREs). However, despite their functional importance, nothing is known about sequence features that may act as TREs in mammalian genomic DNA. By analyzing results of reported DNA binding assays, we identified several CpG rich motifs as potential MLL1 binding units (defined as morphemes). We find that these morphemes are dispersed within a relatively large collection of human promoter sequences and appear densely packed near transcription start sites of protein-coding genes. Genome wide analyses localized frequent morpheme occurrences to CpG islands. In the human HOX loci, the morphemes are spread across CpG islands and in some cases tail into the surrounding shores and shelves of the islands. By analyzing results of chromatin immunoprecipitation assays, we found a connection between morpheme occurrences, CpG islands, and chromatin segments reported to be associated with MLL1. Furthermore, we found a correspondence of reported MLL1-driven "bookmarked" regions in chromatin to frequent occurrences of MLL1 morphemes in CpG islands. Our results implicate the MLL1 morphemes in sequence-features that define the mammalian TREs and provide a novel function for CpG islands. Apparently, our findings offer the first evidence for existence of potential TREs in mammalian genomic DNA and the first evidence for a connection between CpG islands and gene-bookmarking by MLL1 to transmit the memory of highly active genes during mitosis. Our results further suggest a role for overlapping morphemes in producing closely packed and multiple MLL1 binding events in genomic DNA so that MLL1 molecules could interact and reside simultaneously on extended potential transcriptional maintenance elements in human chromosomes to transmit the memory of highly active genes

  15. Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved.

    Science.gov (United States)

    Long, Hannah K; King, Hamish W; Patient, Roger K; Odom, Duncan T; Klose, Robert J

    2016-08-19

    DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. CpG adjuvant enhances the mucosal immunogenicity and efficacy of a Treponema pallidum DNA vaccine in rabbits.

    Science.gov (United States)

    Zhao, Feijun; Liu, Shuangquan; Zhang, Xiaohong; Yu, Jian; Zeng, Tiebing; Gu, Weiming; Cao, Xunyu; Chen, Xi; Wu, Yimou

    2013-04-01

    The protective response against Treponema pallidum (Tp) infection of a DNA vaccine enhanced by an adjuvant CpG ODN was investigated. The mucosal adjuvant CpG ODN enhanced the production of higher levels of anti-TpGpd antibodies induced by pcD/Gpd-IL-2 in rabbits. It also resulted in higher levels of secretion of IL-2 and IFN-γ, and facilitated T cell proliferation and differentiation (p0.05). Furthermore, CpG ODN stimulated the production of mucosa-specific anti-sIgA antibodies and resulted in the lowest Tp-positive rate (6.7%) for Tp-infection of skin lesions and the lowest rates (8.3%) of ulceration lesions, thus achieving better protective effects. New Zealand rabbits were immunized with the eukaryotic vector encoding recombinant pcD/Gpd-IL-2 using intramuscular multi-injection or together with mucosal enhancement via a nasal route. The effect of the mucosal adjuvant CpG ODN was examined. The CpG ODN adjuvant significantly enhances the humoral and cellular immune effects of the immunization by pcD/Gpd-IL-2 with mucosal enhancement via nasal route. It also stimulates strong mucosal immune effects, thus initiating more efficient immune-protective effects.

  17. Gold nanoparticle delivery of modified CpG stimulates macrophages and inhibits tumor growth for enhanced immunotherapy.

    Directory of Open Access Journals (Sweden)

    Adam Yuh Lin

    Full Text Available Gold nanoparticle accumulation in immune cells has commonly been viewed as a side effect for cancer therapeutic delivery; however, this phenomenon can be utilized for developing gold nanoparticle mediated immunotherapy. Here, we conjugated a modified CpG oligodeoxynucleotide immune stimulant to gold nanoparticles using a simple and scalable self-assembled monolayer scheme that enhanced the functionality of CpG in vitro and in vivo. Nanoparticles can attenuate systemic side effects by enhancing CpG delivery passively to innate effector cells. The use of a triethylene glycol (TEG spacer on top of the traditional poly-thymidine spacer increased CpG macrophage stimulatory effects without sacrificing DNA content on the nanoparticle, which directly correlates to particle uptake. In addition, the immune effects of modified CpG-AuNPs were altered by the core particle size, with smaller 15 nm AuNPs generating maximum immune response. These TEG modified CpG-AuNP complexes induced macrophage and dendritic cell tumor infiltration, significantly inhibited tumor growth, and promoted survival in mice when compared to treatments with free CpG.

  18. Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation.

    Science.gov (United States)

    Kamalakaran, Sitharthan; Kendall, Jude; Zhao, Xiaoyue; Tang, Chunlao; Khan, Sohail; Ravi, Kandasamy; Auletta, Theresa; Riggs, Michael; Wang, Yun; Helland, Aslaug; Naume, Bjørn; Dimitrova, Nevenka; Børresen-Dale, Anne-Lise; Hicks, Jim; Lucito, Robert

    2009-07-01

    Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25,000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter-associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species.

  19. Clinical application of CpG-, non-CpG-, and antisense oligodeoxynucleotides as immunomodulators.

    Science.gov (United States)

    Dorn, Annette; Kippenberger, Stefan

    2008-02-01

    Cytosine-phosphate-guanosine (CpG) motifs, found mainly in bacterial DNA, have immunostimulatory effects in humans and have offered new perspectives in the treatment of clinical conditions, including viral and bacterial infections, vaccination, allergy and asthma, and in antitumor therapy. Three classes of CpG-oligodeoxynucleotides (ODNs), CpG-A, -B, and -C, with distinct biological properties and which differ in their sequence and nucleotide backbone, have been characterized. Typically, CpG-ODNs bind to TLR9 in the endosomal compartment and initiate a signaling cascade that leads to activation of proinflammatory transcription factors such as NFkappaB. In addition, non-CpG-ODNs have been shown to modulate the immune system and, although these molecules are devoid of CpG motifs, their biological action appears to require a functional TLR9. In this review, advances in the clinical therapy and prevention of infectious diseases using ODNs, as well as the use of antisense ODNs that specifically target genes and control exaggerated immune responses, are discussed. In addition, an update of selected ODNs that have entered clinical trials is provided.

  20. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos.

    Science.gov (United States)

    Smallwood, Sébastien A; Tomizawa, Shin-Ichi; Krueger, Felix; Ruf, Nico; Carli, Natasha; Segonds-Pichon, Anne; Sato, Shun; Hata, Kenichiro; Andrews, Simon R; Kelsey, Gavin

    2011-06-26

    Elucidating how and to what extent CpG islands (CGIs) are methylated in germ cells is essential to understand genomic imprinting and epigenetic reprogramming. Here we present, to our knowledge, the first integrated epigenomic analysis of mammalian oocytes, identifying over a thousand CGIs methylated in mature oocytes. We show that these CGIs depend on DNMT3A and DNMT3L but are not distinct at the sequence level, including in CpG periodicity. They are preferentially located within active transcription units and are relatively depleted in H3K4me3, supporting a general transcription-dependent mechanism of methylation. Very few methylated CGIs are fully protected from post-fertilization reprogramming but, notably, the majority show incomplete demethylation in embryonic day (E) 3.5 blastocysts. Our study shows that CGI methylation in gametes is not entirely related to genomic imprinting but is a strong factor in determining methylation status in preimplantation embryos, suggesting a need to reassess mechanisms of post-fertilization demethylation.

  1. CpG Motifs in Porphyromonas gingivalis DNA Stimulate Interleukin-6 Expression in Human Gingival Fibroblasts

    Science.gov (United States)

    Takeshita, Akira; Imai, Kenichi; Hanazawa, Shigemasa

    1999-01-01

    We suggest here that Porphyromonas gingivalis DNA may function as a virulence factor in periodontal disease through expression of inflammatory cytokine. The bacterial DNA markedly stimulated in a dose-dependent manner interleukin-6 (IL-6) production by human gingival fibroblasts. The stimulatory action was eliminated by treatment with DNase but not RNase. The stimulatory effect was not observed in the fibroblasts treated with eucaryotic DNAs. The bacterial DNA also stimulated in dose- and treatment time-dependent manners the expression of the IL-6 gene in the cells. In addition, the stimulatory effect was eliminated when the DNA was methylated with CpG motif methylase. Interestingly, a 30-base synthetic oligonucleotide containing the palindromic motif GACGTC could stimulate expression of the IL-6 gene and production of its protein in the cells. Furthermore, the synthetic oligonucleotide-induced expression of this cytokine gene was blocked by pyrrolidine dithiocarbamate and N-acetyl-l-cystine, potent inhibitors of transcriptional factor NF-κB. Gel mobility shift assay showed increased binding of NF-κB to its consensus sequence in the synthetic oligonucleotide-treated cells. Also, using specific antibody against p50 and p65, which compose NF-κB, we showed the consensus sequence-binding proteins to be NF-κB. These results are the first to demonstrate that the internal CpG motifs in P. gingivalis DNA stimulate IL-6 expression in human gingival fibroblasts via stimulation of NF-κB. PMID:10456872

  2. Frequency Modulation and Spatiotemporal Stability of the sCPG in Preterm Infants with RDS

    Directory of Open Access Journals (Sweden)

    Steven M. Barlow

    2012-01-01

    Full Text Available The nonnutritive suck (NNS is an observable and accessible motor behavior which is often used to make inference about brain development and pre-feeding skill in preterm and term infants. The purpose of this study was to model NNS burst compression pressure dynamics in the frequency and time domain among two groups of preterm infants, including those with respiratory distress syndrome (RDS, N=15 and 17 healthy controls. Digitized samples of NNS compression pressure waveforms recorded at a 1-week interval were collected 15 minutes prior to a scheduled feed. Regression analysis and ANOVA revealed that healthy preterm infants produced longer NNS bursts and the mean burst initiation cycle frequencies were higher when compared to the RDS group. Moreover, the initial 5 cycles of the NNS burst manifest a frequency modulated (FM segment which is a significant feature of the suck central pattern generator (sCPG, and differentially expressed in healthy and RDS infants. The NNS burst structure revealed significantly lower spatiotemporal index values for control versus RDS preterm infants during FM, and provides additional information on the microstructure of the sCPG which may be used to gauge the developmental status and progression of oromotor control systems among these fragile infants.

  3. Nanopores suggest a negligible influence of CpG methylation on nucleosome packaging and stability.

    Science.gov (United States)

    Langecker, Martin; Ivankin, Andrey; Carson, Spencer; Kinney, Shannon R M; Simmel, Friedrich C; Wanunu, Meni

    2015-01-14

    Nucleosomes are the fundamental repeating units of chromatin, and dynamic regulation of their positioning along DNA governs gene accessibility in eukaryotes. Although epigenetic factors have been shown to influence nucleosome structure and dynamics, the impact of DNA methylation on nucleosome packaging remains controversial. Further, all measurements to date have been carried out under zero-force conditions. In this paper, we present the first automated force measurements that probe the impact of CpG DNA methylation on nucleosome stability. In solid-state nanopore force spectroscopy, a nucleosomal DNA tail is captured into a pore and pulled on with a time-varying electrophoretic force until unraveling is detected. This is automatically repeated for hundreds of nucleosomes, yielding statistics of nucleosome lifetime vs electrophoretic force. The force geometry, which is similar to displacement forces exerted by DNA polymerases and helicases, reveals that nucleosome stability is sensitive to DNA sequence yet insensitive to CpG methylation. Our label-free method provides high-throughput data that favorably compares with other force spectroscopy experiments and is suitable for studying a variety of DNA-protein complexes.

  4. FPGA implementation of a configurable neuromorphic CPG-based locomotion controller.

    Science.gov (United States)

    Barron-Zambrano, Jose Hugo; Torres-Huitzil, Cesar

    2013-09-01

    Neuromorphic engineering is a discipline devoted to the design and development of computational hardware that mimics the characteristics and capabilities of neuro-biological systems. In recent years, neuromorphic hardware systems have been implemented using a hybrid approach incorporating digital hardware so as to provide flexibility and scalability at the cost of power efficiency and some biological realism. This paper proposes an FPGA-based neuromorphic-like embedded system on a chip to generate locomotion patterns of periodic rhythmic movements inspired by Central Pattern Generators (CPGs). The proposed implementation follows a top-down approach where modularity and hierarchy are two desirable features. The locomotion controller is based on CPG models to produce rhythmic locomotion patterns or gaits for legged robots such as quadrupeds and hexapods. The architecture is configurable and scalable for robots with either different morphologies or different degrees of freedom (DOFs). Experiments performed on a real robot are presented and discussed. The obtained results demonstrate that the CPG-based controller provides the necessary flexibility to generate different rhythmic patterns at run-time suitable for adaptable locomotion. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Excluded-volume effects in the diffusion of hard spheres

    KAUST Repository

    Bruna, Maria

    2012-01-03

    Excluded-volume effects can play an important role in determining transport properties in diffusion of particles. Here, the diffusion of finite-sized hard-core interacting particles in two or three dimensions is considered systematically using the method of matched asymptotic expansions. The result is a nonlinear diffusion equation for the one-particle distribution function, with excluded-volume effects enhancing the overall collective diffusion rate. An expression for the effective (collective) diffusion coefficient is obtained. Stochastic simulations of the full particle system are shown to compare well with the solution of this equation for two examples. © 2012 American Physical Society.

  6. Increase in CpG DNA-induced inflammatory responses by DNA oxidation in macrophages and mice.

    Science.gov (United States)

    Yoshida, Hiroyuki; Nishikawa, Makiya; Kiyota, Tsuyoshi; Toyota, Hiroyasu; Takakura, Yoshinobu

    2011-07-15

    Unmethylated CpG dinucleotide (CpG motif) is involved in the exacerbation of DNA-associated autoimmune diseases. We investigated the effect of DNA containing 8-hydroxydeoxyguanosine (oxo-dG), a representative DNA biomarker for oxidative stress in the diseases, on CpG motif-dependent inflammatory responses. ODN1668 and ODN1720 were selected as CpG-DNA and non-CpG DNA, respectively. Deoxyguanosine in the CpG motif (G9) or outside the motif (G15) of ODN1668 was substituted with oxo-dG to obtain oxo(G9)-1668 and oxo(G15)-1668, respectively. Oxo(G15)-1668 induced a significantly higher amount of tumor necrosis factor (TNF)-α from RAW264.7 macrophage-like cells than ODN1668, whereas oxo(G9)-1668, oxo(G8)-1720, or oxo(G15)-1720 hardly did. CpG DNA-induced TNF-α production was significantly increased by addition of oxo(G8)-1720 or oxo(G15)-1720, but not of ODN1720. This oxo-dG-containing DNA-induced increase in TNF-α production was also observed in primary cultured macrophages isolated from wild-type mice, but not observed in those from Toll-like receptor (TLR)-9 knockout mice. In addition, TNF-α production by ligands for TLR3, TLR4, or TLR7 was not affected by oxo-dG-containing DNA. Then, the footpad swelling induced by subcutaneous injection of ODN1668 into mice was increased by coinjection with oxo(G8)-1720, but not with ODN1720. These results indicate that oxo-dG-containing DNA increases the CpG motif-dependent inflammatory responses, which would exacerbate DNA-related autoimmune diseases. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. General implications for CpG hot spot mutations: methylation patterns of the human iduronate-2-sulfatase gene locus.

    Science.gov (United States)

    Tomatsu, Shunji; Orii, Koji O; Bi, Y; Gutierrez, Monica A; Nishioka, Tatsuo; Yamaguchi, Seiji; Kondo, Naomi; Orii, Tadao; Noguchi, Akihiko; Sly, William S

    2004-06-01

    The methylation pattern at CpG sites of a housekeeping gene correlates with the likelihood of mutation. Mucopolysaccharidosis (MPS) type II, an X-linked disorder, results from the deficiency of iduronate-2-sulfatase (IDS). In these patients, over 35% of independent point mutations at the IDS gene locus were found at CpG sites as transitional events. To gain insight into the relationship between methylation status and CpG hot spot mutations, we investigated patterns of cytosine methylation in the entire IDS gene, except for introns 4-8. Bisulfite genomic sequencing was performed on the normal leukocyte DNA. Our data show that: 1) cytosine methylation at the CpG sites was extensive, except for those present from the promoter region to a portion of intron 3; 2) a sharp boundary of methylated-nonmethylated regions was observed at the 5'-flanking region, whereas a gradual change in methylation was observed in the 2.0-kb segment in the 3'-flanking region; 3) the boundary of the 5'-flanking region contained multiple Sp1 sites and the TATA box; 4) the CpG sites in exons 1 and 2 were hypomethylated and were associated only with rare transitional mutations, while the CpG sites in exon 3 were also hypomethylated, yet were associated with a high rate of transitional mutations; 5) there was no striking sex difference in the methylation patterns in active alleles; and, 6) the methylation in both strands was symmetrical, except at the boundary of methylated-unmethylated regions. Copyright 2004 Wiley-Liss, Inc.

  8. Prophylactic application of CpG oligonucleotides augments the early host response and confers protection in acute melioidosis.

    Directory of Open Access Journals (Sweden)

    Barbara M Judy

    Full Text Available Prophylactic administration of CpG oligodeoxynucleotides (CpG ODNs is known to confer protection against lethal sepsis caused by Burkholderia pseudomallei in the mouse model. The mechanisms whereby CpG regulates the innate immune response to provide protection against B. pseudomallei, however, are poorly characterized. In the present study, we demonstrate that intranasal treatment of mice with Class C CpG, results in recruitment of inflammatory monocytes and neutrophils to the lung at 48 h post-treatment. Mice infected with B. pseudomallei 48 h post-CpG treatment had reduced organ bacterial load and significantly altered cytokine and chemokine profiles concomitant with protection as compared to control animals. CpG administration reduced the robust production of chemokines and pro-inflammatory cytokines in blood, lung and spleen, observed following infection of non-treated animals. Death of control animals coincided with the time of peak cytokine production (day 1-3, while a moderate; sustained cytokine production in CpG-treated animals was associated with survival. In general, CpG treatment resulted in diminished expression of cytokines and chemokines post-infection, though IL-12p40 was released in larger quantities in CpG treated animals. In contrast to CpG-treated animals, the lungs of infected control animals were infiltrated with leukocytes, especially neutrophils, and large numbers of necrotic lesions were observed in lung sections. Therapeutic treatment of B. pseudomallei-infected animals with CpG at 24 h post-infection did not impact survival compared to control animals. In summary, protection of CpG-treated animals was associated with recruitment of inflammatory monocytes and neutrophils into the lungs prior to infection. These responses correspond with early control of bacterial growth, a dampened inflammatory cytokine/chemokine response, reduced lung pathology, and greatly increased survival. In contrast, a delay in recruitment of

  9. 5 CFR 2634.203 - Persons excluded by rule.

    Science.gov (United States)

    2010-01-01

    ... FINANCIAL DISCLOSURE, QUALIFIED TRUSTS, AND CERTIFICATES OF DIVESTITURE Persons Required To File Public Financial Disclosure Reports § 2634.203 Persons excluded by rule. (a) In general. Any individual or group of... not affect adversely the integrity of the Government or the public's confidence in the integrity of...

  10. 40 CFR 240.201 - Solid wastes excluded.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Solid wastes excluded. 240.201 Section 240.201 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES GUIDELINES FOR THE THERMAL PROCESSING OF SOLID WASTES Requirements and Recommended Procedures § 240.201 Solid...

  11. 42 CFR 412.25 - Excluded hospital units: Common requirements.

    Science.gov (United States)

    2010-10-01

    ... decreased at any time during a cost reporting period if the hospital notifies its fiscal intermediary and... chief medical officer of the hospital in which it is located. (B) It maintains admission and discharge... 42 Public Health 2 2010-10-01 2010-10-01 false Excluded hospital units: Common requirements. 412...

  12. 8 CFR 1240.38 - Fingerprinting of excluded aliens.

    Science.gov (United States)

    2010-01-01

    ... 8 Aliens and Nationality 1 2010-01-01 2010-01-01 false Fingerprinting of excluded aliens. 1240.38 Section 1240.38 Aliens and Nationality EXECUTIVE OFFICE FOR IMMIGRATION REVIEW, DEPARTMENT OF JUSTICE IMMIGRATION REGULATIONS PROCEEDINGS TO DETERMINE REMOVABILITY OF ALIENS IN THE UNITED STATES Exclusion of...

  13. The public space and the right to exclude

    Directory of Open Access Journals (Sweden)

    Verónica Urzúa Bastida

    2012-03-01

    Full Text Available This paper raises that the notion of «public space», as is currently used, legitimize, at the same time is the base of what might be called the right to exclude. This is not happening by law, but culture. To argue this, there will develop three ideas: comfort, planning and civic order, presents in the above mentioned notion.

  14. 26 CFR 1.410(b)-6 - Excludable employees.

    Science.gov (United States)

    2010-04-01

    ... section 861(a)(3)) is treated as an excludable employee. (2) Special treaty rule. In addition, an employee... year (for purposes of this paragraph (f)(1)(v), a plan that uses the elapsed time method of determining... provided for such term by 29 CFR 2530.200b-2 under the general method of crediting service for the employee...

  15. 29 CFR 548.305 - Excluding certain additions to wages.

    Science.gov (United States)

    2010-07-01

    ... excluded are: modest housing, bonuses or prizes of various sorts, tuition paid by the employer for the... business. It may also include such things as payment by the employer of the employee's social security tax...-of-living bonus of $260 each calendar quarter, or $20 per week. The employee works overtime in only 2...

  16. University Benefits Survey. Part I (All Benefits Excluding Pensions).

    Science.gov (United States)

    University of Western Ontario, London.

    Results of a 1986 survey of benefits, excluding pensions, for 17 Ontario, Canada, universities are presented. Information is provided on the following areas: whether the university self- administers insurance plans, communication of benefits, proposed changes in benefits, provision of accidental death and dismemberment insurance, maternity leave…

  17. University Benefits Survey. Part 1 (All Benefits Excluding Pensions).

    Science.gov (United States)

    University of Western Ontario, London.

    Results of a 1983 survey of benefits, excluding pensions, for 17 Ontario, Canada, universities are presented. Information is provided on the following areas: whether the university self-administers insurance plans, communication of benefits, proposed changes in benefits, provision of life and dismemberment insurance, maternity leave policy,…

  18. DMPD: Signal transduction pathways mediated by the interaction of CpG DNA withToll-like receptor 9. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 14751759 Signal transduction pathways mediated by the interaction of CpG DNA withTo...;16(1):17-22. (.png) (.svg) (.html) (.csml) Show Signal transduction pathways mediated by the interaction of... CpG DNA withToll-like receptor 9. PubmedID 14751759 Title Signal transduction pathways media

  19. Long-range autocorrelations of CpG islands in the human genome.

    Directory of Open Access Journals (Sweden)

    Benjamin Koester

    Full Text Available In this paper, we use a statistical estimator developed in astrophysics to study the distribution and organization of features of the human genome. Using the human reference sequence we quantify the global distribution of CpG islands (CGI in each chromosome and demonstrate that the organization of the CGI across a chromosome is non-random, exhibits surprisingly long range correlations (10 Mb and varies significantly among chromosomes. These correlations of CGI summarize functional properties of the genome that are not captured when considering variation in any particular separate (and local feature. The demonstration of the proposed methods to quantify the organization of CGI in the human genome forms the basis of future studies. The most illuminating of these will assess the potential impact on phenotypic variation of inter-individual variation in the organization of the functional features of the genome within and among chromosomes, and among individuals for particular chromosomes.

  20. Regulation of a Mammalian Gene Bearing a CpG Island Promoter and a Distal Enhancer

    Directory of Open Access Journals (Sweden)

    Georgina Berrozpe

    2013-08-01

    Full Text Available A quantitative nucleosome occupancy assay revealed rules for nucleosome disposition in yeast and showed how disposition affects regulation of the GAL genes. Here, we show how those findings apply to the control of Kit, a mammalian gene. The Kit promoter lies in a CpG island, and its enhancer (active in mast cells lies some 150 kb upstream. Nucleosomes form with especially high avidities at the Kit promoter, a reaction that, we surmise, ensures extremely low basal expression. In mast cells, transcriptional activators displace nucleosomes that are less tightly formed at the Kit enhancer. In turn, the active enhancer replaces a single Kit promoter nucleosome with the transcriptional machinery, thereby inducing transcription over 1,000-fold. As at the yeast GAL genes, the inhibitory effects of nucleosomes facilitate high factors of induction by mammalian activators working in the absence of specific repressors.

  1. CpG Type A Induction of an Early Protective Environment in Experimental Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    James Crooks

    2017-01-01

    Full Text Available Experimental autoimmune encephalomyelitis (EAE is an inflammatory, demyelinating disease of the CNS that mimics human multiple sclerosis (MS, and it is thought to be driven by Th1 and Th17 myelin-reactive cells. Although adaptive immunity is clearly pivotal in the pathogenesis of EAE, with an essential role of CD4+ T cells, little is known of early, innate responses in this experimental setting. CpG-rich oligodeoxynucleotides (ODNs, typically found in microbial genomes, are potent activators of TLR9 in plasmacytoid dendritic cells (pDCs. In this study, we compared the effects of two types of CpG, namely, type A and type B, on EAE. We found that treatment with CpG type A ODN (CpG-A, known to induce high amounts of IFN-α in pDCs, significantly reduced disease severity in EAE, relative to controls (12.63±1.86 versus 23.49±1.46, resp.; p=0.001. Treatment also delayed onset of neurological deficits and reduced spinal cord demyelination, while increasing the percentage of splenic regulatory (Foxp3+ CD4+ T cells. CpG-A likewise reduced the levels of IL-17 and IFN-γ in the CNS. Mechanistic insight into those events showed that CpG-A promoted a regulatory phenotype in pDCs. Moreover, adoptive transfer of pDCs isolated from CpG-A-treated mice inhibited CNS inflammation and induced disease remission in acute-phase EAE. Our data thus identify a link between TLR9 activation by specific ligands and the induction of tolerance via innate immunity mechanisms.

  2. Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation.

    Directory of Open Access Journals (Sweden)

    Carrie V Breton

    Full Text Available Smoking while pregnant is associated with a myriad of negative health outcomes in the child. Some of the detrimental effects may be due to epigenetic modifications, although few studies have investigated this hypothesis in detail.To characterize site-specific epigenetic modifications conferred by prenatal smoking exposure within asthmatic children.Using Illumina HumanMethylation27 microarrays, we estimated the degree of methylation at 27,578 distinct DNA sequences located primarily in gene promoters using whole blood DNA samples from the Childhood Asthma Management Program (CAMP subset of Asthma BRIDGE childhood asthmatics (n = 527 ages 5-12 with prenatal smoking exposure data available. Using beta-regression, we screened loci for differential methylation related to prenatal smoke exposure, adjusting for gender, age and clinical site, and accounting for multiple comparisons by FDR.Of 27,578 loci evaluated, 22,131 (80% passed quality control assessment and were analyzed. Sixty-five children (12% had a history of prenatal smoke exposure. At an FDR of 0.05, we identified 19 CpG loci significantly associated with prenatal smoke, of which two replicated in two independent populations. Exposure was associated with a 2% increase in mean CpG methylation in FRMD4A (p = 0.01 and Cllorf52 (p = 0.001 compared to no exposure. Four additional genes, XPNPEP1, PPEF2, SMPD3 and CRYGN, were nominally associated in at least one replication group.These data suggest that prenatal exposure to tobacco smoke is associated with reproducible epigenetic changes that persist well into childhood. However, the biological significance of these altered loci remains unknown.

  3. Nanoparticle conjugation and pulmonary delivery enhance the protective efficacy of Ag85B and CpG against tuberculosis.

    Science.gov (United States)

    Ballester, Marie; Nembrini, Chiara; Dhar, Neeraj; de Titta, Alexandre; de Piano, Cyntia; Pasquier, Miriella; Simeoni, Eleonora; van der Vlies, André J; McKinney, John D; Hubbell, Jeffrey A; Swartz, Melody A

    2011-09-16

    Vaccines that drive robust T-cell immunity against Mycobacterium tuberculosis (Mtb) are needed both for prophylactic and therapeutic purposes. We have recently developed a synthetic vaccine delivery platform with Pluronic-stabilized polypropylene sulfide nanoparticles (NPs), which target lymphoid tissues by their small size (∼ 30 nm) and which activate the complement cascade by their surface chemistry. Here we conjugated the tuberculosis antigen Ag85B to the NPs (NP-Ag85B) and compared their efficacy in eliciting relevant immune responses in mice after intradermal or pulmonary administration. Pulmonary administration of NP-Ag85B with the adjuvant CpG led to enhanced induction of antigen-specific polyfunctional Th1 responses in the spleen, the lung and lung-draining lymph nodes as compared to soluble Ag85B with CpG and to the intradermally-delivered formulations. Mucosal and systemic Th17 responses were also observed with this adjuvanted NP formulation and vaccination route, especially in the lung. We then evaluated protection induced by the adjuvanted NP formulation following a Mtb aerosol challenge and found that vaccination with NP-Ag85B and CpG via the pulmonary route displayed a substantial reduction of the lung bacterial burden, both compared to soluble Ag85B with CpG and to the corresponding intradermally delivered formulations. These findings highlight the potential of administrating NP-based formulations by the pulmonary route for TB vaccination. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Promoter CpG Island Hypermethylation in Dysplastic Nevus and Melanoma: CLDN11 as an Epigenetic Biomarker for Malignancy

    NARCIS (Netherlands)

    Gao, L.; Hurk, K. van den; Moerkerk, P.T.; Goeman, J.J.; Beck, S.; Gruis, N.A.; Oord, J.J. van den; Winnepenninckx, V.J.; Engeland, M. van; Doorn, R. van

    2014-01-01

    Dysplastic nevi are melanocytic lesions that represent an intermediate stage between common nevus and melanoma. Histopathological distinction of dysplastic nevus from melanoma can be challenging and there is a requirement for molecular diagnostic markers. In this study, we examined promoter CpG

  5. Loss of human ribosomal gene CpG methylation enhances cryptic RNA polymerase II transcription and disrupts ribosomal RNA processing.

    Science.gov (United States)

    Gagnon-Kugler, Thérèse; Langlois, Frédéric; Stefanovsky, Victor; Lessard, Frédéric; Moss, Tom

    2009-08-28

    Epigenetic methyl-CpG silencing of the ribosomal RNA (rRNA) genes is thought to downregulate rRNA synthesis in mammals. In contrast, we now show that CpG methylation in fact positively influences rRNA synthesis and processing. Human HCT116 cells, inactivated for DNMT1 and DNMT3b or treated with aza-dC, lack CpG methylation and reactivate a large fraction of normally silent rRNA genes. Unexpectedly, these cells display reduced rRNA synthesis and processing and accumulate unprocessed 45S rRNA. Reactivation of the rRNA genes is associated with their cryptic transcription by RNA polymerase II. Ectopic expression of cryptic rRNA gene transcripts recapitulates the defects associated with loss of CpG methylation. The data demonstrate that rRNA gene silencing prevents cryptic RNA polymerase II transcription of these genes. Lack of silencing leads to the partial disruption of rRNA synthesis and rRNA processing, providing an explanation for the cytotoxic effects of loss of CpG methylation.

  6. Deletions of a differentially methylated CpG island at SNRPN define a putative imprinting control region

    Energy Technology Data Exchange (ETDEWEB)

    Sutcliffe, J.S.,; Nakao, M.; Beaudet, A.L. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1994-09-01

    Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are associated with paternal and maternal deficiencies, respectively, of gene expression within human chromosome 15q11-q13, and are caused by deletion, uniparental disomy, or other mutations. Four transcripts designated PAR-5, PAR-7, PAR-1 and PAR-4 were isolated and localized to a region within 300 kb telomeric to the gene encoding small nuclear ribonucleoprotein-associated polypeptide N (SNRPN). Analysis of the transcripts in cultured fibroblasts and lymphoblasts from deletion patients demonstrated that SNRPN, PAR-5 and PAR-1 are expressed exclusively from the paternal chromosome, defining an imprinted domain that spans at least 200 kb. All three imprinted transcripts were absent in cells from three PWS patients (one pair of sibs and one sporadic case) with small deletions that involve a differentially methylated CpG island containing a previously undescribed 5{prime} untranslated exon ({alpha}) of SNRPN. Methylation of the CpG island is specific for the maternal chromosome consistent with paternal expression of the imprinted domain. One deletion, which is benign when maternally transmitted, extends upstream <30 kb from the CpG island, and is associated with altered methylation centromeric to SNRPN, and loss of transcription telomeric to SNRPN, implying the presence of an imprinting control region around the CpG island containing exon {alpha}.

  7. CPG-Based Locomotion Control of a Robotic Fish : Using Linear Oscillators and Reducing Control Parameters via PSO

    NARCIS (Netherlands)

    Wang, Chen; Xie, G.; Wang, L.; Cao, M.

    The aim of the present study is to investigate the locomotion control of a robotic fish. To achieve this goal, we design a control architecture based on a novel central pattern generator (CPG) and implement it as a system of coupled linear oscillators. This design differs significantly from the

  8. Investigation of a CPG-array CdZnTe γ-ray imaging detector with single collecting electrodes readout.

    Science.gov (United States)

    Ma, Yuedong; Xiao, Shali; Yang, Guoqiang; Zhang, Liuqiang

    2015-11-01

    The single-electrode readout method has been applied to a coplanar grid (CPG) array CdZnTe detector in order to halve the number of preamplifiers previously needed and to facilitate imaging applications of CPG detectors. A method of predetermining the width of the optimum collecting electrodes has also been proposed, using the calculated optimum relative gain factor G. Meanwhile, a detailed process for calculating the charge induction efficiency (CIE) is presented. To simplify the calculation process, the computational formula of the CIE was deduced through the integration of the weighting potential. For performance evaluation, a 2 × 2 CPG-array CdZnTe detector was elaborately designed and tested with (137)Cs at 662 keV. Experimental results showed the capability of using the CPG-array CdZnTe detector with single collecting electrode readout for γ-ray imaging applications, with the same complexity of associated readout electronics as that of the pixelated CdZnTe detectors.

  9. Efficacy of QCDCR formulated CpG ODN 2007 in Nile tilapia against Streptococcus iniae and identification of upregulated genes

    Science.gov (United States)

    The potential of using a QCDCR (quilA:cholesterol:dimethyl dioctadecyl ammonium bromide:carbopol:R1005 glycolipid) formulated CpG oligodeoxynucleotide (ODN), ODN 2007, to confer protection in Nile tilapia against Streptococcus iniae infection was evaluated in this study. At two days post treatment, ...

  10. Protection of Balb/c mice against infection with FMDV by immunostimulation with CpG oligonucleotides

    DEFF Research Database (Denmark)

    Kamstrup, Søren; Frimann, Tine; Barfoed, Annette Malene

    2006-01-01

    Oligodeoxynucleotides (ODN) containing unmethylated CpG motifs are potent stimulators of the innate immune system, and are capable of aborting several infections in a non-specific manner. We here report studies of the capacity of such ODN to protect mice against infection with foot and mouth...

  11. CpG promoter methylation status is not a prognostic indicator of gene expression in beryllium challenge.

    Science.gov (United States)

    Tooker, Brian C; Ozawa, Katherine; Newman, Lee S

    2016-05-01

    Individuals exposed to beryllium (Be) may develop Be sensitization (BeS) and progress to chronic beryllium disease (CBD). Recent studies with other metal antigens suggest epigenetic mechanisms may be involved in inflammatory disease processes, including granulomatous lung disorders and that a number of metal cations alter gene methylation. The objective of this study was to determine if Be can exert an epigenetic effect on gene expression by altering methylation in the promoter region of specific genes known to be involved in Be antigen-mediated gene expression. To investigate this objective, three macrophage tumor mouse cell lines known to differentially produce tumor necrosis factor (TNF)-α, but not interferon (IFN)-γ, in response to Be antigen were cultured with Be or controls. Following challenges, ELISA were performed to quantify induced TNFα and IFNγ expression. Bisulfate-converted DNA was evaluated by pyrosequencing to quantify CpG methylation within the promoters of TNFα and IFNγ. Be-challenged H36.12J cells expressed higher levels of TNFα compared to either H36.12E cells or P388D.1 cells. However, there were no variations in TNFα promoter CpG methylation levels between cell lines at the six CpG sites tested. H36.12J cell TNFα expression was shown to be metal-specific by the induction of significantly more TNFα when exposed to Be than when exposed to aluminum sulfate, or nickel (II) chloride, but not when exposed to cobalt (II) chloride. However, H36.12J cell methylation levels at the six CpG sites examined in the TNFα promoter did not correlate with cytokine expression differences. Nonetheless, all three cell lines had significantly more promoter methylation at the six CpG sites investigated within the IFNγ promoter (a gene that is not expressed) when compared to the six CpG sites investigated in the TNFα promoter, regardless of treatment condition (p methylation may be necessary to allow expression of metal-induced TNFα and that promoter

  12. Empowering the digitally excluded: learning initiatives for (invisible groups

    Directory of Open Access Journals (Sweden)

    Jane Seale

    2012-12-01

    Full Text Available There is growing evidence that some digitally excluded groups of learners are receiving more attention than others. Discussions regarding why some digitally excluded learners are more visible than others and therefore worthy of more committed digital inclusion interventions raises important questions about how we define and conceptualise digital inclusion and digital inclusion practice; particularly in relation to empowerment. In this article, we draw on a range of research, practice and policy literature to examine two important questions: what is empowerment and in whose hands does empowerment lie? We argue that empowerment involves making informed choices about technology use, but that learners often require support- human intervention- to make these choices. However, current digital inclusion research has failed to produce a detailed critique of what constitutes empowering support from educational institutions and their staff. A lack of open and reflexive accounts of practice means that we are no closer to identifying and understanding the kinds of empowering practices that are required to challenge the kinds of prejudices, stereotypes, risk-aversiveness and low aspirations associated with the most invisible of digitally excluded learners.

  13. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context.

    Directory of Open Access Journals (Sweden)

    Brock C Christensen

    2009-08-01

    Full Text Available Epigenetic control of gene transcription is critical for normal human development and cellular differentiation. While alterations of epigenetic marks such as DNA methylation have been linked to cancers and many other human diseases, interindividual epigenetic variations in normal tissues due to aging, environmental factors, or innate susceptibility are poorly characterized. The plasticity, tissue-specific nature, and variability of gene expression are related to epigenomic states that vary across individuals. Thus, population-based investigations are needed to further our understanding of the fundamental dynamics of normal individual epigenomes. We analyzed 217 non-pathologic human tissues from 10 anatomic sites at 1,413 autosomal CpG loci associated with 773 genes to investigate tissue-specific differences in DNA methylation and to discern how aging and exposures contribute to normal variation in methylation. Methylation profile classes derived from unsupervised modeling were significantly associated with age (P<0.0001 and were significant predictors of tissue origin (P<0.0001. In solid tissues (n = 119 we found striking, highly significant CpG island-dependent correlations between age and methylation; loci in CpG islands gained methylation with age, loci not in CpG islands lost methylation with age (P<0.001, and this pattern was consistent across tissues and in an analysis of blood-derived DNA. Our data clearly demonstrate age- and exposure-related differences in tissue-specific methylation and significant age-associated methylation patterns which are CpG island context-dependent. This work provides novel insight into the role of aging and the environment in susceptibility to diseases such as cancer and critically informs the field of epigenomics by providing evidence of epigenetic dysregulation by age-related methylation alterations. Collectively we reveal key issues to consider both in the construction of reference and disease

  14. Systemic immune responses to an inactivated, whole H9N2 avian influenza virus vaccine using class B CpG oligonucleotides in chickens.

    Science.gov (United States)

    Singh, Shirene M; Alkie, Tamiru N; Hodgins, Douglas C; Nagy, Éva; Shojadoost, Bahram; Sharif, Shayan

    2015-07-31

    Commercial vaccines against avian influenza viruses (AIV) in chickens consist mainly of inactivated AIV, requiring parenteral administration and co-delivery of an adjuvant. Limitations in T helper 1 or T helper 2 biased responses generated by these vaccines emphasize the need for alternative, more efficacious adjuvants. The Toll-like receptor (TLR) 21 ligand, CpG oligodeoxynucleotides (ODN), has been established as immunomodulatory in chickens. Therefore, the objective of this study was to investigate the adjuvant potential of high (20μg) and low (2μg) doses of CpG ODN 2007 (CpG 2007) and CpG ODN 1826 (CpG 1826) when administered to chickens with a formalin-inactivated H9N2 AIV. Antibody responses in sera were evaluated in 90 specific pathogen free (SPF) chickens after intramuscular administration of vaccine formulations at 7 and 21 days post-hatch. Antibody responses were assessed based on haemagglutination inhibition (HI) and virus neutralization (VN) assays; virus-specific IgM and IgY antibody responses were evaluated by ELISA. The results suggest that the vaccine formulation containing low dose CpG 2007 was significantly more effective at generating neutralizing (both HI and VN) responses than formulations with high or low doses of CpG 1826 or high dose CpG 2007. Neutralizing responses elicited by low dose CpG 2007 significantly exceeded those generated by a squalene-based adjuvanted vaccine formulation during peak responses. A significantly higher IgM response was elicited by the formulation containing low dose CpG 2007 compared to high and low doses of 1826. Although the low dose of CpG 2007 elicited a higher IgY response than CpG 1826, the difference was not statistically significant. In conclusion, 2μg of CpG 2007 is potentially promising as a vaccine adjuvant when delivered intramuscularly with inactivated H9N2 virus to chickens. Future studies may be directed at determining the mucosal antibody responses to the same vaccine formulations. Copyright

  15. Excluded volume effect enhances the homology pairing of model chromosomes

    Science.gov (United States)

    Takamiya, Kazunori; Yamamoto, Keisuke; Isami, Shuhei; Nishimori, Hiraku; Awazu, Akinori

    To investigate the structural dynamics of the homology pairing of polymers, we mod- eled the scenario of homologous chromosome pairings during meiosis in Schizosaccharomyces pombe, one of the simplest model organisms of eukaryotes. We consider a simple model consist- ing of pairs of homologous polymers with the same structures that are confined in a cylindrical container, which represents the local parts of chromosomes contained in an elongated nucleus of S. pombe. Brownian dynamics simulations of this model showed that the excluded volume effects among non-homological chromosomes and the transitional dynamics of nuclear shape serve to enhance the pairing of homologous chromosomes.

  16. Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content.

    Science.gov (United States)

    Mugal, Carina F; Ellegren, Hans

    2011-06-22

    A major goal in the study of molecular evolution is to unravel the mechanisms that induce variation in the germ line mutation rate and in the genome-wide mutation profile. The rate of germ line mutation is considerably higher for cytosines at CpG sites than for any other nucleotide in the human genome, an increase commonly attributed to cytosine methylation at CpG sites. The CpG mutation rate, however, is not uniform across the genome and, as methylation levels have recently been shown to vary throughout the genome, it has been hypothesized that methylation status may govern variation in the rate of CpG mutation. Here, we use genome-wide methylation data from human sperm cells to investigate the impact of DNA methylation on the CpG substitution rate in introns of human genes. We find that there is a significant correlation between the extent of methylation and the substitution rate at CpG sites. Further, we show that the CpG substitution rate is positively correlated with non-CpG divergence, suggesting susceptibility to factors responsible for the general mutation rate in the genome, and negatively correlated with GC content. We only observe a minor contribution of gene expression level, while recombination rate appears to have no significant effect. Our study provides the first direct empirical support for the hypothesis that variation in the level of germ line methylation contributes to substitution rate variation at CpG sites. Moreover, we show that other genomic features also impact on CpG substitution rate variation.

  17. Diffusion of multiple species with excluded-volume effects

    KAUST Repository

    Bruna, Maria

    2012-01-01

    Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results. © 2012 American Institute of Physics.

  18. HLA region excluded by linkage analyses of early onset periodontitis

    Energy Technology Data Exchange (ETDEWEB)

    Sun, C.; Wang, S.; Lopez, N.

    1994-09-01

    Previous studies suggested that HLA genes may influence susceptibility to early-onset periodontitis (EOP). Segregation analyses indicate that EOP may be due to a single major gene. We conducted linkage analyses to assess possible HLA effects on EOP. Fifty families with two or more close relatives affected by EOP were ascertained in Virginia and Chile. A microsatellite polymorphism within the HLA region (at the tumor necrosis factor beta locus) was typed using PCR. Linkage analyses used a donimant model most strongly supported by previous studies. Assuming locus homogeneity, our results exclude a susceptibility gene within 10 cM on either side of our marker locus. This encompasses all of the HLA region. Analyses assuming alternative models gave qualitatively similar results. Allowing for locus heterogeneity, our data still provide no support for HLA-region involvement. However, our data do not statistically exclude (LOD <-2.0) hypotheses of disease-locus heterogeneity, including models where up to half of our families could contain an EOP disease gene located in the HLA region. This is due to the limited power of even our relatively large collection of families and the inherent difficulties of mapping genes for disorders that have complex and heterogeneous etiologies. Additional statistical analyses, recruitment of families, and typing of flanking DNA markers are planned to more conclusively address these issues with respect to the HLA region and other candidate locations in the human genome. Additional results for markers covering most of the human genome will also be presented.

  19. Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

    OpenAIRE

    Mugal, Carina F.; Ellegren, Hans

    2011-01-01

    Background A major goal in the study of molecular evolution is to unravel the mechanisms that induce variation in the germ line mutation rate and in the genome-wide mutation profile. The rate of germ line mutation is considerably higher for cytosines at CpG sites than for any other nucleotide in the human genome, an increase commonly attributed to cytosine methylation at CpG sites. The CpG mutation rate, however, is not uniform across the genome and, as methylation levels have recently been s...

  20. Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks.

    Science.gov (United States)

    Wang, Yiheng; Liu, Tong; Xu, Dong; Shi, Huidong; Zhang, Chaoyang; Mo, Yin-Yuan; Wang, Zheng

    2016-01-22

    The hypo- or hyper-methylation of the human genome is one of the epigenetic features of leukemia. However, experimental approaches have only determined the methylation state of a small portion of the human genome. We developed deep learning based (stacked denoising autoencoders, or SdAs) software named "DeepMethyl" to predict the methylation state of DNA CpG dinucleotides using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. We used the experimental data from immortalised myelogenous leukemia (K562) and healthy lymphoblastoid (GM12878) cell lines to train the learning models and assess prediction performance. We have tested various SdA architectures with different configurations of hidden layer(s) and amount of pre-training data and compared the performance of deep networks relative to support vector machines (SVMs). Using the methylation states of sequentially neighboring regions as one of the learning features, an SdA achieved a blind test accuracy of 89.7% for GM12878 and 88.6% for K562. When the methylation states of sequentially neighboring regions are unknown, the accuracies are 84.82% for GM12878 and 72.01% for K562. We also analyzed the contribution of genome topological features inferred from Hi-C. DeepMethyl can be accessed at http://dna.cs.usm.edu/deepmethyl/.

  1. Universal informative CpG sites for inferring tumor purity from DNA methylation microarray data.

    Science.gov (United States)

    Dou, Haixia; Fang, Yun; Zheng, Xiaoqi

    2017-12-28

    Tumor purity is an intrinsic property of tumor samples and potentially has severe impact on many types of data analysis. We have previously developed a statistical method, InfiniumPurify, which could infer purity of a tumor sample given its tumor type (available in TCGA) or a set of informative CpG (iDMC) sites. However, in many clinical practices, researchers may focus on a specific type of tumor samples that is not included in TCGA, and samples which are too few to identify reliable iDMCs. This greatly restricts the application of InfiniumPurify in cancer research. In this paper, we proposed an updated version of InfiniumPurify (termed as uiInfiniumPurify) through identifying a universal set of iDMCs (uiDMCs) and redesigning the algorithm to determine hyper- and hypo-methylation status of each uiDMC. Through the application, we estimated tumor purities of 8830 tumor samples from TCGA. Result shows that our estimates are highly consistent with those by other available methods. Consequently, the updated uiInfiniumPurify, can be applied to a single sample (or a few samples) of interest whose tumor type is not included in TCGA. This characteristic will greatly broaden the application of uiInfiniumPurify in cancer research.

  2. Prediction of CpG island methylation status by integrating DNA physicochemical properties.

    Science.gov (United States)

    Feng, Pengmian; Chen, Wei; Lin, Hao

    2014-10-01

    As an inheritable epigenetic modification, DNA methylation plays important roles in many biological processes. The non-uniform distribution of DNA methylation across the genome implies that characterizing genome-wide DNA methylation patterns is necessary to better understand the regulatory mechanisms of DNA methylation. Although a series of experimental technologies have been proposed, they are cost-ineffective for DNA methylation status detection. As complements to experimental techniques, computational methods will facilitate the identification of DNA methylation status. In the present study, we proposed a Naïve Bayes model to predict CpG island methylation status. In this model, DNA sequences are formulated by "pseudo trinucleotide composition" into which three DNA physicochemical properties were incorporated. It was observed by the jack-knife test that the overall success rate achieved by the proposed model in predicting the DNA methylation status was 88.22%. This result indicates that the proposed model is a useful tool for DNA methylation status prediction. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Promoter CpG methylation status in porcine Lyn is associated with its expression levels.

    Science.gov (United States)

    Xiao, Zhengzhong; Wang, Chong; Mo, Delin; Li, Jiaqi; Chen, Yaosheng; Zhang, Zongwu; Cong, Peiqing

    2012-12-10

    Resistance to disease and improvement of product quality are important goals in pig farming. Tyrosine Protein Kinase Lyn (LYN) is one of several Src-family tyrosine kinases in immune cells. This protein functions both as a positive and negative regulator of B cell activation, and regulates signaling pathways through phosphorylation of inhibitory receptors, enzymes and adaptors, which suggested that LYN could be correlated with immunity and can be considered as a candidate gene to study in disease resistance. Until now, the profiles of expression and transcriptional regulation of the LYN gene in pig breeds different in immune capacity remain unclear. Using real-time PCR, it indicated that porcine LYN mRNA expressed mainly in immune organs including the spleen, duodenum and liver. Furthermore, Dahuabai pigs (a kind of Chinese indigenous pig breeds with higher immune capacity) showed significant higher LYN mRNA expression levels than that in Landrace. Methylation analysis indicates that LYN expression levels were associated with the methylation status of the LYN promoter, and methylation of the novel CpG site at -1268C/-1267G generated by transposition at -1267 (A→G) results in up-regulating transcriptional activity of this gene. Interestingly, the base A located in -1267 mainly exhibited in landrace while the base G mainly in Dahuabai pigs. These results might contribute to study the function of this gene in pig breeding for disease resistance. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. Incorrect DNA methylation of the DAZL promoter CpG island associates with defective human sperm†

    Science.gov (United States)

    Navarro-Costa, Paulo; Nogueira, Paulo; Carvalho, Marta; Leal, Fernanda; Cordeiro, Isabel; Calhaz-Jorge, Carlos; Gonçalves, João; Plancha, Carlos E.

    2010-01-01

    BACKGROUND Successful gametogenesis requires the establishment of an appropriate epigenetic state in developing germ cells. Nevertheless, an association between abnormal spermatogenesis and epigenetic disturbances in germline-specific genes remains to be demonstrated. METHODS In this study, the DNA methylation pattern of the promoter CpG island (CGI) of two germline regulator genes—DAZL and DAZ, was characterized by bisulphite genomic sequencing in quality-fractioned ejaculated sperm populations from normozoospermic (NZ) and oligoasthenoteratozoospermic (OAT) men. RESULTS OAT patients display increased methylation defects in the DAZL promoter CGI when compared with NZ controls. Such differences are recorded when analyzing sperm fractions enriched either in normal or defective germ cells (P< 0.001 in both cases). Significant differences in DNA methylation profiles are also observable when comparing the qualitatively distinct germ cell fractions inside the NZ and OAT groups (P= 0.003 and P= 0.007, respectively). Contrastingly, the unmethylation pattern of the DAZ promoter CGI remains correctly established in all experimental groups. CONCLUSIONS An association between disrupted DNA methylation of a key spermatogenesis gene and abnormal human sperm is described here for the first time. These results suggest that incorrect epigenetic marks in germline genes may be correlated with male gametogenic defects. PMID:20685756

  5. CpG island methylation of TMS1/ASC and CASP8 genes in cervical cancer

    Directory of Open Access Journals (Sweden)

    Tamandani DM

    2009-02-01

    Full Text Available Abstract Background Gene silencing associated with aberrant methylation of promoter region CpG islands is an acquired epigenetic alteration that serves as an alternative to genetic defects in the inactivation of tumor suppressor and other genes in human cancers. Aims This study describes the methylation status of TMS1/ASC and CASP8 genes in cervical cancer. We also examined the prevalence of TMS1/ASC and CASP8 genes methylation in cervical cancer tissue and none - neo plastic samples in an effort to correlate with smoking habit and clinicopathological features. Method Target DNA was modified by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequently amplified by Methylation Specific (MS PCR with primers specific for methylated versus unmethylated DNA. The PCR product was detected by gel electrophoresis and combined with the clinical records of patients. Results The methylation pattern of the TMS1/ASC and CASP8 genes in specimens of cervical cancer and adjacent normal tissues were detected [5/80 (6.2%, 3/80 (3.75%-2/80 (2.5%, 1/80 (1.2% respectively]. No statistical differences were seen in the extent of differentiation, invasion, pathological type and smoking habit between the methylated and unmethylated tissues (P > 0.05. Conclusion The present study conclude that the frequency of TMS1/ASC and CASP8 genes methylation in cervical cancer are rare (

  6. Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks

    Science.gov (United States)

    Wang, Yiheng; Liu, Tong; Xu, Dong; Shi, Huidong; Zhang, Chaoyang; Mo, Yin-Yuan; Wang, Zheng

    2016-01-01

    The hypo- or hyper-methylation of the human genome is one of the epigenetic features of leukemia. However, experimental approaches have only determined the methylation state of a small portion of the human genome. We developed deep learning based (stacked denoising autoencoders, or SdAs) software named “DeepMethyl” to predict the methylation state of DNA CpG dinucleotides using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. We used the experimental data from immortalised myelogenous leukemia (K562) and healthy lymphoblastoid (GM12878) cell lines to train the learning models and assess prediction performance. We have tested various SdA architectures with different configurations of hidden layer(s) and amount of pre-training data and compared the performance of deep networks relative to support vector machines (SVMs). Using the methylation states of sequentially neighboring regions as one of the learning features, an SdA achieved a blind test accuracy of 89.7% for GM12878 and 88.6% for K562. When the methylation states of sequentially neighboring regions are unknown, the accuracies are 84.82% for GM12878 and 72.01% for K562. We also analyzed the contribution of genome topological features inferred from Hi-C. DeepMethyl can be accessed at http://dna.cs.usm.edu/deepmethyl/.

  7. Correlating CpG islands, motifs, and sequence variants in human chromosome 21

    Directory of Open Access Journals (Sweden)

    Cercone Nick

    2011-07-01

    Full Text Available Abstract Background CpG islands are important regions in DNA. They usually appear at the 5’ end of genes containing GC-rich dinucleotides. When DNA methylation occurs, gene regulation is affected and it sometimes leads to carcinogenesis. We propose a new detection program using a hidden-markov model alongside the Viterbi algorithm. Methods Our solution provides a graphical user interface not seen in many of the other CGI detection programs and we unify the detection and analysis under one program to allow researchers to scan a genetic sequence, detect the significant CGIs, and analyze the sequence once the scan is complete for any noteworthy findings. Results Using human chromosome 21, we show that our algorithm finds a significant number of CGIs. Running an analysis on a dataset of promoters discovered that the characteristics of methylated and unmethylated CGIs are significantly different. Finally, we detected significantly different motifs between methylated and unmethylated CGI promoters using MEME and MAST. Conclusions Developing this new tool for the community using powerful algorithms has shown that combining analysis with CGI detection will improve the continued research within the field of epigenetics.

  8. Racial Differences in DNA-Methylation of CpG Sites Within Preterm-Promoting Genes and Gene Variants.

    Science.gov (United States)

    Salihu, H M; Das, R; Morton, L; Huang, H; Paothong, A; Wilson, R E; Aliyu, M H; Salemi, J L; Marty, P J

    2016-08-01

    Objective To evaluate the role DNA methylation may play in genes associated with preterm birth for higher rates of preterm births in African-American women. Methods Fetal cord blood samples from births collected at delivery and maternal demographic and medical information were used in a cross-sectional study to examine fetal DNA methylation of genes implicated in preterm birth among black and non-black infants. Allele-specific DNA methylation analysis was performed using a methylation bead array. Targeted maximum likelihood estimation was applied to examine the relationship between race and fetal DNA methylation of candidate preterm birth genes. Receiver-operating characteristic analyses were then conducted to validate the CpG site methylation marker within the two racial groups. Bootstrapping, a method of validation and replication, was employed. Results 42 CpG sites were screened within 20 candidate gene variants reported consistently in the literature as being associated with preterm birth. Of these, three CpG sites on TNFAIP8 and PON1 genes (corresponding to: cg23917399; cg07086380; and cg07404485, respectively) were significantly differentially methylated between black and non-black individuals. The three CpG sites showed lower methylation status among infants of black women. Bootstrapping validated and replicated results. Conclusion for Practice Our study identified significant differences in levels of methylation on specific genes between black and non-black individuals. Understanding the genetic/epigenetic mechanisms that lead to preterm birth may lead to enhanced prevention strategies to reduce morbidity and mortality by eventually providing a means to identify individuals with a genetic predisposition to preterm labor.

  9. In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases

    Science.gov (United States)

    Arand, Julia; Spieler, David; Karius, Tommy; Branco, Miguel R.; Meilinger, Daniela; Meissner, Alexander; Jenuwein, Thomas; Xu, Guoliang; Leonhardt, Heinrich; Wolf, Verena; Walter, Jörn

    2012-01-01

    The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements (LINE1, B1, IAP-LTR-retrotransposons, and major satellites). The analysis unambiguously identifies a substantial amount of regional incomplete methylation maintenance, i.e. hemimethylated CpG positions, with variant degrees among cell types. Moreover, non-CpG cytosine methylation is confined to ESCs and exclusively catalysed by Dnmt3a and Dnmt3b. This sequence position–, cell type–, and region-dependent non-CpG methylation is strongly linked to neighboring CpG methylation and requires the presence of Dnmt3L. The generation of a comprehensive data set of 146,000 CpG dyads was used to apply and develop parameter estimated hidden Markov models (HMM) to calculate the relative contribution of DNA methyltransferases (Dnmts) for de novo and maintenance DNA methylation. The comparative modelling included wild-type ESCs and mutant ESCs deficient for Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3a/3b, respectively. The HMM analysis identifies a considerable de novo methylation activity for Dnmt1 at certain repetitive elements and single copy sequences. Dnmt3a and Dnmt3b contribute de novo function. However, both enzymes are also essential to maintain symmetrical CpG methylation at distinct repetitive and single copy sequences in ESCs. PMID:22761581

  10. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases.

    Directory of Open Access Journals (Sweden)

    Julia Arand

    2012-06-01

    Full Text Available The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements (LINE1, B1, IAP-LTR-retrotransposons, and major satellites. The analysis unambiguously identifies a substantial amount of regional incomplete methylation maintenance, i.e. hemimethylated CpG positions, with variant degrees among cell types. Moreover, non-CpG cytosine methylation is confined to ESCs and exclusively catalysed by Dnmt3a and Dnmt3b. This sequence position-, cell type-, and region-dependent non-CpG methylation is strongly linked to neighboring CpG methylation and requires the presence of Dnmt3L. The generation of a comprehensive data set of 146,000 CpG dyads was used to apply and develop parameter estimated hidden Markov models (HMM to calculate the relative contribution of DNA methyltransferases (Dnmts for de novo and maintenance DNA methylation. The comparative modelling included wild-type ESCs and mutant ESCs deficient for Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3a/3b, respectively. The HMM analysis identifies a considerable de novo methylation activity for Dnmt1 at certain repetitive elements and single copy sequences. Dnmt3a and Dnmt3b contribute de novo function. However, both enzymes are also essential to maintain symmetrical CpG methylation at distinct repetitive and single copy sequences in ESCs.

  11. CpG Oligodeoxynucleotide and Montanide ISA 51 Adjuvant Combination Enhanced the Protective Efficacy of a Subunit Malaria Vaccine

    Science.gov (United States)

    2004-02-01

    and cancers to immune enhancement of synthetic peptide- and recombinant protein-based vaccines. We investigated the adjuvant effect of murine CpG ODN...parasites. Briefly, the IFA test was done on 12-well toxoplasmosis slides (Bellco Glass, Vineland, N.J.). Twofold dilutions of test sera were added to P...to enhance the immunoge- nicity of recombinant antigens (13, 22, 33) or as monotherapy for cancers (4, 25, 42). In conclusion, our results show

  12. Methylation status of CpG islands at sites −59 to +96 in exon 1 of the ...

    Indian Academy of Sciences (India)

    Cancer 3,. 33 (http//www.molecular-cancer.com/content/3/1/33). Fearon E. R. 1997 Human cancer syndromes: clues to the origin and nature of cancer. Science 278, 1043–1050. Gonzales-Zulueta M., Bender C. M., Yang A. S., Ngyen T., Beart. R. W., Van Tornaut J. M. and Jones P. A. 1995 Methylation of the 5 CpG island of ...

  13. DNA methylation-based age prediction from saliva: High age predictability by combination of 7 CpG markers.

    Science.gov (United States)

    Hong, Sae Rom; Jung, Sang-Eun; Lee, Eun Hee; Shin, Kyoung-Jin; Yang, Woo Ick; Lee, Hwan Young

    2017-07-01

    DNA methylation is currently one of the most promising age-predictive biomarkers. Many studies have reported DNA methylation-based age predictive models, but most of these are based on DNA methylation patterns from blood. Only a few studies have examined age-predictive DNA patterns in saliva, which is one of the most frequently-encountered body fluids at crime scenes. In this study, we generated genome-wide DNA methylation profiles of saliva from 54 individuals and identified CpG markers that showed a high correlation between methylation and age. Because the age-associated marker candidates from saliva differed from those of blood, we investigated DNA methylation patterns of 6 age-associated CpG marker candidates (cg00481951, cg19671120, cg14361627, cg08928145, cg12757011, and cg07547549 of the SST, CNGA3, KLF14, TSSK6, TBR1, and SLC12A5 genes, respectively) in addition to a cell type-specific CpG marker (cg18384097 of the PTPN7 gene) in an independent set of saliva samples obtained from 226 individuals aged 18 to 65 years. Multiplex methylation SNaPshot reactions were used to generate the data. We then generated a linear regression model with age information and the methylation profile from the 113 training samples. The model exhibited a 94.5% correlation between predicted and chronological age with a mean absolute deviation (MAD) from chronological age of 3.13 years. In subsequent validation using 113 test samples, we also observed a high correlation between predicted and chronological age (Spearman's rho=0.952, MAD from chronological age=3.15years). The model composed of 7 selected CpG sites enabled age prediction in saliva with high accuracy, which will be useful in saliva analysis for investigative leads. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Identification of the porcine XIST gene and its differential CpG methylation status in male and female pig cells.

    Directory of Open Access Journals (Sweden)

    Jae Yeon Hwang

    Full Text Available XIST, a long non-coding RNA, plays an important role in triggering X chromosome inactivation in eutherians, and is used extensively for qualifying stem cells and cloned embryos. However, a porcine XIST has not yet been thoroughly identified despite its biological importance in a wide variety of research fields. Here, we present a full-length porcine XIST sequence assembled using known sequences (GenBank, RNA-Seq data (NCBI SRA, and PCR/sequencing. The proposed porcine XIST gene model encodes a 25,215-bp transcript consisting of 7 exons, including two conserved and two porcine-specific repeat regions. Transcription covering the entire XIST region was observed specifically in female cells, but not in male cells. We also identified eight transcription starting sites (TSSs and evaluated CpG methylation patterns in the upstream (+2.0 kb and downstream (-2.0 kb regions. Sixty-seven CG di-nucleotides identified in the target region were considered to be candidate CpG sites, and were enriched in the following two regions: -284 to +53 bp (13 sites and +285 to +1,727 bp (54 sites from the selected TSS. Male 5` region of XIST (64.5 sites, 96.26% had a higher level of CpG methylation than female DNA (33.4 sites, 49.85%. Taken together, our results revealed that the porcine XIST gene is expressed exclusively in female cells, which is influenced by the lower level of CpG methylation in the putative promoter region compared with male cells. The porcine XIST presented in this study represents a useful tool for related research areas such as porcine embryology and stem cell biology.

  15. Dengue-1 envelope protein domain III along with PELC and CpG oligodeoxynucleotides synergistically enhances immune responses.

    Directory of Open Access Journals (Sweden)

    Chen-Yi Chiang

    Full Text Available The major weaknesses of subunit vaccines are their low immunogenicity and poor efficacy. Adjuvants can help to overcome some of these inherent defects with subunit vaccines. Here, we evaluated the efficacy of the newly developed water-in-oil-in-water multiphase emulsion system, termed PELC, in potentiating the protective capacity of dengue-1 envelope protein domain III. Unlike aluminum phosphate, dengue-1 envelope protein domain III formulated with PELC plus CpG oligodeoxynucleotides induced neutralizing antibodies against dengue-1 virus and increased the splenocyte secretion of IFN-γ after in vitro re-stimulation. The induced antibodies contained both the IgG1 and IgG2a subclasses. A rapid anamnestic neutralizing antibody response against a live dengue virus challenge was elicited at week 26 after the first immunization. These results demonstrate that PELC plus CpG oligodeoxynucleotides broaden the dengue-1 envelope protein domain III-specific immune responses. PELC plus CpG oligodeoxynucleotides is a promising adjuvant for recombinant protein based vaccination against dengue virus.

  16. CpG ODN and ISCOMATRIX Adjuvant: A Synergistic Adjuvant Combination Inducing Strong T-Cell IFN-γ Responses

    Directory of Open Access Journals (Sweden)

    Michael J. McCluskie

    2013-01-01

    Full Text Available For the induction of robust humoral and cellular immune responses, a strong rationale exists to use vaccine-adjuvant combinations possessing both immune modulatory and enhanced delivery capabilities. Herein, we evaluated the combination of 2 different adjuvants, a TLR9 agonist, composed of synthetic oligodeoxynucleotides (ODN containing immunostimulatory CpG motifs (CpG, and ISCOMATRIX adjuvant (ISCOMATRIX, composed of saponin, phospholipid, and cholesterol, which possesses both immunostimulatory and delivery properties. While both individual adjuvants have been shown effective in numerous preclinical and clinical studies, it is likely that for optimal adjuvant activity a combined adjuvant approach will be necessary. Herein, using three different antigens, namely, hepatitis B surface antigen (HBsAg, ovalbumin (OVA, and influenza A haemagglutinin antigen (HA, we show in mice that some adjuvant effects of CpG and ISCOMATRIX are further enhanced if they are used in combination. In particular, with all three antigens, IFN-γ levels were greatly increased with the CpG/ISCOMATRIX combination. The ability of the CpG/ISCOMATRIX combination to induce antitumor responses when administered with OVA following administration to mice of a highly metastatic OVA-secreting tumor cell line (B16-OVA melanoma was also demonstrated. Thus the CpG/ISCOMATRIX combination may prove to be a valuable tool in the development of novel or improved vaccines.

  17. Cationic liposomes containing soluble Leishmania antigens (SLA) plus CpG ODNs induce protection against murine model of leishmaniasis.

    Science.gov (United States)

    Heravi Shargh, Vahid; Jaafari, Mahmoud Reza; Khamesipour, Ali; Jalali, Seyed Amir; Firouzmand, Hengameh; Abbasi, Azam; Badiee, Ali

    2012-07-01

    Development of an effective vaccine against leishmaniasis is possible due to the fact that individuals cured from cutaneous leishmaniasis (CL) are protected from further infection. First generation Leishmania vaccines consisting of whole killed parasites reached to phase 3 clinical trials but failed to show enough efficacies mainly due to the lack of an appropriate adjuvant. In this study, an efficient liposomal protein-based vaccine against Leishmania major infection was developed using soluble Leishmania antigens (SLA) as a first generation vaccine and cytidine phosphate guanosine oligodeoxynucleotides (CpG ODNs) as an immunostimulatory adjuvant. 1, 2-Dioleoyl-3-trimethylammonium-propane was used as a cationic lipid to prepare the liposomes due to its intrinsic adjuvanticity. BALB/c mice were immunized subcutaneously (SC), three times in 2-week intervals, with Lip-SLA-CpG, Lip-SLA, SLA + CpG, SLA, or HEPES buffer. As criteria for protection, footpad swelling at the site of challenge and spleen parasite loads were assessed, and the immune responses were evaluated by determination of IFN-γ and IL-4 levels of cultured splenocytes, and IgG subtypes. The group of mice that received Lip-SLA-CpG showed a significantly smaller footpad swelling, lower spleen parasite burden, higher IgG2a antibody, and lower IL-4 level compared to the control groups. It is concluded that cationic liposomes containing SLA and CpG ODNs are appropriate to induce Th1 type of immune response and protection against leishmaniasis.

  18. Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines.

    Science.gov (United States)

    Chae, Heejoon; Lee, Sangseon; Nephew, Kenneth P; Kim, Sun

    2016-12-23

    Aberrant epigenetic modifications, including DNA methylation, are key regulators of gene activity in tumorigenesis. Breast cancer is a heterogeneous disease, and large-scale analyses indicate that tumor from normal and benign tissues, as well as molecular subtypes of breast cancer, can be distinguished based on their distinct genomic, transcriptomic, and epigenomic profiles. In this study, we used affinity-based methylation sequencing data in 30 breast cancer cell lines representing functionally distinct cancer subtypes to investigate methylation and mutation patterns at the whole genome level. Our analysis revealed significant differences in CpG island (CpGI) shore methylation and mutation patterns among breast cancer subtypes. In particular, the basal-like B type, a highly aggressive form of the disease, displayed distinct CpGI shore hypomethylation patterns that were significantly associated with downstream gene regulation. We determined that mutation rates at CpG sites were highly correlated with DNA methylation status and observed distinct mutation rates among the breast cancer subtypes. These findings were validated by using targeted bisulfite sequencing of differentially expressed genes (n=85) among the cell lines. Our results suggest that alterations in DNA methylation play critical roles in gene regulatory process as well as cytosine substitution rates at CpG sites in molecular subtypes of breast cancer.

  19. A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray

    Directory of Open Access Journals (Sweden)

    Qiao Yingjuan

    2008-01-01

    Full Text Available Abstract Background DNA methylation based techniques are important tools in both clinical diagnostics and therapeutics. But most of these methods only analyze a few CpG sites in a target region. Indeed, difference of site-specific methylation may also lead to a change of methylation density in many cases, and it has been found that the density of methylation is more important than methylation of single CpG site for gene silencing. Results We have developed a novel approach for quantitative analysis of CpG methylation density on the basis of microarray-based hybridization and incorporation of Cy5-dCTP into the Cy3 labeled target DNA by using Taq DNA Polymerase on microarray. The quantification is achieved by measuring Cy5/Cy3 signal ratio which is proportional to methylation density. This methylation-sensitive technique, termed RMEAM (regional methylation elongation assay on microarray, provides several advantages over existing methods used for methylation analysis. It can determine an exact methylation density of the given region, and has potential of high throughput. We demonstrate a use of this method in determining the methylation density of the promoter region of the tumor-related gene MLH1, TERT and MGMT in colorectal carcinoma patients. Conclusion This technique allows for quantitative analysis of regional methylation density, which is the representative of all allelic methylation patterns in the sample. The results show that this technique has the characteristics of simplicity, rapidness, specificity and high-throughput.

  20. A Comparative Study of Five Association Tests Based on CpG Set for Epigenome-Wide Association Studies.

    Directory of Open Access Journals (Sweden)

    Qiuyi Zhang

    Full Text Available An epigenome-wide association study (EWAS is a large-scale study of human disease-associated epigenetic variation, specifically variation in DNA methylation. High throughput technologies enable simultaneous epigenetic profiling of DNA methylation at hundreds of thousands of CpGs across the genome. The clustering of correlated DNA methylation at CpGs is reportedly similar to that of linkage-disequilibrium (LD correlation in genetic single nucleotide polymorphisms (SNP variation. However, current analysis methods, such as the t-test and rank-sum test, may be underpowered to detect differentially methylated markers. We propose to test the association between the outcome (e.g case or control and a set of CpG sites jointly. Here, we compared the performance of five CpG set analysis approaches: principal component analysis (PCA, supervised principal component analysis (SPCA, kernel principal component analysis (KPCA, sequence kernel association test (SKAT, and sliced inverse regression (SIR with Hotelling's T2 test and t-test using Bonferroni correction. The simulation results revealed that the first six methods can control the type I error at the significance level, while the t-test is conservative. SPCA and SKAT performed better than other approaches when the correlation among CpG sites was strong. For illustration, these methods were also applied to a real methylation dataset.

  1. LINE-1 hypomethylation is inversely associated with microsatellite instability and CpG island methylator phenotype (CIMP) in colorectal cancer

    Science.gov (United States)

    Ogino, Shuji; Kawasaki, Takako; Nosho, Katsuhiko; Ohnishi, Mutsuko; Suemoto, Yuko; Kirkner, Gregory J.; Fuchs, Charles S.

    2009-01-01

    The CpG island methylator phenotype (CIMP) with widespread promoter CpG island methylation is a phenotype in colorectal cancer, associated with microsatellite instability (MSI) and BRAF mutation. Genome-wide hypomethylation may also play an important role in genomic instability. However, the relation between global DNA methylation level and methylation in individual CpG islands remains uncertain. Utilizing 869 population-based colorectal cancers, we measured LINE-1 (long interspersed nucleotide element-1) methylation level by Pyrosequencing, which correlates with global DNA methylation level. We quantified DNA methylation in 8 CIMP-specific promoters (CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1) by real-time PCR (MethyLight technology). LINE-1 methylation levels in tumors were approximately normally distributed (mean 61.4%, median 62.3%, standard deviation 9.6%). Among the 869 tumors, 128 (15%) were classified as CIMP-high (≥6/8 methylated promoters). The mean LINE-1 methylation level was higher in CIMP-high tumors (65.1%, pcolorectal cancer. Our data also support a possible link between global hypomethylation and chromosomal instability. PMID:18366060

  2. LINE-1 hypomethylation is inversely associated with microsatellite instability and CpG island methylator phenotype in colorectal cancer.

    Science.gov (United States)

    Ogino, Shuji; Kawasaki, Takako; Nosho, Katsuhiko; Ohnishi, Mutsuko; Suemoto, Yuko; Kirkner, Gregory J; Fuchs, Charles S

    2008-06-15

    The CpG island methylator phenotype (CIMP) with widespread promoter CpG island methylation is a phenotype in colorectal cancer, associated with microsatellite instability (MSI) and BRAF mutation. Genome-wide hypomethylation may also play an important role in genomic instability. However, the relation between global DNA methylation level and methylation in individual CpG islands remains uncertain. Utilizing 869 population-based colorectal cancers, we measured long interspersed nucleotide element-1 (LINE-1) methylation level by Pyrosequencing, which correlates with global DNA methylation level. We quantified DNA methylation in 8 CIMP-specific promoters (CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1) by real-time PCR (MethyLight technology). LINE-1 methylation levels in tumors were approximately normally distributed (mean, 61.4%; median, 62.3%; standard deviation, 9.6%). Among the 869 tumors, 128 (15%) were classified as CIMP-high (>or=6/8 methylated promoters). The mean LINE-1 methylation level was higher in CIMP-high tumors (65.1%, p colorectal cancer. Our data also support a possible link between global hypomethylation and chromosomal instability. (c) 2008 Wiley-Liss, Inc.

  3. Dualism of gene GC content and CpG pattern in regard to expression in the human genome: magnitude versus breadth.

    Science.gov (United States)

    Vinogradov, Alexander E

    2005-12-01

    In this article, I show that, in the human genome, the GC content in genes (but not the CpG island in the promoter) is related to the maximum level of gene expression among tissues, whereas the promoter CpG island and gene CpG level are more strongly related to the breadth of expression among tissues. The relevance of gene GC content to expression cannot be a consequence (i.e. a byproduct) of transcription because it does not correlate with expression in the germline. The variation of GC content and CpG level can determine the characteristics of gene expression in a synergistic interplay with transcription-factor-binding sites (mediated by chromatin condensation).

  4. Phase 1 trial of AMA1-C1/Alhydrogel plus CPG 7909: an asexual blood-stage vaccine for Plasmodium falciparum malaria.

    Directory of Open Access Journals (Sweden)

    Gregory E D Mullen

    2008-08-01

    Full Text Available Apical Membrane Antigen 1 (AMA1, a polymorphic merozoite surface protein, is a leading blood-stage malaria vaccine candidate. This is the first reported use in humans of an investigational vaccine, AMA1-C1/Alhydrogel, with the novel adjuvant CPG 7909.A phase 1 trial was conducted at the University of Rochester with 75 malaria-naive volunteers to assess the safety and immunogenicity of the AMA1-C1/Alhydrogel+CPG 7909 malaria vaccine. Participants were sequentially enrolled and randomized within dose escalating cohorts to receive three vaccinations on days 0, 28 and 56 of either 20 microg of AMA1-C1/Alhydrogel+564 microg CPG 7909 (n = 15, 80 microg of AMA1-C1/Alhydrogel (n = 30, or 80 microg of AMA1-C1/Alhydrogel+564 microg CPG 7909 (n = 30.Local and systemic adverse events were significantly more likely to be of higher severity with the addition of CPG 7909. Anti-AMA1 immunoglobulin G (IgG were detected by enzyme-linked immunosorbent assay (ELISA, and the immune sera of volunteers that received 20 microg or 80 microg of AMA1-C1/Alhydrogel+CPG 7909 had up to 14 fold significant increases in anti-AMA1 antibody concentration compared to 80 microg of AMA1-C1/Alhydrogel alone. The addition of CPG 7909 to the AMA1-C1/Alhydrogel vaccine in humans also elicited AMA1 specific immune IgG that significantly and dramatically increased the in vitro growth inhibition of homologous parasites to levels as high as 96% inhibition.The safety profile of the AMA1-C1/Alhydrogel+CPG 7909 malaria vaccine is acceptable, given the significant increase in immunogenicity observed. Further clinical development is ongoing.ClinicalTrials.gov NCT00344539.

  5. Intranasal administration of CpG induces a rapid and transient cytokine response followed by dendritic and natural killer cell activation and recruitment in the mouse lung.

    Science.gov (United States)

    Pesce, Isabella; Monaci, Elisabetta; Muzzi, Alessandro; Tritto, Elaine; Tavarini, Simona; Nuti, Sandra; De Gregorio, Ennio; Wack, Andreas

    2010-01-01

    CpG-containing oligodeoxynucleotides are potent mucosal adjuvants and effective as stand-alone treatment of respiratory infections in mice. Although CpG is also used as a type 1 helper immunomodulator in the treatment of asthma and allergic disease, immune modulation following intranasal application has not been fully characterized yet. Using a B-type CpG, we monitored RNA expression profiles, cytokine production and cellular activation in lung tissue and bronchoalveolar lavages ex vivo and cytokine production of purified cell populations in vitro. CpG triggered the upregulation of many transcripts, including interferon response genes and proinflammatory cytokine genes, between 3 h and 4 days. Overlapping subsets of these cytokine proteins were induced in vitro in purified CD11c+ cells, B cells and alveolar macrophages from the lung, thus identifying these cells as direct targets of CpG. While lung B cells strongly respond to CpG in vitro, less activation is found ex vivo, suggesting efficient CpG sequestering or rapid B cell migration after activation. In contrast, a type II alveolar epithelial cell line did not respond to CpG in vitro. We noted selective recruitment of plasmacytoid dendritic cells (DCs) into the lung tissue, and of conventional DCs and natural killer (NK) cells into the lung tissue and bronchoalveolar space. Furthermore, CpG induced activation of intrapulmonary DCs, NK and T cells. We hypothesize that CpG-linked adjuvanticity and clearance of respiratory pathogens are mediated by two major mechanisms: transient induction of the interferon pathway limiting microbial survival and selective recruitment of DCs and NK cells, which allows for better adaptive responses.

  6. CpG island clusters and pro-epigenetic selection for CpGs in protein-coding exons of HOX and other transcription factors

    OpenAIRE

    Branciamore, Sergio; Chen, Zhao-Xia; Riggs, Arthur D.; Rodin, Sergei N.

    2010-01-01

    CpG dinucleotides contribute to epigenetic mechanisms by being the only site for DNA methylation in mammalian somatic cells. They are also mutation hotspots and ∼5-fold depleted genome-wide. We report here a study focused on CpG sites in the coding regions of Hox and other transcription factor genes, comparing methylated genomes of Homo sapiens, Mus musculus, and Danio rerio with nonmethylated genomes of Drosophila melanogaster and Caenorhabditis elegans. We analyzed 4-fold degenerate, synony...

  7. CpG island clusters and pro-epigenetic selection for CpGs in protein-coding exons of HOX and other transcription factors.

    Science.gov (United States)

    Branciamore, Sergio; Chen, Zhao-Xia; Riggs, Arthur D; Rodin, Sergei N

    2010-08-31

    CpG dinucleotides contribute to epigenetic mechanisms by being the only site for DNA methylation in mammalian somatic cells. They are also mutation hotspots and approximately 5-fold depleted genome-wide. We report here a study focused on CpG sites in the coding regions of Hox and other transcription factor genes, comparing methylated genomes of Homo sapiens, Mus musculus, and Danio rerio with nonmethylated genomes of Drosophila melanogaster and Caenorhabditis elegans. We analyzed 4-fold degenerate, synonymous codons with the potential for CpG. That is, we studied "silent" changes that do not affect protein products but could damage epigenetic marking. We find that DNA-binding transcription factors and other developmentally relevant genes show, only in methylated genomes, a bimodal distribution of CpG usage. Several genetic code-based tests indicate, again for methylated genomes only, that the frequency of silent CpGs in Hox genes is much greater than expectation. Also informative are NCG-GNN and NCC-GNN codon doublets, for which an unusually high rate of G to C and C to G transversions was observed at the third (silent) position of the first codon. Together these results are interpreted as evidence for strong "pro-epigenetic" selection acting to preserve CpG sites in coding regions of many genes controlling development. We also report that DNA-binding transcription factors and developmentally important genes are dramatically overrepresented in or near clusters of three or more CpG islands, suggesting a possible relationship between evolutionary preservation of CpG dinucleotides in both coding regions and CpG islands.

  8. Enhanced antibody responses elicited by a CpG adjuvant do not improve the protective effect of an aldrithiol-2-inactivated simian immunodeficiency virus therapeutic AIDS vaccine.

    Science.gov (United States)

    Wang, Yichuan; Blozis, Shelley A; Lederman, Michael; Krieg, Arthur; Landay, Alan; Miller, Christopher J

    2009-04-01

    The potential benefit of using unmethylated CpG oligoribodeoxynucleotides (ODN) as an adjuvant in a therapeutic simian immunodeficiency virus (SIV) vaccine consisting of AT2-inactivated SIVmac239 was evaluated in SIV-infected rhesus macaques receiving antiretroviral therapy (ART). We hypothesized that using CpG ODN as an adjuvant in therapeutic vaccination would enhance SIV-specific immune responses and suppress SIV replication after ART was stopped. To test our hypothesis, we immunized chronically SIV-infected rhesus macaques receiving ART with one of the following therapeutic vaccines: (i) AT2-inactivated SIVmac239, (ii) CpG10103 plus AT2-inactivated SIVmac239, (iii) CpG10103, and (iv) saline. While immunization with CpG plus AT2-SIVmac239 significantly increased SIV-specific immunoglobulin G (IgG) antibody titers, the mean plasma viral RNA (vRNA) level in these animals after ART did not differ from those of saline-treated animals. The AT2-inactivated SIVmac239-immunized animal group had a significantly higher mean SIV-specific gamma interferon T-cell response after three immunizations and lower plasma vRNA levels for 6 weeks after ART was withdrawn compared to the saline-treated animal group. Compared to the saline control group, the animal group treated with CpG alone had a significantly higher mean SIV-specific lymphocyte proliferation index and a higher rate of plasma vRNA rebound after ART. These results demonstrate that while the use of CpG as an adjuvant enhances SIV-specific antibody responses, this does not improve the control of SIV replication after ART is stopped. The lack of benefit may be related to the high levels of SIV-specific lymphocyte proliferation in the CpG adjuvant group.

  9. CpG oligonucleotides induce an immune response of odontoblasts through the TLR9, MyD88 and NF-kappaB pathways.

    Science.gov (United States)

    He, Wenxi; Yu, Qing; Zhou, Zeyuan; Wang, Ping

    2010-08-20

    Odontoblasts are the first-line defense cells against invading microorganisms. Toll-like receptors (TLRs) play a crucial role in innate immunity, and TLR9 is involved in the recognition of microbial DNA. This study aimed to investigate whether odontoblasts can respond to CpG DNA and to determine the intracellular signaling pathways triggered by CpG DNA. We found that the mouse odontoblast-like cell line MDPC-23 constitutively expressed TLR9. Exposure to CpG ODN induced a potent proinflammatory response based on an increase of IL-6 and TNF-alpha expression. Pretreatment with an inhibitory MyD88 peptide or a specific inhibitor for TLR9, NF-kappaB or IkappaBalpha markedly inhibited CpG ODN-induced IL-6 and TNF-alpha expression. Moreover, the CpG ODN-mediated increase of kappaB-luciferase activity in MDPC-23 cells was suppressed by the overexpression of dominant negative mutants of TLR9, MyD88 and IkappaBalpha, but not by the dominant negative mutant of TLR4. This result suggests a possible role for the CpG DNA-mediated immune response in odontoblasts and indicates that TLR9, MyD88 and NF-kappaB are involved in this process. Crown Copyright 2010. Published by Elsevier Inc. All rights reserved.

  10. Transcriptomic Insights into the Response of Placenta and Decidua Basalis to the CpG Oligodeoxynucleotide Stimulation in Non-Obese Diabetic Mice and Wild-Type Controls

    Directory of Open Access Journals (Sweden)

    Xiao-Rui Liu

    2016-08-01

    Full Text Available Intrauterine infection is one of the most frequent causes of miscarriage. CpG oligodeoxynucleotide (CpG ODN can mimic intrauterine infection. CpG ODN-induced embryo-resorption was observed consistently in the NK-cell deficient non-obese diabetic (NOD mice but not in the wild-type (WT mice. To elucidate the molecular mechanisms of differential pregnancy outcomes, differentially expressed genes (DEGs in the placenta and decidua basalis was revealed by RNA-Seq with CpG ODN or control ODN treatment. Common DEGs in the WT and NOD mice were enriched in antimicrobial/antibacterial humoral responses that may be activated as a primary response to bacterial infection. The susceptibility to CpG ODN-induced embryo-resorption in the NOD mice might mainly be attributed to M1 macrophage polarization and the immunodeficient status, such as the down-regulation in antigen processing and presentation, allograft rejection, and natural killer cell mediated cytotoxicity. In contrast, the WT mice with normal immune systems could activate multiple immune responses and be resistant to CpG ODN-induced embryo-resorption, such as M2 macrophage differentiation and activation regulated by complement component C1q and peroxisome proliferation-activated receptor (PPAR signaling pathways. Collectively, this study suggests that the immunodeficient status of NOD mice and the macrophage polarization regulated by C1q and PPAR signaling might be the basis for differential pregnancy outcomes between the NOD and WT mice.

  11. The rates of G:C[yields]T:A and G:C[yields]C:G transversions at CpG dinucleotides in the human factor IX gene

    Energy Technology Data Exchange (ETDEWEB)

    Ketterling, R.P.; Vielhaber, E.; Sommer, S.S. (Mayo Clinic/Foundation, Rochester, MN (United States))

    1994-05-01

    The authors have identified eight independent transversions at CpG in 290 consecutive families with hemophilia B. These eight transversions account for 16.3% of all independent transversions in the sample, yet the expected frequency of CpG transversions at random in the factor IX gene is only 2.6% (P<0.1). The aggregate data suggest that the two types of CpG transversions (G:C[yields]T:A and G:C[yields]C:G) possess similar mutation rates (24.8 [times] 10[sup [minus]10] and 20.6 [times] 10[sup [minus]10], respectively), which are about fivefold greater than the comparable rates for transversions at non-CpG dinucleotides. The enhancement of transversions at CpG suggest that the model by which mutations occur at CpG may need to be reevaluated. The relationship, if any, between deamination of 5-methyl cytosine and enhancement of transversions at CpG remains to be defined. 28 refs., 2 tabs.

  12. Organosilane and Polyethylene Glycol Functionalized Magnetic Mesoporous Silica Nanoparticles as Carriers for CpG Immunotherapy In Vitro and In Vivo.

    Directory of Open Access Journals (Sweden)

    Hengrui Zheng

    Full Text Available Cytosine-guanine (CpG containing oligodeoxynucleotides (ODN have significant clinical potential as immunotherapeutics. However, limitations exist due to their transient biological stability in vivo, lack of specificity for target cells, and poor cellular uptake. To address these issues, we prepared amine magnetic mesoporous silica nanoparticles (M-MSN-A then further modified with polyethylene glycol (PEG for use as CpG delivery vectors. The PEG modified M-MSN-A (M-MSN-P had notable CpG ODN loading capacity, negligible cytotoxicity, and were easily internalized into cells where they released the loaded CpG into the cytoplasm. As a result, such complexes were effective in activating macrophages and inhibiting tumor cells when combined with chemotherapeutics in vitro. Furthermore, these complexes had excellent immuno-stimulating activity in vivo, compared to the free CpG therapeutics. We report here a highly effective MSNs-based delivery system with great potential as a therapeutic CpG formulation in cancer immunotherapy.

  13. CpG oligodeoxynucleotides augment the murine immune response to the Yersinia pestis F1-V vaccine in bubonic and pneumonic models of plague.

    Science.gov (United States)

    Amemiya, Kei; Meyers, Jennifer L; Rogers, Taralyn E; Fast, Randy L; Bassett, Anthony D; Worsham, Patricia L; Powell, Bradford S; Norris, Sarah L; Krieg, Arthur M; Adamovicz, Jeffrey J

    2009-04-06

    The current U.S. Department of Defense candidate plague vaccine is a fusion between two Yersinia pestis proteins: the F1 capsular protein, and the low calcium response (Lcr) V-protein. We hypothesized that an immunomodulator, such as CpG oligodeoxynucleotide (ODN)s, could augment the immune response to the plague F1-V vaccine in a mouse model for plague. CpG ODNs significantly augmented the antibody response and efficacy of a single dose of the plague vaccine in murine bubonic and pneumonic models of plague. In the latter study, we also found an overall significant augmentation the immune response to the individual subunits of the plague vaccine by CpG ODN 2006. In a long-term, prime-boost study, CpG ODN induced a significant early augmentation of the IgG response to the vaccine. The presence of CpG ODN induced a significant increase in the IgG2a subclass response to the vaccine up to 5 months after the boost. Our studies showed that CpG ODNs significantly augmented the IgG antibody response to the plague vaccine, which increased the probability of survival in murine models of plague (P<0.0001).

  14. The Impact of CpG Island on Defining Transcriptional Activation of the Mouse L1 Retrotransposable Elements

    Science.gov (United States)

    Lee, Sung-Hun; Cho, Soo-Young; Shannon, M. Frances; Fan, Jun; Rangasamy, Danny

    2010-01-01

    Background L1 retrotransposable elements are potent insertional mutagens responsible for the generation of genomic variation and diversification of mammalian genomes, but reliable estimates of the numbers of actively transposing L1 elements are mostly nonexistent. While the human and mouse genomes contain comparable numbers of L1 elements, several phylogenetic and L1Xplore analyses in the mouse genome suggest that 1,500–3,000 active L1 elements currently exist and that they are still expanding in the genome. Conversely, the human genome contains only 150 active L1 elements. In addition, there is a discrepancy among the nature and number of mouse L1 elements in L1Xplore and the mouse genome browser at the UCSC and in the literature. To date, the reason why a high copy number of active L1 elements exist in the mouse genome but not in the human genome is unknown, as are the potential mechanisms that are responsible for transcriptional activation of mouse L1 elements. Methodology/Principal Findings We analyzed the promoter sequences of the 1,501 potentially active mouse L1 elements retrieved from the GenBank and L1Xplore databases and evaluated their transcription factors binding sites and CpG content. To this end, we found that a substantial number of mouse L1 elements contain altered transcription factor YY1 binding sites on their promoter sequences that are required for transcriptional initiation, suggesting that only a half of L1 elements are capable of being transcriptionally active. Furthermore, we present experimental evidence that previously unreported CpG islands exist in the promoters of the most active TF family of mouse L1 elements. The presence of sequence variations and polymorphisms in CpG islands of L1 promoters that arise from transition mutations indicates that CpG methylation could play a significant role in determining the activity of L1 elements in the mouse genome. Conclusions A comprehensive analysis of mouse L1 promoters suggests that the

  15. The role of the CpG island methylator phenotype on survival outcome in colon cancer.

    Science.gov (United States)

    Kang, Ki Joo; Min, Byung Hoon; Ryu, Kyung Ju; Kim, Kyoung Mee; Chang, Dong Kyung; Kim, Jae J; Rhee, Jong Chul; Kim, Young Ho

    2015-03-01

    CpG island methylator phenotype (CIMP)- high colorectal cancers (CRCs) have distinct clinicopathologi-cal features from their CIMP-low/negative CRC counterparts. However, controversy exists regarding the prognosis of CRC according to the CIMP status. Therefore, this study examined the prognosis of Korean patients with colon cancer according to the CIMP status. Among a previous cohort pop-ulation with CRC, a total of 154 patients with colon cancer who had available tissue for DNA extraction were included in the study. CIMP-high was defined as ≥3/5 methylated mark-ers using the five-marker panel (CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1). CIMP-high and CIMP-low/neg-ative cancers were observed in 27 patients (17.5%) and 127 patients (82.5%), respectively. Multivariate analysis adjust-ing for age, gender, tumor location, tumor stage and CIMP and microsatellite instability (MSI) statuses indicated that CIMP-high colon cancers were associated with a significant increase in colon cancer-specific mortality (hazard ratio [HR], 3.23; 95% confidence interval [CI], 1.20 to 8.69; p=0.02). In microsatellite stable cancers, CIMP-high cancer had a poor survival outcome compared to CIMP-low/negative cancer (HR, 2.91; 95% CI, 1.02 to 8.27; p=0.04). Re-gardless of the MSI status, CIMP-high cancers had poor sur-vival outcomes in Korean patients. (Gut Liver, 2015;9202-207).

  16. Determinants of prosocial behavior in included versus excluded contexts

    Directory of Open Access Journals (Sweden)

    Esther eCuadrado

    2016-01-01

    Full Text Available Prosocial behavior is increasingly becoming necessary as more and more individuals experience exclusion. In this context it is important to understand the motivational determinants of prosocial behavior. Here we report two experiments which analyzed the influence of dispositional (prosocialness; rejection sensitivity and motivational variables (prosocial self-efficacy; prosocial collective efficacy; trust; anger; social affiliation motivation on prosocial behavior under neutral contexts (Study 1, and once under inclusion or exclusion conditions (Study 2. Both studies provided evidence for the predicted mediation of prosocial behavior. Results in both neutral and inclusion and exclusion conditions supported our predictive model of prosocial behavior. In the model dispositional variables predicted motivational variables, which in turn predicted prosocial behavior. We showed that the investigated variables predicted prosocial behavior; this suggests that to promote prosocial behavior one could (1 foster prosocialness, prosocial self and collective efficacy, trust in others and affiliation motivation and (2 try to reduce negative feelings and the tendency to dread rejection in an attempt to reduce the negative impact that these variables have on prosocial behavior. Moreover, the few differences that emerged in the model between the inclusion and exclusion contexts suggested that in interventions with excluded individuals special care emphasis should be placed on addressing rejection sensitivity and lack of trust.

  17. Should the Standard Count Be Excluded from Neutron Probe Calibration?

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhuanfang

    2017-10-12

    About 6 decades after its introduction, the neutron probe remains one of the most accurate methods for indirect measurement of soil moisture content. Traditionally, the calibration of a neutron probe involves the ratio of the neutron count in the soil to a standard count, which is the neutron count in the fixed environment such as the probe shield or a specially-designed calibration tank. The drawback of this count-ratio-based calibration is that the error in the standard count is carried through to all the measurements. An alternative calibration is to use the neutron counts only, not the ratio, with proper correction for radioactive decay and counting time. To evaluate both approaches, the shield counts of a neutron probe used for three decades were analyzed. The results show that the surrounding conditions have a substantial effect on the standard count. The error in the standard count also impacts the calculation of water storage and could indicate false consistency among replicates. The analysis of the shield counts indicates negligible aging effect of the instrument over a period of 26 years. It is concluded that, by excluding the standard count, the use of the count-based calibration is appropriate and sometimes even better than ratio-based calibration. The count-based calibration is especially useful for historical data when the standard count was questionable or absent

  18. Polder maps: improving OMIT maps by excluding bulk solvent.

    Science.gov (United States)

    Liebschner, Dorothee; Afonine, Pavel V; Moriarty, Nigel W; Poon, Billy K; Sobolev, Oleg V; Terwilliger, Thomas C; Adams, Paul D

    2017-02-01

    The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. The tools described in this manuscript have been implemented and are available in PHENIX.

  19. The politics of corruption, inequality, and the socially excluded.

    Science.gov (United States)

    Santos Salas, Anna

    2013-07-01

    In this article, the production of knowledge in the context of socially excluded people exposed to inequality, oppression, and exploitation is problematized. The analysis follows Enrique Dussel's philosophical exegesis of the politics of power and corruption and his vision of a critical transformation of the social political order. The argument is also informed by the work of critical educator Paulo Freire, who elucidates the conditions of oppression and marginalization and highlights the importance of conscientization to develop a critical awareness of these conditions. Hannah Arendt's work on the politics of understanding totalitarianism also assists in the elucidation of the machinery that operates behind oppression to sustain power and inequality. The article emphasizes the need to recognize the inequality of conditions that exists between the producer of knowledge and those who live through inequality and oppression in their lived corporality. A critical transformation of the process of production of knowledge is needed to both acknowledge the conditions that sustain this endeavour in the first place and avoid the corruption of knowledge. A work of conscientization is also necessary among knowledge producers to undertake a critical analysis of inequality that exposes the corruption of power. This analysis needs to examine and unmask the hidden mechanisms that perpetuate inequality and oppression and serve only the interests of a few. The abysmal gaps between the wealthy and the poor within and among countries bespeak a degree of human indifference that reflects a most serious and complex phenomenon that perverts something profoundly human in our societies. © 2013 John Wiley & Sons Ltd.

  20. 75 FR 49528 - Freescale Semiconductor, Inc., Networking and Multimedia Group (“NMG”) Excluding the Multimedia...

    Science.gov (United States)

    2010-08-13

    ... Employment and Training Administration Freescale Semiconductor, Inc., Networking and Multimedia Group (``NMG'') Excluding the Multimedia Applications Division Including On- Site Leased Workers of Synergy Services..., applicable to workers of Freescale Semiconductor, Inc., Networking and Multimedia Group (``NMG''), excluding...

  1. CpG island methylator phenotype in plasma is associated with hepatocellular carcinoma prognosis

    Science.gov (United States)

    Liu, Ji-Bin; Zhang, Yi-Xin; Zhou, Shu-Hui; Shi, Min-Xin; Cai, Jin; Liu, Yan; Chen, Ke-Ping; Qiang, Fu-Lin

    2011-01-01

    AIM: To evaluate the clinical significance of CpG island methylator phenotype (CIMP) in plasma and its association with hepatocellular carcinoma (HCC) progress. METHODS: CIMP status of 108 HCC patients was analyzed using a methylation marker panel in tumor tissues and plasma with methylation-specific polymerase chain reaction. Fifteen samples of non-neoplastic liver tissues and 60 of plasma from healthy persons were examined simultaneously. Examined genes included APC, WIF-1, RUNX-3, DLC-1, SFRP-1, DKK and E-cad. RESULTS: The frequencies of high-level methylation in HCC tissue and plasma were at least 15% for the seven genes: APC, 48/108, 44.44% in tissue and 26/108, 24.07% in plasma; WIF-1, 53/108, 49.07% in tissue and 35/108, 32.41% in plasma; RUNX-3, 52/108, 48.14% in tissue and 42/108, 38.89% in plasma; DLC-1, 38/108, 35.18% in tissue and 23/108, 21.30% in plasma; SFRP-1, 40/108, 37.04% in tissue and 31/108, 28.7% in plasma; DKK, 39/108, 36.1% in tissue and 25/108, 23.14% in plasma; and E-cad, 37/108, 34.3% in tissue and 18/108, 16.67% in plasma. CIMP+ (≥ 3 methylated genes) was detected in 68 (60.2%) tumor tissue samples and 62 (57.4%) plasma samples. CIMP was not detected in non-neoplastic liver tissues or plasma of healthy persons. CIMP status in tumor tissues differed significantly in gender, hepatitis B surface antigen, alpha-fetoprotein, and tumor-node-metastasis stage (P < 0.05). Similar results were obtained with plasma samples (P < 0.05). There was no difference in CIMP status in age, presence of hepatitis C virus antibody, cirrhosis, number of nodes, number of tumors, tumor size, or Edmondson-Steiner stage. A one-year follow-up found that the metastatic rate and recurrence rate in the CIMP+ group were significantly higher than in the CIMP- group as assessed with plasma samples (P < 0.05). CONCLUSION: Plasma DNA can be a reliable sample source for CIMP analysis. CIMP in plasma may serve as a molecular marker of late-stage and poor-prognosis HCC. PMID

  2. CpG island methylator phenotype and Helicobacter pylori infection associated with gastric cancer

    Science.gov (United States)

    Liu, Ji-Bin; Wu, Xu-Ming; Cai, Jin; Zhang, Jin-Ye; Zhang, Jin-Lin; Zhou, Shu-Hui; Shi, Min-Xin; Qiang, Fu-Lin

    2012-01-01

    AIM: To investigate the association between the CpG island methylator phenotype (CIMP) and serum Helicobacter pylori (H. pylori) levels for clinical prediction of gastric cancer (GC) progression. METHODS: We analyzed the serum CIMP status of 75 patients with GC using a methylation marker panel and a methylation-specific polymerase chain reaction. Serum samples from 40 healthy persons were examined at the same time. The genes examined were APC, WIF-1, RUNX-3, DLC-1, SFRP-1, DKK and E-cad. H. pylori infection in serum was assayed with an anti-H. pylori immunoglobulin G antibody test and a rapid urease test. RESULTS: The frequencies of high-level methylation in GC tissues for the seven genes were: 48% for APC, 57.33% for WIF-1, 56% for RUNX-3, 50.67% for DLC-1, 52% for SFRP-1, 54.67% for DKK, and 48% for E-cad. The frequencies in GC serum were 30.67% for APC, 34.67% for WIF-1, 37.33% for RUNX-3, 29.33% for DLC-1, 33.33% for SFRP-1, 32% for DKK, and 26.67% for E-cad. CIMP+ (defined as ≥ 3 methylated genes) was associated with 47 (62.67%) GC tissue samples and 44 (58.67%) GC serum samples. CIMP+ was not associated with non-neoplastic mucosal tissues or the serum of healthy persons. Of the 75 GC cases, 51 (68%) were H. pylori+, and 24 (32%) were H. pylori-. Of the 51 H. pylori+ cases, 36 were CIMP+ and 15 were CIMP-. In contrast, for the 24 H. pylori- cases, 11 were CIMP+, and 13 were CIMP-. The difference was significant between the H. pylori+ and H. pylori- groups (χ2 = 4.27, P < 0.05). Of the 51 H. pylori+ GC patients, 34 were CIMP+ and 17 were CIMP-, while among the 24 H. pylori- GC cases, 10 were CIMP+ and 14 were CIMP-. The difference was significant between the H. pylori+ and H. pylori- groups (χ2 = 4.21, P < 0.05). A 2-year follow-up showed significant difference in the rates of metastasis and recurrence between H. pylori+/CIMP+ cases and the H. pylori+/CIMP- cases or CIMP- cases associated with H. pylori assayed in serum (P < 0.05). However, there were no

  3. hTERT promoter activity and CpG methylation in HPV-induced carcinogenesis

    Directory of Open Access Journals (Sweden)

    Snijders Peter JF

    2010-06-01

    Full Text Available Abstract Background Activation of telomerase resulting from deregulated hTERT expression is a key event during high-risk human papillomavirus (hrHPV-induced cervical carcinogenesis. In the present study we examined hTERT promoter activity and its relation to DNA methylation as one of the potential mechanisms underlying deregulated hTERT transcription in hrHPV-transformed cells. Methods Using luciferase reporter assays we analyzed hTERT promoter activity in primary keratinocytes, HPV16- and HPV18-immortalized keratinocyte cell lines and cervical cancer cell lines. In the same cells as well as cervical specimens we determined hTERT methylation by bisulfite sequencing analysis of the region spanning -442 to +566 (relative to the ATG and quantitative methylation specific PCR (qMSP analysis of two regions flanking the hTERT core promoter. Results We found that in most telomerase positive cells increased hTERT core promoter activity coincided with increased hTERT mRNA expression. On the other hand basal hTERT promoter activity was also detected in telomerase negative cells with no or strongly reduced hTERT mRNA expression levels. In both telomerase positive and negative cells regulatory sequences flanking both ends of the core promoter markedly repressed exogenous promoter activity. By extensive bisulfite sequencing a strong increase in CpG methylation was detected in hTERT positive cells compared to cells with no or strongly reduced hTERT expression. Subsequent qMSP analysis of a larger set of cervical tissue specimens revealed methylation of both regions analyzed in 100% of cervical carcinomas and 38% of the high-grade precursor lesions, compared to 9% of low grade precursor lesions and 5% of normal controls. Conclusions Methylation of transcriptionally repressive sequences in the hTERT promoter and proximal exonic sequences is correlated to deregulated hTERT transcription in HPV-immortalized cells and cervical cancer cells. The detection of DNA

  4. Epigenetic regulation of CpG promoter methylation in invasive prostate cancer cells

    Directory of Open Access Journals (Sweden)

    Farrar William L

    2010-10-01

    Full Text Available Abstract Background Recently, much attention has been focused on gaining a better understanding of the different populations of cells within a tumor and their contribution to cancer progression. One of the most commonly used methods to isolate a more aggressive sub-population of cells utilizes cell sorting based on expression of certain cell adhesion molecules. A recently established method we developed is to isolate these more aggressive cells based on their properties of increased invasive ability. These more invasive cells have been previously characterized as tumor initiating cells (TICs that have a stem-like genomic signature and express a number of stem cell genes including Oct3/4 and Nanog and are more tumorigenic compared to their 'non-invasive' counterpart. They also have a profile reminiscent of cells undergoing a classic pattern of epithelial to mesenchymal transition or EMT. Using this model of invasion, we sought to investigate which genes are under epigenetic control in this rare population of cells. Epigenetic modifications, specifically DNA methylation, are key events regulating the process of normal human development. To determine the specific methylation pattern in these invasive prostate cells, and if any developmental genes were being differentially regulated, we analyzed differences in global CpG promoter methylation. Results Differentially methylated genes were determined and select genes were chosen for additional analyses. The non-receptor tyrosine kinase BMX and transcription factor SOX1 were found to play a significant role in invasion. Ingenuity pathway analysis revealed the methylated gene list frequently displayed genes from the IL-6/STAT3 pathway. Cells which have decreased levels of the targets BMX and SOX1 also display loss of STAT3 activity. Finally, using Oncomine, it was determined that more aggressive metastatic prostate cancers in humans also have higher levels of both Stat3 and Sox1. Conclusions Using this

  5. Casino Self- and Forced Excluders' Gambling Behavior Before and After Exclusion.

    Science.gov (United States)

    Kotter, Roxana; Kräplin, Anja; Bühringer, Gerhard

    2017-11-11

    Casino exclusion programs are intended to prevent or limit gambling-related harm. Although previous research showed that self-exclusion is associated with reduced gambling, it remains unknown whether self- and forced excluded subjects show different patterns of gambling behavior and if exclusion from casino gambling affects all gambling activities. The present study retrospectively investigated (1) the role of voluntariness of exclusion for the first time, and (2) general gambling behavior of excluded individuals before and after exclusion. A total of N = 215 casino excluders (self-excluders: n = 187, forced excluders: n = 28) completed an online survey or a face-to-face interview up to 8 years after enrollment. Self- and forced excluders showed similar rates of abstinence (self-excluders: 19.3%, forced excluders: 28.6%) and reduction (self-excluders: 67.4%, forced excluders: 60.7%), even though forced excluders reported a significantly greater initial gambling intensity compared to self-excluders (e.g., pre-exclusion gambling time; self-excluders: 3.2 days/week, forced excluders: 4.3 days/week). Overall, results indicated that 20.5% of excluders stopped all gambling activities and another 66.5% reduced their gambling. Those who continued gambling significantly reduced this behavior in every segment, except for gambling halls. Findings indicate that self- and forced exclusion are associated with similarly reduced gambling behavior, even in non-excluded segments. However, unchanged gambling in gambling halls emphasizes the importance to implement consistent exclusion programs over all gambling segments.

  6. 5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation.

    Directory of Open Access Journals (Sweden)

    David K Kranzhöfer

    Full Text Available Cardiomyocytes undergo major changes in DNA methylation during maturation and transition to a non-proliferative state after birth. 5'-hydroxylation of methylated cytosines (5hmC is not only involved in DNA loss of CpG methylation but is also thought to be an epigenetic mark with unique distribution and functions. Here, we sought to get insight into the dynamics of 5'-hydroxymethylcytosine in newborn and adult cardiomyocytes.Cardiomyocyte nuclei from newborn and adult C57BL/6 mice were purified by flow cytometric sorting. 5hmC-containing DNA was captured by selective chemical labeling, followed by deep sequencing. Sequencing reads of library replicates were mapped independently (n = 3 for newborn, n = 2 for adult mice and merged for further analysis steps. 5hmC coverage was normalized to read length and the total number of mapped reads (RPKM. MethylC-Seq, ChIP-Seq and RNA-Seq data sets of newborn and adult cardiomyocytes served to elucidate specific features of 5hmC at gene bodies and around low methylated regions (LMRs representing regulatory genomic regions with enhancer function.163,544 and 315,220 5hmC peaks were identified in P1 and adult cardiomyocytes, respectively. Of these peaks, 66,641 were common between P1 and adult cardiomyocytes with more than 50% reciprocal overlap. P1 and adult 5hmC peaks were overrepresented in genic features such as exons, introns, 3'- and 5'-untranslated regions (UTRs, promotors and transcription end sites (TES. During cardiomyocyte maturation, 5hmC was found to be enriched at sites of subsequent DNA loss of CpG methylation such as gene bodies of upregulated genes (i.e. Atp2a2, Tnni3, Mb, Pdk4. Additionally, centers of postnatally established enhancers were premarked by 5hmC before DNA loss of CpG methylation.Simultaneous analysis of 5hmC-Seq, MethylC-Seq, RNA-Seq and ChIP-Seq data at two defined time points of cardiomyocyte maturation demonstrates that 5hmC is positively associated with gene expression and

  7. 21 CFR 1308.26 - Excluded veterinary anabolic steroid implant products.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Excluded veterinary anabolic steroid implant... SCHEDULES OF CONTROLLED SUBSTANCES Excluded Veterinary Anabolic Steroid Implant Products § 1308.26 Excluded veterinary anabolic steroid implant products. (a) Products containing an anabolic steroid, that are expressly...

  8. De novo CpG methylation on an artificial chromosome-like vector maintained for a long-term in mammalian cells.

    Science.gov (United States)

    Nishioka, Keisuke; Kishida, Tsunao; Masui, Shinji; Mazda, Osam

    2016-04-01

    To examine whether an autonomously replicating, artificial chromosome-like vector containing a long genomic DNA sequence (namely, Epigenosome-Nanog) undergoes de novo CpG methylation after maintenance in cultured cells for more than a half year. Epigenosome-Nanog efficiently replicated in iPS cells after transfection. In HeLa and C2C12 cells Epigenosome-Nanog was stably maintained for more than eight months. The CpG methylation occurred de novo at the Nanog gene promoter region on the epigenosome in C2C12 cells but the degrees of methylation were much lower than those at the same CpG sites on the chromosomes. Among the four CpG sites at the region, the upstream two CpGs underwent methylation in a correlated manner while methylation at the downstream two CpGs was also correlated to each other, and these correlations were commonly shared between the epigenosome and the chromosome. CpG methylation thus was not solely dependent on the nucleotide sequence at the DNA locus. The epigenosome may become a useful tool to study the mechanisms of epigenetic regulation of a genetic region of interest in mammalian cells.

  9. Prevention and Treatment of Cutaneous Leishmaniasis in Primates by Using Synthetic Type D/A Oligodeoxynucleotides Expressing CpG Motifs

    Science.gov (United States)

    Flynn, Barbara; Wang, Vivian; Sacks, David L.; Seder, Robert A; Verthelyi, Daniela

    2005-01-01

    Oligodeoxynucleotides (ODN) containing CpG motifs mimic microbial DNA and are recognized by toll-like receptor 9 on immune cells. The resulting response limits the early spread of infectious organisms and promotes the development of adaptive immunity. In this regard, CpG ODN show promise as immunoprotective agents and as vaccine adjuvants. Previous studies of nonhuman primates showed that administration of CpG ODN type D (also known as type A) at the site of infection 3 days before and after a challenge with Leishmania major enhanced host resistance and reduced the lesion's severity. In this study, we show that systemic administration of D/A ODN limits the size of lesions following an intradermal infection with L. major. Importantly, the reduced morbidity was not associated with a reduction in long-term immunity, as such treated macaques were still protected following a secondary challenge. Finally, administration of D/A ODN to macaques that had established cutaneous lesions reduced the severity of the lesions, suggesting a potential role for CpG ODN in L. major treatment. Together, these findings support the development of clinical studies to assess the use of CpG ODN types D/A as immunoprotective and therapeutic agents. PMID:16041009

  10. Determination of methylated CpG sites in the promoter region of catechol-O-methyltransferase (COMT and their involvement in the etiology of tobacco smoking

    Directory of Open Access Journals (Sweden)

    Qing Xu

    2010-06-01

    Full Text Available We previously reported that catechol-O-methyltransferase (COMT is significantly associated with nicotine dependence (ND in humans. In this study, we examined whether there exists any difference in the extent of methylation of CpG dinucleotides in the promoter region of COMT in smokers and nonsmokers by analyzing the methylation status of cytosines at 33 CpG sites through direct sequencing of bisulfite-treated DNA (N = 50 per group. The cytosine was methylated at 13 of 33 CpG sites, and two of these sites showed significant differences between smokers and matched nonsmoker controls. Specifically, in the -193 CpG site, the degree of methylation was 19.1% in smokers and 13.2% in nonsmokers (P < 0.01. This finding was confirmed by methylation-specific PCR using an additional 100 smoker and 100 nonsmoker control samples, which showed the degree of methylation to be 22.2% in smokers and 18.3% in nonsmokers (P < 0.01. For the -39 CpG site, the degree of methylation was 9.2% in smokers, whereas no methylation was found in nonsmoker controls. Together, our findings provide the first molecular explanation at the epigenetic level for the association of ND with methylation of the COMT promoter, implying that methylation plays a role in smoking dependence.

  11. Proinflammatory Stimulation of Toll-Like Receptor 9 with High Dose CpG ODN 1826 Impairs Endothelial Regeneration and Promotes Atherosclerosis in Mice.

    Directory of Open Access Journals (Sweden)

    Alexander O Krogmann

    Full Text Available Toll-like receptors (TLR of the innate immune system have been closely linked with the development of atherosclerotic lesions. TLR9 is activated by unmethylated CpG motifs within ssDNA, but also by CpG motifs in nucleic acids released during vascular apoptosis and necrosis. The role of TLR9 in vascular disease remains controversial and we sought to investigate the effects of a proinflammatory TLR9 stimulation in mice.TLR9-stimulation with high dose CpG ODN at concentrations between 6.25 nM to 30 nM induced a significant proinflammatory cytokine response in mice. This was associated with impaired reendothelialization upon acute denudation of the carotid and increased numbers of circulating endothelial microparticles, as a marker for amplified endothelial damage. Chronic TLR9 agonism in apolipoprotein E-deficient (ApoE-/- mice fed a cholesterol-rich diet increased aortic production of reactive oxygen species, the number of circulating endothelial microparticles, circulating sca-1/flk-1 positive cells, and most importantly augmented atherosclerotic plaque formation when compared to vehicle treated animals. Importantly, high concentrations of CpG ODN are required for these proatherogenic effects.Systemic stimulation of TLR9 with high dose CpG ODN impaired reendothelialization upon acute vascular injury and increased atherosclerotic plaque development in ApoE-/- mice. Further studies are necessary to fully decipher the contradictory finding of TLR9 agonism in vascular biology.

  12. Methylation of a CpG Island within the Uroplakin Ib Promoter: A Possible Mechanism for Loss of Uroplakin lb Expression in Bladder Carcinoma

    Directory of Open Access Journals (Sweden)

    Andrea E. Varga

    2004-03-01

    Full Text Available Uroplakin Ib is a structural protein on the surface of urothelial cells. Expression of uroplakin Ib mRNA is reduced or absent in many transitional cell carcinomas (TCCs but molecular mechanisms underlying loss of expression remain to be determined. Analysis of the uroplakin Ib promoter identified a weak CpG island spanning the proximal promoter, exon 1, and the beginning of intron 1. This study examined the hypothesis that methylation of this CpG island regulates uroplakin Ib expression. Uroplakin Ib mRNA levels were determined by reverse transcription polymerase chain reaction and CpG methylation was assessed by bisulfite modification of DNA, PCR, and sequencing. A correlation was demonstrated in 15 TCC lines between uroplakin Ib mRNA expression and lack of CpG methylation. In support of a regulatory role for methylation, incubating uroplakin Ib-negative lines with 5-aza-2′ -deoxycytidine reactivated uroplakin Ib mRNA expression. A trend between uroplakin Ib mRNA expression and CpG methylation was also observed in normal urothelium and bladder carcinomas. In particular, loss of uroplakin Ib expression correlated with methylation of a putative Spi/NFκB binding motif. The data are consistent with the hypothesis that methylation of specific sites within the uroplakin Ib promoter may be an important factor in the loss of uroplakin Ib expression in TCCs.

  13. CpG loaded MoS2 nanosheets as multifunctional agents for photothermal enhanced cancer immunotherapy.

    Science.gov (United States)

    Han, Qiusen; Wang, Xinhuan; Jia, Xinghang; Cai, Shuangfei; Liang, Wei; Qin, Yan; Yang, Rong; Wang, Chen

    2017-05-11

    Single or few-layered MoS2 nanosheets, as a novel class of 2D nanomaterials, have received tremendous attention due to their fantastic physical and chemical properties. Here, we fabricated MoS2-PEG-CpG with a small and uniform size as a multifunctional platform for photothermal enhanced immunotherapy. MoS2 nanosheets were fabricated by chemical exfoliation and further probe sonication. To realize MoS2-based adjuvant delivery, MoS2 nanosheets were functionalized with cytosine-phosphate-guanine (CpG) and polyethylene glycol (PEG) to form MoS2-PEG-CpG nanoconjugates. As an efficient nanocarrier with excellent near infrared-light (NIR) absorbing performance, MoS2-PEG-CpG significantly promotes CpG intracellular accumulation and the effect can be further enhanced by photothermal treatment. In addition, the enhanced uptake can stimulate the production of proinflammatory cytokines and remarkably elevate the immune response level. Finally, we found that MoS2-PEG-CpG could reduce the proliferative activity of cancer cells when co-cultured with a macrophage-like cell upon NIR irradiation, implying a novel strategy for multifunctional therapeutics against cancers.

  14. Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level.

    Science.gov (United States)

    Fatemi, Mehrnaz; Pao, Martha M; Jeong, Shinwu; Gal-Yam, Einav Nili; Egger, Gerda; Weisenberger, Daniel J; Jones, Peter A

    2005-11-27

    Promoters are molecular 'modules', which are controlled as individual entities yet are often analyzed by nuclease digestion methodologies which, a priori, destroy this modularity. About 40% of mammalian genes contain CpG islands in their promoters and exonic regions, which are normally unmethylated. We developed a footprinting strategy to map the chromatin structure at unmethylated CpG islands by treatment of isolated nuclei with the CpG-specific DNA methyltransferase SssI (M.SssI), followed by genomic bisulfite sequencing of individual progeny DNA molecules. This gave single molecule resolution over the promoter region and allowed for the physical linkage between binding sites on individual promoter molecules to be maintained. Comparison of the p16 promoters in two human cell lines, J82 and LD419, expressing the p16 gene at 25-fold different levels showed that the two cell lines contain remarkably different, heterogeneously positioned nucleosomes over the promoter region, which were not distinguishable by standard methods using nucleases. Our high resolution approach gives a 'digitized' visualization of each promoter providing information regarding nucleosome occupancy and may be utilized to define transcription factor binding and chromatin remodeling.

  15. Polymorphism in folate- and methionine-metabolizing enzyme and aberrant CpG island hypermethylation in uterine cervical cancer.

    Science.gov (United States)

    Kang, Sokbom; Kim, Jae Weon; Kang, Gyeong Hoon; Park, Noh Hyun; Song, Yong Sang; Kang, Soon Beom; Lee, Hyo Pyo

    2005-01-01

    This study was conducted to explore the association between the CpG island hypermethylation of tumor-associated genes and the polymorphisms of methyl group metabolizing enzymes in uterine cervical cancer. We analyzed CpG island hypermethylation in 15 genes (APC, CDH1, COX2, DAPK, FHIT, GSTP1, HLTF1, hMLH1, MGMT, p14, p16, RASSF1A, RUNX3, THBS1, and TIMP3) and its association with the methylene-tetrahydrofolate reductase (MTHFR) C677T and A1298C and the methionine synthase (MS) A2756G polymorphisms in 82 Korean women with uterine cervical cancer. All uterine cervical cancer samples had at least one gene methylated. The average number of methylated genes was lower in patients with the heterozygous genotype of MTHFR and MS than in those with the common homozygous genotype, although this difference was not significant. The MTHFR 677 CT genotype was significantly associated with the decreased promoter hypermethylation of O(6)-methylguanine DNA methyltransferase (MGMT) (OR = 0.22, 95% confidence interval (CI) 0.07-0.70, P = 0.011). However, the MTHFR C677T and A1298C and the MS A2756G polymorphisms were not associated with an increased risk of uterine cervical cancer. These findings suggest that there is a possible interaction between epigenetic and genetic factors in uterine cervical cancer.

  16. Detection and discrimination of maintenance and de novo CpG methylation events using MethylBreak.

    Science.gov (United States)

    Hsu, William; Mercado, Augustus T; Hsiao, George; Yeh, Jui-Ming; Chen, Chung-Yung

    2017-05-15

    Understanding the principles governing the establishment and maintenance activities of DNA methyltransferases (DNMTs) can help in the development of predictive biomarkers associated with genetic disorders and diseases. A detection system was developed that distinguishes and quantifies methylation events using methylation-sensitive endonucleases and molecular beacon technology. MethylBreak (MB) is a 22-mer oligonucleotide with one hemimethylated and two unmethylated CpG sites, which are also recognition sites for Sau96I and SacII, and is attached to a fluorophore and a quencher. Maintenance methylation was quantified by fluorescence emission due to the digestion of SacII when the hemimethylated CpG site is methylated, which inhibits Sau96I cleavage. The signal difference between SacII digestion of both MB substrate and maintenance methylated MB corresponds to de novo methylation event. Our technology successfully discriminated and measured both methylation activities at different concentrations of MB and achieved a high correlation coefficient of R(2)=0.997. Additionally, MB was effectively applied to normal and cancer cell lines and in the analysis of enzymatic kinetics and RNA inhibition of recombinant human DNMT1. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. A hybrid CPG-ZMP control system for stable walking of a simulated flexible spine humanoid robot.

    Science.gov (United States)

    Or, Jimmy

    2010-04-01

    Biped humanoid robots have gained much popularity in recent years. These robots are mainly controlled by two major control methods, the biologically-inspired approach based on Central Pattern Generator (CPG) and the engineering-oriented approach based on Zero Moment Point (ZMP). Given that flexibility in the body torso is required in some human activities, we believe that it is beneficial for the next generation of humanoid robots to have a flexible spine as humans do. In order to cope with the increased complexity in controlling this type of robot, a new kind of control system is necessary. Currently, there is no controller that allows a flexible spine humanoid robot to maintain stability in real-time while walking with dynamic spine motions. This paper presents a new hybrid CPG-ZMP control system for the walking of a realistically simulated flexible spine humanoid robot. Experimental results showed that using our control method, the robot is able to adapt its spine motions in real-time to allow stable walking. Our control system could be used for the control of the next generation humanoid robots. Copyright 2009 Elsevier Ltd. All rights reserved.

  18. Methylation of the estrogen receptor CpG island distinguishes spontaneous and plutonium-induced tumors from nitrosamine-induced lung tumors

    Energy Technology Data Exchange (ETDEWEB)

    Belinsky, S.A.; Baylin, S.B.; Issa, J.J. [Johns Hopkins Univ., Baltimore, MD (United States)

    1995-12-01

    CpG islands located in the promoter region of genes constitute one mechanism for regulating transcription. These islands are normally free of methylation, regardless of the expression state of the gene. Hypermethylation of CpG islands, the addition of a methyl group to the internal cytosine within CpG dinucleotides, can cause silencing of a gene. Hypermethylation has been detected as an early event at specific chromosome loci during the development of colon cancer and represents one mechanism used by neoplatic cells to inactivate tumor suppressor genes. Recent studies have demonstrated this mechanism in inactivation of the VHL tumor suppressor gene in 19% of sporadic renal tumors and the p16 {sup INK4a} tumor suppressor gene in 30% of non-small cell lung cancers. A recent report indicates that the estrogen receptor gene could also be inactivated through methylation. In addition, estrogen receptor CpG island methylation arises as a direct function of age in normal colonic mucosa and is present in virtually all colonic tumors. In cultured colon cancer cells, methylation-associated loss of expression of the estrogen receptor gene results in deregulated growth, suggesting a role for the estrogen receptor in colon cancer development. These results provide further evidence that gene silencing through methylation could be a predominant epigenetic mechanism underlying the development of many different types of cancer. The purpose of the current investigation was to determine whether estrogen receptor CpG island methylation is involved in the development of lung cancer. The frequency for methylation of the estrogen receptor CpG island in rodent lung tumors is summarized.

  19. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.

    Directory of Open Access Journals (Sweden)

    Zhifu Sun

    Full Text Available We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+ and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A, and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER- cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER- cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5 kb of the 5' end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER- breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.

  20. Combined CpG and poly I:C stimulation of monocytes results in unique signaling activation not observed with the individual ligands.

    Science.gov (United States)

    Arsenault, Ryan J; Kogut, Michael H; He, Haiqi

    2013-11-01

    Toll-like receptors (TLRs) bind to components of microbes, activate cellular signal transduction pathways and stimulate innate immune responses. Previously, we have shown in chicken monocytes that the combination of CpG, the ligand for TLR21 (the chicken equivalent of TLR9), and poly I:C, the ligand for TLR3, results in a synergistic immune response. In order to further characterize this synergy, kinome analysis was performed on chicken monocytes stimulated with either unmethylated CpG oligodeoxynucleotides (CpG) and polyinosinic-polycytidylic acid (poly I:C) individually or in combination for either 1h or 4h. The analysis was carried out using chicken species-specific peptide arrays to study the kinase activity induced by the two ligands. The arrays are comprised of kinase target sequences immobilized on an array surface. Active kinases phosphorylate their respective target sequences, and these phosphorylated peptides are then visualized and quantified. A significant number of peptides exhibited altered phosphorylation when CpG and poly I:C were given together, that was not observed when either CpG or poly I:C was given separately. The unique, synergistic TLR agonist affected peptides represent protein members of signaling pathways including calcium signaling pathway, cytokine-cytokine receptor interaction and Endocytosis at the 1h time point. At the 4h time point, TLR agonist synergy influenced pathways included Adipocytokine signaling pathway, cell cycle, calcium signaling pathway, NOD-like receptor signaling pathway and RIG-I-like receptor signaling pathway. Using nitric oxide (NO) production as the readout, TLR ligand synergy was also investigated using signaling protein inhibitors. A number of inhibitors were able to inhibit NO response in cells given CpG alone but not in cells given both CpG and poly I:C, as poly I:C alone does not elicit a significant NO response. The unique peptide phosphorylation induced by the combination of CpG and poly I:C and the

  1. Protection of Mice from Lethal Vaccinia Virus Infection by Vaccinia Virus Protein Subunits with a CpG Adjuvant

    Directory of Open Access Journals (Sweden)

    Sarah Reeman

    2017-12-01

    Full Text Available Smallpox vaccination carries a high risk of adverse events in recipients with a variety of contra-indications for live vaccines. Although alternative non-replicating vaccines have been described in the form of replication-deficient vaccine viruses, DNA vaccines, and subunit vaccines, these are less efficacious than replicating vaccines in animal models. DNA and subunit vaccines in particular have not been shown to give equivalent protection to the traditional replicating smallpox vaccine. We show here that combinations of the orthopoxvirus A27, A33, B5 and L1 proteins give differing levels of protection when administered in different combinations with different adjuvants. In particular, the combination of B5 and A27 proteins adjuvanted with CpG oligodeoxynucleotides (ODN gives a level of protection in mice that is equivalent to the Lister traditional vaccine in a lethal vaccinia virus challenge model.

  2. Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells

    KAUST Repository

    Takahashi, Yuta

    2017-05-05

    CpG islands (CGIs) are primarily promoter-associated genomic regions and are mostly unmethylated within highly methylated mammalian genomes. The mechanisms by which CGIs are protected from de novo methylation remain elusive. Here we show that insertion of CpG-free DNA into targeted CGIs induces de novo methylation of the entire CGI in human pluripotent stem cells (PSCs). The methylation status is stably maintained even after CpG-free DNA removal, extensive passaging, and differentiation. By targeting the DNA mismatch repair gene MLH1 CGI, we could generate a PSC model of a cancer-related epimutation. Furthermore, we successfully corrected aberrant imprinting in induced PSCs derived from an Angelman syndrome patient. Our results provide insights into how CpG-free DNA induces de novo CGI methylation and broaden the application of targeted epigenome editing for a better understanding of human development and disease.

  3. Induction of anti-glioma NK cell response following multiple low-dose intracerebral CpG therapy

    Science.gov (United States)

    Alizadeh, Darya; Zhang, Leying; Brown, Christine E.; Farrukh, Omar; Jensen, Michael C.; Badie, Behnam

    2010-01-01

    Purpose Stimulation of toll-like receptor-9 (TLR9) by CpG oligodeoxynucleotides (CpG-ODN) has been shown to counteract the immunosuppressive microenvironment and to inhibit tumor growth in glioma models. These studies, however, have used high doses of CpG-ODN which can induce toxicity in a clinical setting. The goal of this study was to evaluate the anti-tumor efficacy of multiple low-dose intratumoral CpG- ODN in a glioma model. Experimental Design Mice bearing four-day old intracranial GL261 gliomas received a single or multiple (two or four) intratumoral injections of CpG-ODN (3 μg) every 4 days. Tumor growth was measured by bioluminescent imaging, brain histology, and animal survival. Flow cytometry and cytotoxicity assays were used to assess anti-glioma immune response. Results Two and four intracranial injections of low-dose CpG-ODN, but not a single injection, eradicated gliomas in 70% of mice. Moreover, surviving animals exhibited durable tumor free remission (> 3 months), and were protected from intracranial rechallenge with GL21 gliomas, demonstrating the capacity for long-term anti-tumor immunity. Although most inflammatory cells appeared to increase, activated NK cells (i.e. NK+CD107a+) were more frequent than CD8+CD107a+ in the brains of rechallenged CpG-ODN-treated animals and demonstrated a stronger in vitro cytotoxicity against GL261 target cells. Leukocyte depletion studies confirmed that NK cells played an important role in the initial CpG-ODN anti-tumor response, but both CD8 and NK cells were equally important in long-term immunity against gliomas. Conclusions These findings suggest that multiple low-dose intratumoral injections of CpG-ODN can eradicate intracranial gliomas possibly through mechanisms involving NK mediated effector function. PMID:20570924

  4. Metronomic Doses of Temozolomide Enhance the Efficacy of Carbon Nanotube CpG Immunotherapy in an Invasive Glioma Model.

    Directory of Open Access Journals (Sweden)

    Mao Ouyang

    Full Text Available Even when treated with aggressive current therapies, most patients with glioblastoma survive less than two years. Rapid tumor growth, an invasive nature, and the blood-brain barrier, which limits the penetration of large molecules into the brain, all contribute to the poor tumor response associated with conventional therapies. Immunotherapy has emerged as a therapeutic approach that may overcome these challenges. We recently reported that single-walled carbon nanotubes (SWCNTs can be used to dramatically increase the immunotherapeutic efficacy of CpG oligonucleotides in a mouse model of glioma. Following implantation in the mouse brain, the tumor cell line used in these previous studies (GL261 tends to form a spherical tumor with limited invasion into healthy brain. In order to evaluate SWCNT/CpG therapy under more clinically-relevant conditions, here we report the treatment of a more invasive mouse glioma model (K-Luc that better recapitulates human disease. In addition, a CpG sequence previously tested in humans was used to formulate the SWCNT/CpG which was combined with temozolomide, the standard of care chemotherapy for glioblastoma patients. We found that, following two intracranial administrations, SWCNT/CpG is well-tolerated and improves the survival of mice bearing invasive gliomas. Interestingly, the efficacy of SWCNT/CpG was enhanced when combined with temozolomide. This enhanced anti-tumor efficacy was correlated to an increase of tumor-specific cytotoxic activity in splenocytes. These results reinforce the emerging understanding that immunotherapy can be enhanced by combining it with chemotherapy and support the continued development of SWCNT/CpG.

  5. Development of Nonaggregating Poly-A Tailed Immunostimulatory A/D Type CpG Oligodeoxynucleotides Applicable for Clinical Use

    Directory of Open Access Journals (Sweden)

    Taiki Aoshi

    2015-01-01

    Full Text Available Immunostimulatory CpG ODNs have been developed and utilized as TLR9-dependent innate immune activators and vaccine adjuvants. Four different types of immunostimulatory CpG ODNs (A/D, B/K, C, and P type have been reported. A/D type ODNs are characterized by high IFN-α production but intrinsically form aggregates, hindering its good manufacturing practice grade preparation. In this study, we developed several D35-derived ODNs (a commonly used A/D type ODN, which were modified with the addition of a phosphorothioate polynucleotide tail (such as dAs40, and examined their physical properties, solubility in saline, immunostimulatory activity on human PBMCs, and vaccine adjuvant potential in monkeys. We found that two modified ODNs including D35-dAs40 and D35core-dAs40 were immunostimulatory, similar to original D35 in human PBMCs, resulting in high IFN-α secretion in a dose-dependent manner. Physical property analysis by dynamic light scattering revealed that both D35-dAs40 and D35core-dAs40 did not form aggregates in saline, which is currently impossible for the original D35. Furthermore, D35-dAs40 and D35core-dAs40 worked as better vaccine adjuvant in monkeys. These results suggested that D35-dAs40 and D35core-dAs40 are two promising prototypes of nonaggregating A/D type ODN with advantages of ease of drug preparation for clinical applications as vaccine adjuvants or IFN-α inducing immunomodifiers.

  6. Fibronectin inhibits cytokine production induced by CpG DNA in macrophages without direct binding to DNA.

    Science.gov (United States)

    Yoshida, Hiroyuki; Nishikawa, Makiya; Yasuda, Sachiyo; Toyota, Hiroyasu; Kiyota, Tsuyoshi; Takahashi, Yuki; Takakura, Yoshinobu

    2012-10-01

    Fibronectin (FN) is known to have four DNA-binding domains although their physiological significance is unknown. Primary murine peritoneal macrophages have been shown to exhibit markedly lower responsiveness to CpG motif-replete plasmid DNA (pDNA), Toll-like receptor-9 (TLR9) ligand, compared with murine macrophage-like cell lines. The present study was conducted to examine whether FN having DNA-binding domains is involved in this phenomenon. The expression of FN was significantly higher in primary macrophages than in a macrophage-like cell line, RAW264.7, suggesting that abundant FN might suppress the responsiveness in the primary macrophages. However, electrophoretic analysis revealed that FN did not bind to pDNA in the presence of a physiological concentration of divalent cations. Surprisingly, marked tumor necrosis factor - (TNF-)α production from murine macrophages upon CpG DNA stimulation was significantly reduced by exogenously added FN in a concentration-dependent manner but not by BSA, laminin or collagen. FN did not affect apparent pDNA uptake by the cells. Moreover, FN reduced TNF-α production induced by polyI:C (TLR3 ligand), and imiquimod (TLR7 ligand), but not by LPS (TLR4 ligand), or a non-CpG pDNA/cationic liposome complex. The confocal microscopic study showed that pDNA was co-localized with FN in the same intracellular compartment in RAW264.7, suggesting that FN inhibits cytokine signal transduction in the endosomal/lysosomal compartment. Taken together, the results of the present study has revealed, for the first time, a novel effect of FN whereby the glycoprotein modulates cytokine signal transduction via CpG-DNA/TLR9 interaction in macrophages without direct binding to DNA through its putative DNA-binding domains. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Non-invasive detection of fetal trisomy 21 using fetal epigenetic biomarkers with a high CpG density.

    Science.gov (United States)

    Lim, Ji Hyae; Lee, Da Eun; Kim, Kyeong Sun; Kim, Hyun Jin; Lee, Bom Yi; Park, So Yeon; Ahn, Hyun Kyong; Lee, Si Won; Kim, Moon Young; Ryu, Hyun Mee

    2014-05-01

    Non-invasive prenatal test of trisomy 21 (T21) is being researched using fetal specific epigenetic biomarkers present in maternal plasma. We applied a methyl-CpG binding domain-based protein (MBD) method based on epigenetic characteristics of fetal specific-methylated regions with a high CpG density in HLCS on chromosome 21 and RASSF1A on chromosome 3 for the non-invasive detection of fetal T21 and estimated the diagnostic accuracy of the method. A nested case-control study was conducted with maternal plasma collected from 50 pregnant women carrying 40 normal and 10 T21 fetuses. A MBD method was used for enrichment of methylated DNA regions in maternal plasma. The levels of methylated HLCS (M-HLCS) and methylated RASSF1A (M-RASSF1A) were simultaneously measured by multiplex qPCR. Levels of M-HLCS and M-RASSF1A were obtained in all cases. Levels were not different according to fetal gender (p>0.05 in both). The level of M-HLCS was significantly increased in women with a T21 fetus compared with controls (p0.05). In non-invasive fetal T21 detection, the specificity of M-HLCS level and the epigenetic-epigenetic ratio (EER) using M-HLCS and M-RASSF1A levels were 82.5% and 92.5%, respectively, at 90.0% sensitivity. Our findings suggest that the EER may be useful as a potential biomarker for the non-invasive detection of fetal T21, regardless of fetal gender. The MBD method can be used as an effective tool in the detection of methylated fetal specific markers with a high CpG density in maternal plasma.

  8. Asymmetric DNA methylation of CpG dyads is a feature of secondary DMRs associated with the Dlk1/Gtl2 imprinting cluster in mouse.

    Science.gov (United States)

    Guntrum, Megan; Vlasova, Ekaterina; Davis, Tamara L

    2017-01-01

    Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development. To investigate the nature of these more variably methylated secondary differentially methylated regions, we adopted a hairpin linker bisulfite mutagenesis approach to examine CpG dyad methylation at differentially methylated regions associated with the murine Dlk1/Gtl2 imprinting cluster on both complementary strands. We observed homomethylation at greater than 90% of the methylated CpG dyads at the IG-DMR, which serves as the imprinting control element. In contrast, homomethylation was only observed at 67-78% of the methylated CpG dyads at the secondary differentially methylated regions; the remaining 22-33% of methylated CpG dyads exhibited hemimethylation. We propose that this high degree of hemimethylation could explain the variability in DNA methylation patterns at secondary differentially methylated regions associated with imprinted loci. We further suggest that the presence of 5-hydroxymethylation at secondary differentially methylated regions may result in hemimethylation and methylation variability as a result of passive and/or active demethylation mechanisms.

  9. A stable nanoparticulate DDA/MMG formulation acts synergistically with CpG ODN 1826 to enhance the CD4(+) T-cell response

    DEFF Research Database (Denmark)

    Karlsen, Kasper; Korsholm, Karen Smith; Mortensen, Rasmus

    2014-01-01

    /MMG/CpG was the best combination for obtaining increased CD4(+) T-cell responses. However, coformulating CpG and DDA/MMG liposomes led to instability and the formulation was therefore optimized systematically using a design of experiment. CONCLUSION: The nanoparticulate DDA/MMG/CpG adjuvant can be stabilized...

  10. Response of immune response genes to adjuvants poly [di(sodium carboxylatoethylphenoxy)phosphazene] (PCEP), CpG oligodeoxynucleotide and emulsigen at intradermal injection site in pigs.

    Science.gov (United States)

    Magiri, R B; Lai, K; Chaffey, A M; Wilson, H L; Berry, W E; Szafron, M L; Mutwiri, G K

    2016-07-01

    Understanding the mechanisms by which adjuvants mediate their effects provide critical information on how innate immunity influences the development of adaptive immunity. Despite being a critical vaccine component, the mechanisms by which adjuvants mediate their effects are not fully understood and this is especially true when they are used in large animals. This lack of understanding limits our ability to design effective vaccines. In the present study, we administered polyphosphazene (PCEP), CpG oligodeoxynucleotides (CpG), emulsigen or saline via an intradermal injection into pigs and assessed the impact on the expression of reported 'adjuvant response genes' over time. CpG induced a strong upregulation of the chemokine CXL10 several 'Interferon Response Genes', as well as TNFα, and IL-10, and a down-regulation of IL-17 genes. Emulsigen upregulated expression of chemokines CCL2 and CCL5, proinflammatory cytokines IL-6 and TNFα, as well as TLR9, and several IFN response genes. PCEP induced the expression of chemokine CCL2 and proinflammatory cytokine IL-6. These results suggest that emulsigen and CpG may promote recruitment of innate immune cells and Th1 type cytokine production but that PCEP may promote a Th-2 type immune response through the induction of IL-6, an inducer of B cell activity and differentiation. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Signal management in pharmacovigilance and human risk assessment of CpG 7909, integrating embryo-fetal and post-natal developmental toxicity studies in rats and rabbits.

    Science.gov (United States)

    Delannois, Frédérique; Planty, Camille; Giordano, Giulia; Destexhe, Eric; Stanislaus, Dinesh; Da Silva, Fernanda Tavares; Stegmann, Jens-Ulrich; Thacker, Karen; Reynaud, Lucie; Garçon, Nathalie; Segal, Lawrence

    2018-01-01

    The potential reproductive and developmental toxicity of the synthetic oligodeoxynucleotide (ODN) CpG 7909, a component of GSK's AS15 immunostimulant, was examined in rat and rabbit studies following intermittent intramuscular injections. Previous studies using subcutaneous and intraperitoneal injections in mice, rats and rabbits revealed that CpG ODNs induced developmental effects. To analyze the safety signal, GSK conducted additional animal studies using the intended clinical route of administration. CpG 7909 injections were administered intramuscularly to rats or rabbits 28 and 14days before pairing, on 4 or 5 occasions during gestation, and on lactation day 7. The No Observed Adverse Effect Level for female fertility, embryo-fetal and pre- and post-natal development was 4.2mg/kg in both species, approximately 500-fold higher than the anticipated human dose. In conclusion, the anticipated risk to humans is considered low for sporadic intramuscular exposure to CpG 7909. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Targeting of C-type lectin-like receptor 2 or P2Y12 for the prevention of platelet activation by immunotherapeutic CpG oligodeoxynucleotides: comment.

    Science.gov (United States)

    Flierl, U; Nero, T L; Lim, B; Andrews, R K; Parker, M W; Gardiner, E E; Peter, K

    2017-10-20

    We read with great interest the article by Delierneux et al. [1] in the Journal of Thrombosis and Haemostasis. The authors elegantly describe a mechanism of platelet activation by CpG oligodeoxynucleotides (ODNs) through CLEC-2 mediated binding and uptake. This is the second platelet activation mechanism to be attributed to CpG ODNs, the first being the one described by our group involving platelet-specific collagen receptor glycoprotein VI (GPVI) [2]. CpG ODNs are short single-stranded DNA molecules resembling bacterial DNA and they were developed as potential drug candidates, largely due to their immunostimulatory properties via activation of toll-like receptor 9 (TLR9) [3]. These CpG ODNs often have a phosphorothioate (PS) backbone modification, where non-bridging oxygen atoms are replaced with sulfur to prevent rapid degradation by cellular and/or plasma nucleases [4]. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  13. The immunostimulatory effect of CpG oligodeoxynucleotides on peripheral blood mononuclear cells of healthy dogs and dogs with atopic dermatitis

    NARCIS (Netherlands)

    Jassies-van der Lee, Annette; Rutten, Victor; Spiering, Rachel; van Kooten, Peter; Willemse, Ton; Broere, Femke

    2014-01-01

    Synthetic oligodeoxynucleotides containing cytosine phosphatidyl guanine-rich DNA sequences (CpG ODN) can promote T-helper type 1 (Th1) responses, reduce T-helper type 2 (Th2) responses and/or favour regulatory T cell (Treg) responses in vitro and in vivo in humans and animals, by acting via

  14. CpG ODN 1668 induce innate and adaptive immune responses in rock bream (Oplegnathus fasciatus) against rock bream iridovirus (RBIV) infection.

    Science.gov (United States)

    Jung, Myung-Hwa; Jung, Sung-Ju

    2017-10-01

    Rock bream iridovirus (RBIV) causes severe mass mortalities in rock bream in Korea. CpG ODN 1668 showed promise as immunoprotective agents against RBIV infection in rock bream. In this study, we assessed innate/adaptive-related gene expression patterns in RBIV-infected rock bream with and without CpG ODN 1668 administration to determine important immune defense related factors that may affect fish survival. In the CpG ODN 1668+virus-injected group, virus copies were more than 7.4- to 790591-fold lower than in the virus-injected group at 4 d (8.79 × 10 4 and 6.58 × 10 5 /μl, respectively), 7 d (5.30 × 10 2 and 2.29 × 10 7 /μl, respectively) and 10 dpi (7.79 × 10 1 and 6.16 × 10 7 /μl, respectively). Furthermore, in the CpG ODN 1668+virus-injected group, significantly higher levels of MyD88 (6 h, 1 d, 4 d and 7 dpi), IL1β (1 d, 2 d and 7 dpi) and perforin/granzyme (1 dpi) expression were observed, whereas these genes were not significantly expressed in the virus-injected group at that time points. Mx, ISG15 and PKR were significantly highly expressed at 4 d and 7 dpi and reduced when low viral loads at 10 dpi in the CpG ODN 1668+virus-injected group. Conversely, in the virus-injected group, Mx, ISG15 and PKR expression were significantly higher than the control group until 10 dpi. However, MHC class I, CD8, Fas, Fas ligand and caspases (3, 8 and 9) expression levels showed no statistically significant differences between virus- and CpG ODN 1668+virus-injected group. In summary, CpG ODN 1668 administration in fish induces innate immune response or cell death pathway, which could be a major contributing factor to effective fish control over viral transcription on 4 d to 10 dpi. Expression of MyD88, IL1β, perforin and granzyme-related immune gene response is critical factor for inhibition of RBIV replication. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. 20 CFR 404.1323 - Post-World War II service excluded.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Post-World War II service excluded. 404.1323... DISABILITY INSURANCE (1950- ) Wage Credits for Veterans and Members of the Uniformed Services Post-World War II Veterans § 404.1323 Post-World War II service excluded. Your service was not in the active service...

  16. 8 CFR 241.21 - Stay of deportation of excluded alien.

    Science.gov (United States)

    2010-01-01

    ... 8 Aliens and Nationality 1 2010-01-01 2010-01-01 false Stay of deportation of excluded alien. 241.21 Section 241.21 Aliens and Nationality DEPARTMENT OF HOMELAND SECURITY IMMIGRATION REGULATIONS APPREHENSION AND DETENTION OF ALIENS ORDERED REMOVED Deportation of Excluded Aliens (for Hearings Commenced...

  17. 22 CFR 40.102 - Guardian required to accompany excluded alien.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Guardian required to accompany excluded alien. 40.102 Section 40.102 Foreign Relations DEPARTMENT OF STATE VISAS REGULATIONS PERTAINING TO BOTH... Guardian required to accompany excluded alien. INA 212(a)(9)(B) is not applicable at the time of visa...

  18. Bias towards dementia: are hip fracture trials excluding too many patients? A systematic review

    NARCIS (Netherlands)

    Hebert-Davies, Jonah; Laflamme, G.-Yves; Rouleau, Dominique; Bhandari, Mohit; Devereaux, Philip J.; Guyatt, Gordon; Heetveld, Martin J.; Jeray, Kyle; Liew, Susan; Richardson, Martin J.; Schemitsch, Emil H.; Swiontkowski, Marc; Tornetta, Paul; Walter, Stephen; Mohit, Bhandari; Sprague, Sheila; Viveiros, Helena; Simunovic, Nicole; Swinton, Marilyn; Heels-Ansdell, Diane; Buckingham, Lisa; Duraikannan, Aravin; Swiontkowski, Marc F.; Agel, Julie; van Lieshout, Esther M. M.; Zielinski, Stephanie M.; Goslings, J. Carel; Haverlag, Robert; Ponsen, M. J.; de Rijcke, P. A. R.; Koppert, C. L.; Buijk, Steven E.; Groenendijk, Richard P. R.; Dawson, I.; de Rycke, P. A. R.; Tetteroo, G. W. M.; Bruijninckx, M. M. M.; Doornebosch, P.; deGraaf, E. J. R.; Patka, Peter; Eversdijk, Martin; Peters, Rolf; van Waes, Oscar; den Hartog, Dennis; van Waes, O.; Oprel, P.; Gasthuis, Kennemer; Visser, Gijs A.; Stockmann, Heyn; Silvis, Rob; Snellen, J. P.; Rybroek, A.; Scheepers, J. J. G.; Vermeulen, Erik G. J.; Siroen, M. P. C.; Vuylsteke, Ronald; Brom, H. L. F.; Ryna, H.; van Laarhoven, H. A. J.; Haag, Den; Rhemrev, S.; Bosman, C. H. R.; van Otterloo, Alexander Mol; Hoogendoorn, Jochem; Idenburg, Floris; de Vries, A. C.; Meylaerts, S. A. G.; Roukema, Gert R.; Josaputra, H.; Keller, Paul; de Rooij, P. P.; Kuiken, H.; Boxma, H.; Cleffken, B. I.; Liem, Ronald; Poolman, Rudolf W.; Simons, Maarten P.; van der Heijden, F. H. W. M.; Willems, W. J.; de Meulemeester, Frank R. A. J.; van der Hart, Cor; Tarkan, K.; Festen, S.; de Nies, F.; Out, N. J. M.; Bosma, J.; de Graaf Gasthuis, Reinier; van der Elst, Maarten; van der Pol, Carmen C.; van't Reit, Martyne; Karsten, T. M.; de Vries, M. R.; Stassen, P. S.; Schep, N.; Schmidt, Ben; Hoffman, W. H.; Segers, J. M.; Zijl, Jacco; Verhoeven, Bart; Smits, Anke; Theunissen, Evert B. M.; Wille, J.; Govaert, Lonnek; Wittich, Phillippe; Brauw, Maurits; Wille, Jan; Ritchie, Ewan D.; Wittish, H.; Wessel, R. N.; Hammacher, E. R.; Ziekenhuis, Elisabeth; Verhofstad, Michiel H. J.; Meijer, Joast M. R.; van Egmond, Teun; van den Heijden, F. H. W. M.; Campo, Martin; Verhagen, Ronald; van Kampen, A.; Biert, J.; van Vugt, Arie B.; Edwards, Michael; Blokhuis, Taco; Frolke, Jan Paul M.; Geeraidts, L.; de Waal Malefyt, M. C.; Schreurs, B.; Simmermacher, Roger K. J.; van Mulken, Jeroen; van Gaalen, Steven M.; Bronovo, Ziekenhuis; Bronkhorst, Maarten W. G. A.; Guicherit, O. R.; Frihagen, Frede; Nordsletten, Lars; Kibsgaard, Thomas; Haug, Knut Jorgen; Lona, Tariei; Ugland, Stein; Nilsen, Kenneth; Brekke, Anne Christin; Vesterhus, Elise Berg; Tetsworth, Kevin; Weinrauch, Patrick; Pincus, Paul; Donald, Geoff; yang, Steven; Halliday, Brett; Gervais, Trevor; Holt, Michael; Flynn, Annette; Pirpiris, Marinis; Love, David; Bucknill, Andrew; Farrugia, Richard J.; Dowrick, Adam; Donohue, Craig; Bedi, Harvinder; Li, Doug; Edwards, Elton; Csonguray, Steven; Miller, Russell; Wang, Otis; Chia, Andrew; Jain, Arvind; Mammen, Mathan; Moaveni, Ash; Murdock, Zoe; Sage, Claire; Bahadur, Tegh; Jain, Anil Kumar; Pankaj, Amite; Pesantez, Rodrigo; Martinez, Adriana; Novoa, Catherine; Buckley, Richard E.; Duffy, Paul; Korley, Robert; Johnston, Kelly; Puloski, Shannon; Carcary, Kimberly; Avram, Victoria; Bicknell, Ryan; Yach, Jeff; Bardana, Davide; Wood, Gavin; Lambert, Sue; Sanders, David W.; Howard, Jamie; Macleod, Mark; Lawendy, Abdel; Bartley, Debra; Laney, Tim; Tieszer, Christina; Peterson, Devin; Zalzal, Paul; Naumetz, Victor; Brien, Heather; Weening, Brad; Wai, Eugene K.; Papp, Steven; Roffey, Darren; McCormack, Robert; Stone, Trevor; Perey, Bertrand; Viskontas, Darius; Boyer, Dory; Moola, Farhad; Zomar, Mauri; Moon, Karyn; McKee, Michael; Hall, Jeremy; Ahn, Henry; Vicente, Milena R.; Wild, Lisa M.; Kreder, Hans J.; Stephen, David J. G.; Nousianinen, Markku; Kunz, Monica; Syed, Khalid; Azad, Tania; Coles, Chad; Leighton, Ross; Johnstone, David; Glazebrook, Mark; Alexander, David; Coady, Cathy; Trask, Kelly; Dobbin, Gwendolyn; Oliver, Todd M.; Jones, Vicky; Ronan, James; Brown, Desmond T.; Carlilse, Hope; Shaughnessy, Lisa; Schwappach, John; Davis, Craig A.; Weingarten, Peter; Weinerman, Stewart; Newman, Heike; Baker, Janell; Browner, Kieran; Hurley, Meghan; Payton, Krystal; Zura, Robert; Manson, Maria J.; Goetz, David; Broderick, Scott J.; Porter, Scott; Pace, Thomas; Tanner, Stephanie L.; Snider, Becky; Schmidt, Andrew H.; Haas, Jonathan; Templeman, David; Westberg, Jerald R.; Mullis, Brian; Ertl, J. P.; Shively, Karl; Frizzel, Valda; Moore, Molly M.; Marcantonio, Andrew J.; Iorio, Richard; Lobo, Margaret; Kain, Michael; Specht, Lawrence; Tilzey, John; Garfi, John; Prayson, Michael J.; Laughlin, Richard; Rubino, Joe; Lawless, Mathew; DiPaola, Matt; Gayton, Chris; Dulaney-Cripe, Liz; Vallier, Heather A.; Wilber, John; Wilber, Roger G.; Sontich, John H.; Patterson, Brendan; Dolenc, Andrea; Robinson, Chalitha; DePaolo, Charles J.; Alosky, Rachel; Shell, E.; Keeve, Jonathan P.; Anderson, Chris; McDonald, Michael; Hoffman, Jodi; Baele, Joseph; Weber, Tim; Edison, Matt; Musapatika, Dana; Jones, Clifford; Ringler, James; Endres, Terrance; Gelbke, Martin; Jabara, Michael; Sietsema, Debra L.; Engerman, Susan M.; Switzer, Julie A.; Li, Mangnai; Marston, Scott; Cole, Peter; Vang, Sandy X.; Ly, Thuan; Anderson, Sarah; Foley, Amy; McBeth, Jessica; Comstock, Curt; Ziran, Navid; Shaer, James; Hileman, Barbara; Karges, David; Cannada, Lisa; Kuldjanov, Djoldas; Watson, John Tracy; Mills, James Jackman Emily; Hill, Leslie; Simon, Tiffanya; Abdelgawad, Amr; Shunia, Juan; Jenkins, Mark; Zumwalt, Mimi; Romero, Amanda West; Lowe, Jason; Goldstein, Jessica; Zamorano, David P.; Lawson, Deanna; Archdeacon, Michael; Wyrick, John; Hampton, Shelley; Lewis, Courtland G.; Ademi, Arben; Sullivan, Raymond; Caminiti, Stephanie; Graves, Matthew; Smith, Lori; Della Rocca, Gregory J.; Crist, Brett D.; Murtha, Yvonne; Anderson, Linda K.; Kliewer, Toni K.; McPherson, Melinda K.; Sullivan, Kelly M.; Jarrett, Sharon L.; Sagebien, Carlos; Seuffert, Patricia; Mehta, Samir; Esterhai, John; Ahn, Jaimo; Tjoumakaris, Fotios; Horan, Annamarie D.; Kaminski, Christine; Tarkin, Ivan; Siska, Peter; Luther, Arlene; Irrgang, James; Farrell, Dana J.; Gorczyca, John T.; Gross, Jonathan M.; Kates, Stephen Lloyd; Colosi, Jen; Hibsch, Nancy; Noble, Krista; Neu, Sarah; Agarwal, Animesh; Wright, Rebecca; Hsu, Joseph R.; Randall, Gayle M.; Ficke, James R.; Charlton, Michael; Fan, Mary; Garcia, Socorro H.; Obremskey, William T.; Richards, Justin Edward; Robinson, Kenya; Carroll, Eben; Kulp, Brenda; Guyatt, Gordon H.; Devereaux, Philip James; Einhorn, Thomas A.; Koval, Ken J.; Tetsworth, Kevin D.; Culgin, Sarah; Desjardin, Heather; Beimers, Lijkele; de Vries, Jasper; Zurcher, Arthur W.; Albers, G. H. Rob; Rademakers, Maarten; Breugem, Stefan; van der Haven, Ibo; Damen, Peter Jan; Bulstra, Gythe H.; Somford, P.; Haverkamp, Daniël; Gasthuis, Onze Lieve Vrouwe; Molekamp, Willem Jan Kleyn; Kleipool, E. B.; Keizer, Stefan B.; Swen, Jan-Willem A.; Nelissen, Eelco M.; Hollander, Peter H. C. den; Metsaars, Weineke; Thomassen, J. W.; Fontijne, W. Peter J.; Wiersma, Saskia C.; Boetes, Bastiaan; JT, Edgar; Ziekenhuis, Spaarne; Nolte, Peter A.; de Jong, Tjitte; van Noort, Arthur; Vergroesen, Diederik A.; van den Bekerom, Michel P. J.; Schutte, Bernard G.; Schuman, Lein; Hillen, Robert Jan; Cheung, John; van der Heide, Huub J. L.; Nagels, Jochem; Krips, Rover; Mullers, J. Bernard; Schüller, Hans; Ziekenhuis, Amphia; van den Hout, Joost A. A. M.; Joosten, Adrianus J. P.; van der Broek, Chris M.; Bolder, Stefan B. T.; Eygendaal, Denise; Moonen, Adrianus F. C. M.; van Geenen, Rutger C. I.; Hoebink, Eric A.; Wagenmakers, Robert; van Helden, Wouter; Kooijman, Rob; Postema, Roelf R.; Lampe, Harald I. H.; Ziekenhuizen, Gelre; Bolhuis, Hugo W.; Bullens, Pieter H. J.; Hogervorst, Mike; de Kroon, Karin E.; Jansen, Rob H.; Raven, Eric E. J.; van Jonbergen, Hans-Peter W.; Reuver, Joost M.; Barnaart, Alexander F. W.; Roerdink, W. Herbert; van Erve, Ruud H. G. P.; Koorevaar, Rinco; Frima, Anthony Hans; Flikweert, Elvira R.; Falke, Mark L. M.; Kurek, Frans J.; Slingerland, Adrianus C. H.; Vallei, Gelderse; van Dijk, Jan P.; van Helden, Wouter H.; Mauer-Hansen, Espen; Boee, Berte; Clarke-Jensen, Jon; Brekke, Anne Christine; Vestergaard, Elise Berg; Carr, Ashley; Russ, Matthias; Li, Douglas; Doig, Stephen; Laflamme, Yves; Fernandes, Julio C.; Poirier, Marie-France; Bogoch, Earl; Kreder, Hans; Axelrod, Terry; Jenkinson, Richard; Wadey, Veronica; Nousiainen, Markku; Stephen, David; Macnevin, Melanie; Richardson, Glen C.; Biddulph, Michael; Gross, Michael; Dunbar, Michael; Dobbin, Gwen; Zarin, Jeffrey; Parvataneni, Hari; Baker, Janell K.; Roberson, James R.; Erens, Greg; Montelione, Anita; Woodard, Shawndra; Ertl, Janos; Cummings, Judd; Worman, Ripley; Webster, Mark; Parr, Andrew; Frizzell, Valda; Moore, Molly; Wilk, Richard; Torchia, Michael; Cross, William; Sems, Andrew; Taunton, Michael; Sanchez-Satelo, Joaquin; Sierrz, Rafsel; Timm, Kimberly; Foreman, Barbara; DePaolo, Charles; Hill, Rocky; Lewis, Coutland; Srivastava, Ajay; Bakeman, James; Sietsema, Deb; Strathy, Gregg; Johnson, Paul; Peter, Kathleen; Morton, Maeghan E.; Parvizi, Javad; Austin, Matthew; Morrison, Tiffany; Mont, Michael; Copeland, Carol; Delanois, Ronald; Khanuja, Harpal; Weddington, Shaquita; Bacon, Madeline; Mullen, Marylou; Kanlic, Enes; Abdelgawad, Amr Atef; Shunia, Juan Gerardo; Horan, Annamarie

    2012-01-01

    Patients with hip fractures are older and often present many co-morbidities, including dementia. These patients cannot answer quality of life questionnaires and are generally excluded from trials. We hypothesized that a significant number of patients are being excluded from these studies and this

  19. 38 CFR 17.260 - Patient care costs to be excluded from direct costs.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Patient care costs to be excluded from direct costs. 17.260 Section 17.260 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Grants for Exchange of Information § 17.260 Patient care costs to be excluded from...

  20. 40 CFR 1048.20 - What requirements from this part apply to excluded stationary engines?

    Science.gov (United States)

    2010-07-01

    ... of another company you choose to designate. (3) State the engine displacement (in liters) and maximum... to excluded stationary engines? 1048.20 Section 1048.20 Protection of Environment ENVIRONMENTAL...-IGNITION ENGINES Overview and Applicability § 1048.20 What requirements from this part apply to excluded...

  1. 41 CFR 101-30.302 - Types of items excluded from cataloging.

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 2 2010-07-01 2010-07-01 true Types of items excluded...-FEDERAL CATALOG SYSTEM 30.3-Cataloging Items of Supply § 101-30.302 Types of items excluded from...) Items procured in foreign markets for use in overseas activities of Federal agencies. (e) Printed forms. ...

  2. 26 CFR 31.3402(e)-1 - Included and excluded wages.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 15 2010-04-01 2010-04-01 false Included and excluded wages. 31.3402(e)-1... SOURCE Collection of Income Tax at Source § 31.3402(e)-1 Included and excluded wages. (a) If a portion of... not more than 31 consecutive days constitutes wages, and the remainder does not constitute wages, all...

  3. Preventing Inclusion? Inclusive Early Childhood Education and the Option to Exclude

    Science.gov (United States)

    Cologon, Kathy

    2014-01-01

    While there is increasing international commitment to inclusive education, as outlined in the United Nations Convention on the Rights of Persons with Disabilities (CRPD), many children remain excluded at school. One marginalised and frequently excluded group of people are people who experience disability. In the recently released first report on…

  4. In silico enhanced restriction enzyme based methylation analysis of the human glioblastoma genome using Agilent 244K CpG Island microarrays

    Directory of Open Access Journals (Sweden)

    Anh Tran

    2010-01-01

    Full Text Available Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling. We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE assay for use with two-color Agilent 244K CpG island microarrays. In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive and MspI (methylation-insensitive restriction enzymes. Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome. In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments. We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing. Along with additional validation points, we performed a receiver operating characteristics (ROC analysis to determine the optimal threshold (p ≤ 0.001. Based on this threshold, we identified ~2400 CpG islands common to all three samples and 145 CpG islands unique to glioblastoma. These data provide more general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches.

  5. Inheritance of an epigenetic mark: the CpG DNA methyltransferase 1 is required for de novo establishment of a complex pattern of non-CpG methylation.

    Directory of Open Access Journals (Sweden)

    Valérie Grandjean

    Full Text Available Site-specific methylation of cytosines is a key epigenetic mark of vertebrate DNA. While a majority of the methylated residues are in the symmetrical (meCpG:Gp(meC configuration, a smaller, but significant fraction is found in the CpA, CpT and CpC asymmetric (non-CpG dinucleotides. CpG methylation is reproducibly maintained by the activity of the DNA methyltransferase 1 (Dnmt1 on the newly replicated hemimethylated substrates (meCpG:GpC. On the other hand, establishment and hereditary maintenance of non-CpG methylation patterns have not been analyzed in detail. We previously reported the occurrence of site- and allele-specific methylation at both CpG and non-CpG sites. Here we characterize a hereditary complex of non-CpG methylation, with the transgenerational maintenance of three distinct profiles in a constant ratio, associated with extensive CpG methylation. These observations raised the question of the signal leading to the maintenance of the pattern of asymmetric methylation. The complete non-CpG pattern was reinstated at each generation in spite of the fact that the majority of the sperm genomes contained either none or only one methylated non-CpG site. This observation led us to the hypothesis that the stable CpG patterns might act as blueprints for the maintenance of non-CpG DNA methylation. As predicted, non-CpG DNA methylation profiles were abrogated in a mutant lacking Dnmt1, the enzymes responsible for CpG methylation, but not in mutants defective for either Dnmt3a or Dnmt2.

  6. Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

    Directory of Open Access Journals (Sweden)

    Adam G Marsh

    Full Text Available Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera and an anemone (Nematostella vectensis. Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to

  7. Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island.

    Directory of Open Access Journals (Sweden)

    Heather M O'Hagan

    2008-08-01

    Full Text Available Chronic exposure to inducers of DNA base oxidation and single and double strand breaks contribute to tumorigenesis. In addition to the genetic changes caused by this DNA damage, such tumors often contain epigenetically silenced genes with aberrant promoter region CpG island DNA hypermethylation. We herein explore the relationships between such DNA damage and epigenetic gene silencing using an experimental model in which we induce a defined double strand break in an exogenous promoter construct of the E-cadherin CpG island, which is frequently aberrantly DNA hypermethylated in epithelial cancers. Following the onset of repair of the break, we observe recruitment to the site of damage of key proteins involved in establishing and maintaining transcriptional repression, namely SIRT1, EZH2, DNMT1, and DNMT3B, and the appearance of the silencing histone modifications, hypoacetyl H4K16, H3K9me2 and me3, and H3K27me3. Although in most cells selected after the break, DNA repair occurs faithfully with preservation of activity of the promoter, a small percentage of the plated cells demonstrate induction of heritable silencing. The chromatin around the break site in such a silent clone is enriched for most of the above silent chromatin proteins and histone marks, and the region harbors the appearance of increasing DNA methylation in the CpG island of the promoter. During the acute break, SIRT1 appears to be required for the transient recruitment of DNMT3B and subsequent methylation of the promoter in the silent clones. Taken together, our data suggest that normal repair of a DNA break can occasionally cause heritable silencing of a CpG island-containing promoter by recruitment of proteins involved in silencing. Furthermore, with contribution of the stress-related protein SIRT1, the break can lead to the onset of aberrant CpG island DNA methylation, which is frequently associated with tight gene silencing in cancer.

  8. A non-variable L1-peptide displays high sensitivity and specificity for detecting women having human papillomavirus-associated cervical lesions.

    Science.gov (United States)

    Urquiza, Mauricio; Guevara, Tatiana; Sanchez, Ricardo; Vanegas, Magnolia; Patarroyo, Manuel E

    2008-06-01

    Anti-human papillomavirus (HPV) antibody detection is promising technique for detecting women at risk of suffering cervical cancer, since potentially oncogenic, persistent, long-term HPV-infections elicit an antibody response which is rarely detected in transitory HPV-infection patients. We have identified a non-variable C-terminus L1-peptide, belonging to an alpha-helix surface exposed on L1-protein, specifically recognized by antibodies from HPV-associated cervical lesion patients. This peptide tested against 313 sera presented higher reactivity with antibodies from cervical cancer (OD mean 0.43+/-0.13) or cervical lesion patients (OD mean 0.41+/-0.17) than antibodies from normal cytology patients (OD mean 0.17+/-0.03). High-risk HPV-infected patients presented higher antibody reactivity (OD mean 0.36+/-0.17) than high-risk HPV-non-infected patients (OD mean 0.22+/-0.11). This peptide showed 88.36% sensitivity, 99.39% specificity and 94.21% correct classification of high risk-HPV cervical lesion or cervical cancer patients. This peptide should be taken into account for designing serological screening or diagnostic tests for use in a clinical scenario.

  9. Vaccination with heat-killed leishmania antigen or recombinant leishmanial protein and CpG oligodeoxynucleotides induces long-term memory CD4+ and CD8+ T cell responses and protection against leishmania major infection.

    Science.gov (United States)

    Rhee, Elizabeth G; Mendez, Susana; Shah, Javeed A; Wu, Chang-you; Kirman, Joanna R; Turon, Tara N; Davey, Dylan F; Davis, Heather; Klinman, Dennis M; Coler, Rhea N; Sacks, David L; Seder, Robert A

    2002-06-17

    CpG oligodeoxynucleotides (ODN) have potent effects on innate and adaptive cellular immune responses. In this report, the ability of CpG ODN to confer long-term immunity and protection when used as a vaccine adjuvant with a clinical grade of leishmanial antigen, autoclaved Leishmania major (ALM), or a recombinant leishmanial protein was studied. In two different mouse models of L. major infection, vaccination with ALM plus CpG ODN was able to control infection and markedly reduce lesion development in susceptible BALB/c and resistant C57BL/6 (B6) mice, respectively, up to 12 wk after immunization. Moreover, B6 mice immunized with ALM plus CpG ODNs were still protected against infectious challenge even 6 mo after vaccination. In terms of immune correlates of protection, ALM plus CpG ODN-vaccinated mice displayed L. major-specific T helper cell 1 and CD8+ responses. In addition, complete protection was markedly abrogated in mice depleted of CD8+ T cells at the time of vaccination. Similarly, mice vaccinated with a recombinant leishmanial protein plus CpG ODN also had long-term protection that was dependent on CD8+ T cells in vivo. Together, these data demonstrate that CpG ODN, when used as a vaccine adjuvant with either a recombinant protein or heat-killed leishmanial antigen, can induce long-term protection against an intracellular infection in a CD8-dependent manner.

  10. Delivery of an inactivated avian influenza virus vaccine adjuvanted with poly(D,L-lactic-co-glycolic acid) encapsulated CpG ODN induces protective immune responses in chickens.

    Science.gov (United States)

    Singh, Shirene M; Alkie, Tamiru N; Nagy, Éva; Kulkarni, Raveendra R; Hodgins, Douglas C; Sharif, Shayan

    2016-09-14

    In poultry, systemic administration of commercial vaccines consisting of inactivated avian influenza virus (AIV) requires the simultaneous delivery of an adjuvant (water-in-oil emulsion). These vaccines are often limited in their ability to induce quantitatively better local (mucosal) antibody responses capable of curtailing virus shedding. Therefore, more efficacious adjuvants with the ability to provide enhanced immunogenicity and protective anti-AIV immunity in chickens are needed. While the Toll-like receptor (TLR) 21 agonist, CpG oligodeoxynucleotides (ODNs) has been recognized as a potential vaccine adjuvant in chickens, poly(D,L-lactic-co-glycolic acid) (PLGA) nanoparticles, successfully tested as vaccine delivery systems in other species, have not been extensively explored. The present study, therefore, assessed both systemic and mucosal antibody-mediated responses following intramuscular vaccination (administered at 7 and 21days post-hatch) of chickens with PLGA encapsulated H9N2 AIV plus encapsulated CpG ODN 2007 (CpG 2007), and nonencapsulated AIV plus PLGA encapsulated CpG 2007 vaccine formulations. Virus challenge was performed at 2weeks post-secondary vaccination using the oculo-nasal route. Our results showed that chickens vaccinated with the nonencapsulated AIV vaccine plus PLGA encapsulated CpG 2007 developed significantly higher systemic IgY and local (mucosal) IgY antibodies as well as haemagglutination inhibition antibody titres compared to PLGA encapsulated AIV plus encapsulated CpG 2007 vaccinated chickens. Furthermore, chickens that received CpG 2007 as an adjuvant in the vaccine formulation had antibodies exhibiting higher avidity indicating that the TLR21-mediated pathway may enhance antibody affinity maturation qualitatively. Collectively, our data indicate that vaccination of chickens with nonencapsulated AIV plus PLGA encapsulated CpG 2007 results in qualitatively and quantitatively augmented antibody responses leading to a reduction in

  11. An empirically driven data reduction method on the human 450K methylation array to remove tissue specific non-variable CpGs.

    Science.gov (United States)

    Edgar, Rachel D; Jones, Meaghan J; Robinson, Wendy P; Kobor, Michael S

    2017-01-01

    Population based epigenetic association studies of disease and exposures are becoming more common with the availability of economical genome-wide technologies for interrogation of the methylome, such as the Illumina 450K Human Methylation Array (450K). Often, the expected small number of differentially methylated cytosine-guanine pairs (CpGs) in studies of the human methylome presents a statistical challenge, as the large number of CpGs measured on the 450K necessitates careful multiple test correction. While the 450K is a highly useful tool for population epigenetic studies, many of the CpGs tested are not variable and thus of limited information content in the context of the study and tissue. CpGs with observed lack of variability in the tissue under study could be removed to reduce the data dimensionality, limit the severity of multiple test correction and allow for improved detection of differential DNA methylation. Here, we performed a meta-analysis of 450K data from three commonly studied human tissues, namely blood (605 samples), buccal epithelial cells (121 samples) and placenta (157 samples). We developed lists of CpGs that are non-variable in each tissue. These lists are surprisingly large (blood 114,204 CpGs, buccal epithelial cells 120,009 CpGs and placenta 101,367 CpGs) and thus will be valuable filters for epigenetic association studies, considerably reducing the dimensionality of the 450K and subsequently the multiple testing correction severity. We propose this empirically derived method for data reduction to allow for more power in detecting differential DNA methylation associated with exposures in studies on the human methylome.

  12. Differential base stacking interactions induced by trimethylene interstrand DNA cross-links in the 5'-CpG-3' and 5'-GpC-3' sequence contexts.

    Science.gov (United States)

    Huang, Hai; Dooley, Patricia A; Harris, Constance M; Harris, Thomas M; Stone, Michael P

    2009-11-01

    Synthetically derived trimethylene interstrand DNA cross-links have been used as surrogates for the native cross-links that arise from the 1,N(2)-deoxyguanosine adducts derived from alpha,beta-unsaturated aldehydes. The native enal-mediated cross-linking occurs in the 5'-CpG-3' sequence context but not in the 5'-GpC-3' sequence context. The ability of the native enal-derived 1,N(2)-dG adducts to induce interstrand DNA cross-links in the 5'-CpG-3' sequence as opposed to the 5'-GpC-3' sequence is attributed to the destabilization of the DNA duplex in the latter sequence context. Here, we report higher accuracy solution structures of the synthetically derived trimethylene cross-links, which are refined from NMR data with the AMBER force field. When the synthetic trimethylene cross-links are placed into either the 5'-CpG-3' or the 5'-GpC-3' sequence contexts, the DNA duplex maintains B-DNA geometry with structural perturbations confined to the cross-linked base pairs. Watson-Crick hydrogen bonding is conserved throughout the duplexes. Although different from canonical B-DNA stacking, the cross-linked and the neighbor base pairs stack in the 5'-CpG-3' sequence. In contrast, the stacking at the cross-linked base pairs in the 5'-GpC-3' sequence is greatly perturbed. The pi-stacking interactions between the cross-linked and the neighbor base pairs are reduced. This is consistent with remarkable chemical shift perturbations of the C(5) H5 and H6 nucleobase protons that shifted downfield by 0.4-0.5 ppm. In contrast, these chemical shift perturbations in the 5'-CpG-3' sequence are not remarkable, consistent with the stacked structure. The differential stacking of the base pairs at the cross-linking region probably explains the difference in stabilities of the trimethylene cross-links in the 5'-CpG-3' and 5'-GpC-3' sequence contexts and might, in turn, account for the sequence selectivity of the interstrand cross-link formation induced by the native enal-derived 1,N(2)-d

  13. Nicotine induced CpG methylation of Pax6 binding motif in StAR promoter reduces the gene expression and cortisol production

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Tingting [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Chen, Man; Liu, Lian [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Cheng, Huaiyan [Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Yan, You-E [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Feng, Ying-Hong, E-mail: yhfeng@usuhs.edu [Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Wang, Hui, E-mail: wanghui19@whu.edu.cn [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Research Center of Food and Drug Evaluation, Wuhan University, Wuhan 430071 (China)

    2011-12-15

    Steroidogenic acute regulatory protein (StAR) mediates the rate-limiting step in the synthesis of steroid hormones, essential to fetal development. We have reported that the StAR expression in fetal adrenal is inhibited in a rat model of nicotine-induced intrauterine growth retardation (IUGR). Here using primary human fetal adrenal cortex (pHFAC) cells and a human fetal adrenal cell line NCI-H295A, we show that nicotine inhibits StAR expression and cortisol production in a dose- and time-dependent manner, and prolongs the inhibitory effect on cells proliferating over 5 passages after termination of nicotine treatment. Methylation detection within the StAR promoter region uncovers a single site CpG methylation at nt -377 that is sensitive to nicotine treatment. Nicotine-induced alterations in frequency of this point methylation correlates well with the levels of StAR expression, suggesting an important role of the single site in regulating StAR expression. Further studies using bioinformatics analysis and siRNA approach reveal that the single CpG site is part of the Pax6 binding motif (CGCCTGA) in the StAR promoter. The luciferase activity assays validate that Pax6 increases StAR gene expression by binding to the glucagon G3-like motif (CGCCTGA) and methylation of this site blocks Pax6 binding and thus suppresses StAR expression. These data identify a nicotine-sensitive CpG site at the Pax6 binding motif in the StAR promoter that may play a central role in regulating StAR expression. The results suggest an epigenetic mechanism that may explain how nicotine contributes to onset of adult diseases or disorders such as metabolic syndrome via fetal programming. -- Highlights: Black-Right-Pointing-Pointer Nicotine-induced StAR inhibition in two human adrenal cell models. Black-Right-Pointing-Pointer Nicotine-induced single CpG site methylation in StAR promoter. Black-Right-Pointing-Pointer Persistent StAR inhibition and single CpG methylation after nicotine termination

  14. Emulsified nanoparticles containing inactivated influenza virus and CpG oligodeoxynucleotides critically influences the host immune responses in mice.

    Directory of Open Access Journals (Sweden)

    Ming-Hsi Huang

    Full Text Available BACKGROUND: Antigen sparing and cross-protective immunity are regarded as crucial in pandemic influenza vaccine development. Both targets can be achieved by adjuvantation strategy to elicit a robust and broadened immune response. We assessed the immunogenicity of an inactivated H5N1 whole-virion vaccine (A/Vietnam/1194/2004 NIBRG-14, clade 1 formulated with emulsified nanoparticles and investigated whether it can induce cross-clade protecting immunity. METHODOLOGY/PRINCIPAL FINDINGS: After formulation with PELC, a proprietary water-in-oil-in-water nanoemulsion comprising of bioresorbable polymer/Span(R85/squalene, inactivated virus was intramuscularly administered to mice in either one-dose or two-dose schedule. We found that the antigen-specific serum antibody responses elicited after two doses of non-adjuvanted vaccine were lower than those observed after a single dose of adjuvanted vaccine, PELC and the conventional alum adjuvant as well. Moreover, 5 microg HA of PELC-formulated inactivated virus were capable of inducing higher antibodies than those obtained from alum-adjuvanted vaccine. In single-dose study, we found that encapsulating inactivated virus into emulsified PELC nanoparticles could induce better antibody responses than those formulated with PELC-adsorbed vaccine. However, the potency was rather reduced when the inactivated virus and CpG (an immunostimulatory oligodeoxynucleotide containing unmethylated cytosine-guanosine motifs were co-encapsulated within the emulsion. Finally, the mice who received PELC/CpG(adsorption-vaccine could easily and quickly reach 100% of seroprotection against a homologous virus strain and effective cross-protection against a heterologous virus strain (A/Whooper swan/Mongolia/244/2005, clade 2.2. CONCLUSIONS/SIGNIFICANCE: Encapsulating inactivated H5N1 influenza virus and CpG into emulsified nanoparticles critically influences the humoral responses against pandemic influenza. These results demonstrated

  15. GATA5 CpG island methylation in renal cell cancer: a potential biomarker for metastasis and disease progression.

    Science.gov (United States)

    Peters, Inga; Eggers, Hendrik; Atschekzei, Faranaz; Hennenlotter, Jörg; Waalkes, Sandra; Tränkenschuh, Wolfgang; Grosshennig, Anika; Merseburger, Axel S; Stenzl, Arnulf; Kuczyk, Markus A; Serth, Jürgen

    2012-07-01

    GATA5 CpG island (CGI) methylation and transcriptional inactivation is involved in colorectal and gastric cancer. Whether DNA methylation of GATA5 affects clinical pathology is still unclear. In the present study, we analysed, for the first time, CGI methylation in RCC and its association with clinicopathological parameters and progression-free survival of patients. We show for the first time GATA5 CGI hypermethylation in RCC. Moreover, we found out that increased methylation is statistically associated with status of metastasis, progressive disease and shortened progression-free survival. The present study underline the necessity for further functional investigations as well as prospective survival analyses to clarify whether GATA5 promoter methylation can provide independent information for future clinical management of patients with RCC. To investigate whether GATA5 CpG island (CGI) methylation occurs in renal cell carcinoma (RCC) and is associated with clinical, histopathological characteristics or progression-free survival of patients. Methylation was quantified in 117 RCC samples and 89 paired adjacent normal tissues using quantitative combined bisulphite restriction analysis (COBRA). COBRA was evaluated in advance by pyrosequencing analyses of control RCC cell lines (coefficient of correlation, R = 0.95). Statistical analyses were carried out using the paired t-test for matched tumour tissue (TU) and adjacent normal tissue (adN) samples, logistic regression for comparisons of independent sample groups and Cox regression for analysis of progression-free survival. In the present study, we found a significant higher mean relative methylation in TU (20.4%) than in adN (7.9%, P methylation in tumours was associated with metastasis (P = 0.005) and decreased progression-free survival (P = 0.005, HR = 4.59) in the clear-cell RCC (ccRCC) group. CGI methylation in advanced ccRCCs (pT ≥3 and/or N1, M1 or G2-3/G3) exceeds those detected in localized tumours (pT ≤2

  16. NNDSS - Table II. Salmonellosis (excluding typhoid fever and paratyphoid fever) to Shigellosis

    Data.gov (United States)

    U.S. Department of Health & Human Services — NNDSS - Table II. Salmonellosis (excluding typhoid fever and paratyphoid fever) to Shigellosis - 2018. In this Table, provisional cases of selected notifiable...

  17. Listening to excluded young people's perspectives on how digital technologies support and challenge their lives

    OpenAIRE

    Sue Cranmer

    2010-01-01

    Listening to excluded young people’s perspectives on how digital technologies support and challenge their lives This article reports on the perspectives of young people who have been excluded from school on how ICTs support and challenge them in their everyday lives. Qualitative in-depth semistructured interviews were carried out with 13 young people at a Pupil Referral Unit (PRU). The analysis provides a nuanced account of young people’s online activities for those who are already experie...

  18. Equation of State for the Two-component Van der Waals Gas with Relativistic Excluded Volumes

    OpenAIRE

    Zeeb, Gebhard; Bugaev, Kyrill A.; Reuter, Philipp T.; Stöcker, Horst

    2002-01-01

    A canonical partition function for the two-component excluded volume model is derived, leading to two different van der Waals approximations. The one is known as the Lorentz-Berthelot mixture and the other has been proposed recently. Both models are analysed in the canonical and grand canonical ensemble. In comparison with the one-component van der Waals excluded volume model the suppression of particle densities is reduced in these two-component formulations, but in two essentially different...

  19. Vaccination with the Leishmania major ribosomal proteins plus CpG oligodeoxynucleotides induces protection against experimental cutaneous leishmaniasis in mice.

    Science.gov (United States)

    Iborra, Salvador; Parody, Nuria; Abánades, Daniel R; Bonay, Pedro; Prates, Deboraci; Novais, Fernanda O; Barral-Netto, Manoel; Alonso, Carlos; Soto, Manuel

    2008-01-01

    In the present work we analyze the antigenicity of Leishmania major ribosomal proteins (LRP) in infected BALB/c mice. We show that BALB/c mice vaccinated with LRP in the presence of CpG oligodeoxynucleotides (CpG-ODN) were protected against the development of dermal pathology and showed a reduction in the parasite load after challenge with L. major. This protection was associated with the induction of an IL-12 dependent specific-IFN-gamma response mediated mainly by CD4(+) T cell, albeit a minor contribution of CD8(+) T cells cannot be ruled out. Induction of Th1 responses against LRP also resulted in a reversion of the Th2 responses associated with susceptibility. A marked reduction of IgG1 antibody titer against parasite antigens besides an impaired IL-4 and IL-10 cytokine production by parasite specific T cells was observed. In addition, we show that the administration of the LRP plus CpG-ODN preparation also conferred protection in the naturally resistant C57BL/6 mice. In this strain protection was associated with a LRP specific IFN-gamma production in lymph nodes draining the challenge site. We believe that these evolutionary conserved proteins, combined with adjuvants that favor Th1 responses, may be relevant components of a pan-Leishmania vaccine.

  20. Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons.

    Directory of Open Access Journals (Sweden)

    Guilherme M Q Cruz

    Full Text Available Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification.

  1. Immune response to recombinant Leishmania infantum lipophosphoglycan 3 plus CpG oligodeoxynucleotides in BALB/c mice.

    Science.gov (United States)

    Pirdel, L; Zavaran Hosseini, A

    2017-03-01

    Development of a protective antileishmanial vaccine is an urgent priority for successful control of different forms of leishmaniasis. The potential of a recombinant lipophosphoglycan 3 (rLPG3) expressed by Leishmania tarentolae was evaluated in combination with CpG oligodeoxynucleotides (CpG-ODN) as a Th1-promoting adjuvant against Leishmania infantum infection in BALB/c mice. First, mice were immunized subcutaneously with rLPG3 either alone or in combination with CpG-ODN. Next, the immunogenic and protective efficacies of this vaccine were analysed in immunized mice. It was observed that coadministration of rLPG3 with CpG-ODN led to enhance in a Th1 response to rLPG3 induced by itself as the IFN-γ production was promoted in association with the predominant presence of IgG2a antibodies in the sera. However, immunization with rLPG3 plus CpG-ODN induced partial protection against infectious challenge in BALB/c mice. Taken together, further studies are required to improve the protective efficacy using either more potent immune enhancers or vaccination strategies. © 2016 John Wiley & Sons Ltd.

  2. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands

    Directory of Open Access Journals (Sweden)

    Guillermo Barturen

    2013-01-01

    Full Text Available Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.

  3. Promoter CpG island hypermethylation in dysplastic nevus and melanoma: CLDN11 as an epigenetic biomarker for malignancy.

    Science.gov (United States)

    Gao, Linda; van den Hurk, Karin; Moerkerk, Peter T M; Goeman, Jelle J; Beck, Samuel; Gruis, Nelleke A; van den Oord, Joost J; Winnepenninckx, Véronique J; van Engeland, Manon; van Doorn, Remco

    2014-12-01

    Dysplastic nevi are melanocytic lesions that represent an intermediate stage between common nevus and melanoma. Histopathological distinction of dysplastic nevus from melanoma can be challenging and there is a requirement for molecular diagnostic markers. In this study, we examined promoter CpG island methylation of a selected panel of genes, identified in a genome-wide methylation screen, across a spectrum of 405 melanocytic neoplasms. Promoter methylation analysis in common nevi, dysplastic nevi, primary melanomas, and metastatic melanomas demonstrated progressive epigenetic deregulation. Dysplastic nevi were affected by promoter methylation of genes that are frequently methylated in melanoma but not in common nevi. We assessed the diagnostic value of the methylation status of five genes in distinguishing primary melanoma from dysplastic nevus. In particular, CLDN11 promoter methylation was specific for melanoma, as it occurred in 50% of primary melanomas but in only 3% of dysplastic nevi. A diagnostic algorithm that incorporates methylation of the CLDN11, CDH11, PPP1R3C, MAPK13, and GNMT genes was validated in an independent sample set and helped distinguish melanoma from dysplastic nevus (area under the curve 0.81). Melanoma-specific methylation of these genes supports the utility as epigenetic biomarkers and could point to their significance in melanoma development.

  4. Effective melanoma immunotherapy in mice by the skin-depigmenting agent monobenzone and the adjuvants imiquimod and CpG.

    Directory of Open Access Journals (Sweden)

    Jasper G van den Boorn

    2010-05-01

    Full Text Available Presently melanoma still lacks adequate treatment options for metastatic disease. While melanoma is exceptionally challenging to standard regimens, it is suited for treatment with immunotherapy based on its immunogenicity. Since treatment-related skin depigmentation is considered a favourable prognostic sign during melanoma intervention, we here aimed at the reverse approach of directly inducing vitiligo as a shortcut to effective anti-melanoma immunity.We developed an effective and simple to use form of immunotherapy by combining the topical skin-bleaching agent monobenzone with immune-stimulatory imiquimod cream and cytosine-guanine oligodeoxynucleotides (CpG injections (MIC therapy. This powerful new approach promptly induced a melanoma antigen-specific immune response, which abolished subcutaneous B16.F10 melanoma growth in up to 85% of C57BL/6 mice. Importantly, this regimen induced over 100 days of tumor-free survival in up to 60% of the mice, and forcefully suppressed tumor growth upon re-challenge either 65- or 165 days after MIC treatment cessation.MIC therapy is effective in eradicating melanoma, by vigilantly incorporating NK-, B- and T cells in its therapeutic effect. Based on these results, the MIC regimen presents a high-yield, low-cost and simple therapy, readily applicable in the clinic.

  5. Class A CpG Oligonucleotide Priming Rescues Mice from Septic Shock via Activation of Platelet-Activating Factor Acetylhydrolase

    Directory of Open Access Journals (Sweden)

    Yoshinari Yamamoto

    2017-08-01

    Full Text Available Sepsis is a life-threatening, overwhelming immune response to infection with high morbidity and mortality. Inflammatory response and blood clotting are caused by sepsis, which induces serious organ damage and death from shock. As a mechanism of pathogenesis, platelet-activating factor (PAF induces excessive inflammatory responses and blood clotting. In this study, we demonstrate that a Class A CpG oligodeoxynucleotide (CpG-A1585 strongly induced PAF acetylhydrolase, which generates lyso-PAF. CpG-A1585 rescued mice from acute lethal shock and decreased fibrin deposition, a hallmark of PAF-induced disseminated intravascular coagulation. Furthermore, CpG-A1585 improved endotoxin shock induced by lipopolysaccharide, which comprises the cell wall of Gram-negative bacteria and inhibits inflammatory responses induced by cytokines such as interleukin-6 and tumor necrosis factor-α. These results suggest that CpG-A1585 is a potential therapeutic target to prevent sepsis-related induction of PAF.

  6. A nebulized gelatin nanoparticle-based CpG formulation is effective in immunotherapy of allergic horses.

    Science.gov (United States)

    Klier, John; Fuchs, Sebastian; May, Anna; Schillinger, Ulrike; Plank, Christian; Winter, Gerhard; Coester, Conrad; Gehlen, Heidrun

    2012-06-01

    In the recent years, nanotechnology has boosted the development of potential drug delivery systems and material engineering on nanoscale basis in order to increase drug specificity and reduce side effects. A potential delivery system for immunostimulating agents such as cytosine-phosphate-guanine-oligodeoxynucleotides (CpG-ODN) needs to be developed to maximize the efficacy of immunotherapy against hypersensitivity. In this study, an aerosol formulation of biodegradable, biocompatible and nontoxic gelatin nanoparticle-bound CpG-ODN 2216 was used to treat equine recurrent airway obstruction in a clinical study. Bronchoalveolar lavage fluid was obtained from healthy and allergic horses to quantify Th1/Th2 cytokine levels before and after inhalation regimen. Full clinical examinations were performed to evaluate the therapeutic potential of this nebulized gelatin nanoparticle-based CpG formulation. Most remarkable was that regulatory anti-inflammatory and anti-allergic cytokine IL-10 expression was significantly triggered by five consecutive inhalations. Thorough assessment of clinical parameters following nanoparticle treatment indicated a partial remission of the allergic condition. Thus this study, for the first time, showed effectiveness of colloidal nanocarrier-mediated immunotherapy in food-producing animals with potential future applicability to other species including humans.

  7. Mendelian Randomization Analysis Identifies CpG Sites as Putative Mediators for Genetic Influences on Cardiovascular Disease Risk.

    Science.gov (United States)

    Richardson, Tom G; Zheng, Jie; Davey Smith, George; Timpson, Nicholas J; Gaunt, Tom R; Relton, Caroline L; Hemani, Gibran

    2017-10-05

    The extent to which genetic influences on cardiovascular disease risk are mediated by changes in DNA methylation levels has not been systematically explored. We developed an analytical framework that integrates genetic fine mapping and Mendelian randomization with epigenome-wide association studies to evaluate the causal relationships between methylation levels and 14 cardiovascular disease traits. We identified ten genetic loci known to influence proximal DNA methylation which were also associated with cardiovascular traits after multiple-testing correction. Bivariate fine mapping provided evidence that the individual variants responsible for the observed effects on cardiovascular traits at the ADCY3 and ADIPOQ loci were potentially mediated through changes in DNA methylation, although we highlight that we are unable to reliably separate causality from horizontal pleiotropy. Estimates of causal effects were replicated with results from large-scale consortia. Genetic variants and CpG sites identified in this study were enriched for histone mark peaks in relevant tissue types and gene promoter regions. Integrating our results with expression quantitative trait loci data, we provide evidence that variation at these regulatory regions is likely to also influence gene expression levels at these loci. Copyright © 2017 American Society of Human Genetics. All rights reserved.

  8. Differential effects of P-class versus other CpG oligodeoxynucleotide classes on the impaired innate immunity of plasmacytoid dendritic cells in HIV type 1 infection.

    Science.gov (United States)

    Donhauser, Norbert; Helm, Martin; Pritschet, Kathrin; Schuster, Philipp; Ries, Moritz; Korn, Klaus; Vollmer, Jörg; Schmidt, Barbara

    2010-02-01

    Abstract Human plasmacytoid dendritic cells (PDC) are the major producers of type I interferons (IFN) after stimulation with CpG oligodeoxynucleotides (ODN). HIV-1-infected patients show a deficit in PDC numbers and function with progression of disease. CpG ODN appear to be attractive therapeutics to support the impaired innate immunity in HIV-1 infection. PDC counts, phenotype, and function were analyzed in 23 HIV-infected untreated individuals and 16 controls. Markers for migration (CCR7), activation (CD80), maturation (CD83), and endocytosis (BDCA2) were evaluated at baseline and 20 h after in vitro stimulation with class A, B, C, and P ODN. PDC counts and the expression of BDCA2 on these cells were significantly lower in HIV-1-infected subjects compared to controls (both p classes (A > P > C > B) in patients and controls (p class ODN may be effective in reversing this innate immune defect, which should be further evaluated in vivo.

  9. B-CLL cells acquire APC- and CTL-like phenotypic characteristics after stimulation with CpG ODN and IL-21

    Science.gov (United States)

    Hagn, Magdalena; Blackwell, Sue E.; Beyer, Thamara; Ebel, Verena; Fabricius, Dorit; Lindner, Stefanie; Stilgenbauer, Stefan; Simmet, Thomas; Tam, Constantine; Neeson, Paul; Trapani, Joseph A.; Schrezenmeier, Hubert; Weiner, George J.

    2014-01-01

    CpG oligodeoxynucleotides (CpG) and IL-21 are two promising agents for the treatment of B-cell chronic lymphocytic leukemia (B-CLL). Recently, we reported that the combination of CpG and IL-21 (CpG/IL-21) can induce granzyme B (GrB)-dependent apoptosis in B-CLL cells. Here, we demonstrate that treatment of B-CLL cells with CpG and IL-21 results in the development of antigen-presenting cell (APC)-like cells with cytotoxic features. These properties eventually give rise to B-CLL cell apoptosis, independently of their cytogenetic phenotype, whereas normal B-cell survival is not negatively affected by CpG/IL-21. APC- and CTL-typical molecules found to be up-regulated in CpG/IL-21-stimulated B-CLL cells include GrB, perforin, T-bet, monokine-induced by IFN-γ and IFN-γ-inducible protein 10 (IP-10), as well as molecules important for cell adhesion, antigen cross-presentation and costimulation. Also induced are molecules involved in GrB induction, trafficking and processing, whereas the GrB inhibitor Serpin B9 [formerly proteinase inhibitor-9 (PI-9)] is down-modulated by CpG/IL-21. In conclusion, CpG/IL-21-stimulated B-CLL cells acquire features that are reminiscent of killer dendritic cells, and which result in enhanced immunogenicity, cytotoxicity and apoptosis. Our results provide novel insights into the aberrant immune state of B-CLL cells and may establish a basis for the development of an innovative cellular vaccination approach in B-CLL. PMID:24497611

  10. TLR9 Ligand (CpG Oligodeoxynucleotide) Induces CLL B-Cells to Differentiate into CD20(+) Antibody-Secreting Cells.

    Science.gov (United States)

    Ghamlouch, Hussein; Ouled-Haddou, Hakim; Guyart, Aude; Regnier, Aline; Trudel, Stéphanie; Claisse, Jean-François; Fuentes, Vincent; Royer, Bruno; Marolleau, Jean-Pierre; Gubler, Brigitte

    2014-01-01

    B-cell chronic lymphocytic leukemia (CLL) is the most frequent adult leukemia in the Western world. It is a heterogeneous disease characterized by clonal proliferation and the accumulation of CD5(+) mature B lymphocytes. However, the normal counterpart from which the latter cells arise has not yet been identified. CD27 expression and gene expression profiling data suggest that CLL cells are related to memory B-cells. In vitro, memory B-cells differentiate into plasma cells when stimulated with CpG oligodeoxynucleotide (CpG). The objective of the present study was therefore to investigate the ability of CpG, in the context of CD40 ligation, to induce the differentiation of CLL B-cells into antibody-secreting cells (ASCs). CD20(+)CD38(-) CLL B-cells were stimulated with a combination of CpG, CD40 ligand and cytokines (CpG/CD40L/c) in a two-step, 7-day culture system. We found that the CpG/CD40L/c culture system prompted CLL B-cells to differentiate into CD19(+)CD20(+)CD27(+)CD38(-)ASCs. These cells secreted large amounts of IgM and had the same shape as plasma cells. However, only IgMs secreted by ASCs that had differentiated from unmutated CLL B-cells were poly/autoreactive. Class-switch recombination (CSR) to IgG and IgA was detected in cells expressing the activation-induced cytidine deaminase gene (AICDA). Although these ASCs expressed high levels of the transcription factors PRDM1 (BLIMP1), IRF4, and XBP1s, they did not downregulate expression of PAX5. Our results suggest that CLL B-cells can differentiate into ASCs, undergo CSR and produce poly/autoreactive antibodies. Furthermore, our findings may be relevant for (i) identifying the normal counterpart of CLL B-cells and (ii) developing novel treatment strategies in CLL.

  11. B-CLL cells acquire APC- and CTL-like phenotypic characteristics after stimulation with CpG ODN and IL-21.

    Science.gov (United States)

    Hagn, Magdalena; Blackwell, Sue E; Beyer, Thamara; Ebel, Verena; Fabricius, Dorit; Lindner, Stefanie; Stilgenbauer, Stefan; Simmet, Thomas; Tam, Constantine; Neeson, Paul; Trapani, Joseph A; Schrezenmeier, Hubert; Weiner, George J; Jahrsdörfer, Bernd

    2014-07-01

    CpG oligodeoxynucleotides (CpG) and IL-21 are two promising agents for the treatment of B-cell chronic lymphocytic leukemia (B-CLL). Recently, we reported that the combination of CpG and IL-21 (CpG/IL-21) can induce granzyme B (GrB)-dependent apoptosis in B-CLL cells. Here, we demonstrate that treatment of B-CLL cells with CpG and IL-21 results in the development of antigen-presenting cell (APC)-like cells with cytotoxic features. These properties eventually give rise to B-CLL cell apoptosis, independently of their cytogenetic phenotype, whereas normal B-cell survival is not negatively affected by CpG/IL-21. APC- and CTL-typical molecules found to be up-regulated in CpG/IL-21-stimulated B-CLL cells include GrB, perforin, T-bet, monokine-induced by IFN-γ and IFN-γ-inducible protein 10 (IP-10), as well as molecules important for cell adhesion, antigen cross-presentation and costimulation. Also induced are molecules involved in GrB induction, trafficking and processing, whereas the GrB inhibitor Serpin B9 [formerly proteinase inhibitor-9 (PI-9)] is down-modulated by CpG/IL-21. In conclusion, CpG/IL-21-stimulated B-CLL cells acquire features that are reminiscent of killer dendritic cells, and which result in enhanced immunogenicity, cytotoxicity and apoptosis. Our results provide novel insights into the aberrant immune state of B-CLL cells and may establish a basis for the development of an innovative cellular vaccination approach in B-CLL. © The Japanese Society for Immunology. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Matrix protein CCN1 induced by bacterial DNA and CpG ODN limits lung inflammation and contributes to innate immune homeostasis.

    Science.gov (United States)

    Moon, H-G; Qin, Z; Quan, T; Xie, L; Dela Cruz, C S; Jin, Y

    2015-03-01

    To defend against pulmonary infections, lung epithelial cells are equipped with complex innate immunity closely linked to inflammation. Dysregulated innate immunity/inflammation leads to self-perpetuating lung injury. The CpG motif in bacterial DNA is one of the factors involved in bacterial infection-associated inflammation. Bacterial DNA and synthetic CpG oligonucleotide (ODN) induced CCN1 secretion from lung epithelial cells, functioning as a potential "braking" signal to prevent uncontrolled inflammatory responses. CpG ODN-induced endoplasmic reticulum (ER) stress resulted in Src-Y527 phosphorylation (pY527) and Src/CCN1 vWF domain dissociation. Src-Y527 activated caveolin-1 (cav-1) phosphorylation at Y14 and then modulated CCN1 secretion via pCav-1 interaction with the CCN1 IGFbp domain. Functionally, secreted CCN1 promoted anti-inflammatory cytokine interleukin (IL)-10 release from epithelial cells via integrin αVβ6-PKC, and this subsequently suppressed tumor necrosis factor (TNF)-α, macrophage inflammatory protein 2 (MIP-2)-2 secretion and neutrophil infiltration in the lungs. Collectively, bacterial DNA/CpG ODN-stimulated CCN1 secretion via the BiP/GRP78-Src(Y527)-JNK-Cav-1(Y14) pathway and CpG-induced CCN1 conferred anti-inflammatory roles. Our studies suggested a novel paradigm by which the lung epithelium maintains innate immune homeostasis after bacterial infection.

  13. Immortalization of T-Cells Is Accompanied by Gradual Changes in CpG Methylation Resulting in a Profile Resembling a Subset of T-Cell Leukemias

    Directory of Open Access Journals (Sweden)

    Sofie Degerman

    2014-07-01

    Full Text Available We have previously described gene expression changes during spontaneous immortalization of T-cells, thereby identifying cellular processes important for cell growth crisis escape and unlimited proliferation. Here, we analyze the same model to investigate the role of genome-wide methylation in the immortalization process at different time points pre-crisis and post-crisis using high-resolution arrays. We show that over time in culture there is an overall accumulation of methylation alterations, with preferential increased methylation close to transcription start sites (TSSs, islands, and shore regions. Methylation and gene expression alterations did not correlate for the majority of genes, but for the fraction that correlated, gain of methylation close to TSS was associated with decreased gene expression. Interestingly, the pattern of CpG site methylation observed in immortal T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL samples classified as CpG island methylator phenotype positive. These sites were highly overrepresented by polycomb target genes and involved in developmental, cell adhesion, and cell signaling processes. The presence of non-random methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis.

  14. B-cell activation with CD40L or CpG measures the function of B-cell subsets and identifies specific defects in immunodeficient patients.

    Science.gov (United States)

    Marasco, Emiliano; Farroni, Chiara; Cascioli, Simona; Marcellini, Valentina; Scarsella, Marco; Giorda, Ezio; Piano Mortari, Eva; Leonardi, Lucia; Scarselli, Alessia; Valentini, Diletta; Cancrini, Caterina; Duse, Marzia; Grimsholm, Ola; Carsetti, Rita

    2017-01-01

    Around 65% of primary immunodeficiencies are antibody deficiencies. Functional tests are useful tools to study B-cell functions in vitro. However, no accepted guidelines for performing and evaluating functional tests have been issued yet. Here, we report our experience on the study of B-cell functions in infancy and throughout childhood. We show that T-independent stimulation with CpG measures proliferation and differentiation potential of memory B cells. Switched memory B cells respond better than IgM memory B cells. On the other hand, CD40L, a T-dependent stimulus, does not induce plasma cell differentiation, but causes proliferation of naïve and memory B cells. During childhood, the production of plasmablasts in response to CpG increases with age mirroring the development of memory B cells. The response to CD40L does not change with age. In patients with selective IgA deficiency (SIgAD), we observed that switched memory B cells are reduced due to the absence of IgA memory B cells. In agreement, IgA plasma cells are not generated in response to CpG. Unexpectedly, B cells from SIgAD patients show a reduced proliferative response to CD40L. Our results demonstrate that functional tests are an important tool to assess the functions of the humoral immune system. © 2016 The Authors. European Journal of Immunology published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Medicare Star excludes diabetes patients with poor CVD risk factor control.

    Science.gov (United States)

    Schmittdiel, Julie; Raebel, Marsha; Dyer, Wendy; Steiner, John; Goodrich, Glenn; Karter, Andy; Nichols, Gregory

    2014-12-01

    CMS recently added medication adherence to antihypertensives, antihyperlipidemics, and oral antihyperglycemics to its Medicare Star quality measures. These CMS metrics exclude patients with Star adherence metrics and assessed the relationship of both Star-defined adherence and exclusion from Star metrics with CVD risk factor control. Cross-sectional, population-based analysis of 129,040 patients with diabetes aged ≥65 years in 2010 from 3 Kaiser Permanente regions. We estimated adjusted risk ratios to assess the relationship between achieving Star adherence and being excluded from Star adherence metrics, with CVD risk factor control (glycated hemoglobin [A1C]Star metrics excluded 27% of patients with diabetes prescribed oral medications. Star-defined nonadherence was negatively associated with CVD risk factor control (risk ratio [RR], 0.95, 0.84, 0.96 for A1C, LDL-C, and SBP control, respectively; PStar metrics due to early nonadherence was also strongly associated with poor control (RR, 0.83, 0.56, 0.87 for A1C, LDL-C, and SBP control, respectively; PStar adherence measures underestimate the prevalence of medication nonadherence in diabetes and exclude patients at high risk for poor CVD outcomes. Up to 3 million elderly patients with diabetes may be excluded from these measures nationally. Quality measures designed to encourage effective medication use should focus on all patients treated for CVD risk.

  16. Levels of DNA Methylation Vary at CpG Sites across the BRCA1 Promoter, and Differ According to Triple Negative and "BRCA-Like" Status, in Both Blood and Tumour DNA.

    Directory of Open Access Journals (Sweden)

    Sarah L Daniels

    Full Text Available Triple negative breast cancer is typically an aggressive and difficult to treat subtype. It is often associated with loss of function of the BRCA1 gene, either through mutation, loss of heterozygosity or methylation. This study aimed to measure methylation of the BRCA1 gene promoter at individual CpG sites in blood, tumour and normal breast tissue, to assess whether levels were correlated between different tissues, and with triple negative receptor status, histopathological scoring for BRCA-like features and BRCA1 protein expression. Blood DNA methylation levels were significantly correlated with tumour methylation at 9 of 11 CpG sites examined (p<0.0007. The levels of tumour DNA methylation were significantly higher in triple negative tumours, and in tumours with high BRCA-like histopathological scores (10 of 11 CpG sites; p<0.01 and p<0.007 respectively. Similar results were observed in blood DNA (6 of 11 CpG sites; p<0.03 and 7 of 11 CpG sites; p<0.02 respectively. This study provides insight into the pattern of CpG methylation across the BRCA1 promoter, and supports previous studies suggesting that tumours with BRCA1 promoter methylation have similar features to those with BRCA1 mutations, and therefore may be suitable for the same targeted therapies.

  17. Mutation of a Cuticle Protein Gene, BmCPG10, Is Responsible for Silkworm Non-Moulting in the 2nd Instar Mutant.

    Directory of Open Access Journals (Sweden)

    Fan Wu

    Full Text Available In the silkworm, metamorphosis and moulting are regulated by ecdysone hormone and juvenile hormone. The subject in the present study is a silkworm mutant that does not moult in the 2nd instar (nm2. Genetic analysis indicated that the nm2 mutation is controlled by a recessive gene and is homozygous lethal. Based on positional cloning, nm2 was located in a region approximately 275 kb on the 5th linkage group by eleven SSR polymorphism markers. In this specific range, according to the transcriptional expression of thirteen genes and cloning, the relative expression level of the BmCPG10 gene that encodes a cuticle protein was lower than the expression level of the wild-type gene. Moreover, this gene's structure differs from that of the wild-type gene: there is a deletion of 217 bp in its open reading frame, which resulted in a change in the protein it encoded. The BmCPG10 mRNA was detectable throughout silkworm development from the egg to the moth. This mRNA was low in the pre-moulting and moulting stages of each instar but was high in the gluttonous stage and in newly exuviated larvae. The BmCPG10 mRNA showed high expression levels in the epidermis, head and trachea, while the expression levels were low in the midgut, Malpighian tubule, prothoracic gland, haemolymph and ventral nerve cord. The ecdysone titre was determined by ELISA, and the results demonstrated that the ecdysone titre of nm2 larvae was lower than that of the wild-type larvae. The nm2 mutant could be rescued by feeding 20-hydroxyecdysone, cholesterol and 7-dehydrocholesterol (7dC, but the rescued nm2 only developed to the 4th instar and subsequently died. The moulting time of silkworms could be delayed by BmCPG10 RNAi. Thus, we speculated that the mutation of BmCPG10 was responsible for the silkworm mutant that did not moult in the 2nd instar.

  18. [Viral load test conducive to excluding negative subjects from suspects in HIV antibody detections].

    Science.gov (United States)

    Hei, Fa-Xin; Zhang, Qi-Yun; Sun, Wei-Dong; Zhang, Qin; Ye, Jing-Rong; Liu, Hai-Lin; Lu, Hong-Yan

    2008-01-01

    To study whether plasma viral load testing is helpful to exclude ones free from Human immunodeficiency virus (HIV) infections from suspects in HIV antibody detections. 19 Specimens, which showed disconcordant results of the two HIV EIA testing (S/CO test, were selected. Viral load of the specimens were detected. A six-month follow up survey in detecting HIV antibody was conducted in these subjects. None of these 19 cases was observed to be positive HIV viral loads and there was no any progress in WB bands development during the follow-up period. The possibility of HIV infection could be excluded. When the specimens react with very low intensity in both EIA and WB, negative viral load result is conducive to exclude negative subjects from suspects in HIV antibody detections.

  19. Synchrotron Radiation Effects in the IR Solenoid Flux Excluder(LCC-0007)

    Energy Technology Data Exchange (ETDEWEB)

    Tenenbaum, P

    2004-04-22

    We examine the emittance dilution due to synchrotron radiation in the fringing fields at the end of the ''flux excluder'' solenoid which protects the final doublet quadrupoles from the main detector solenoid field, and also the effect of SR in the main solenoid field itself.Because the deflection due to the excluder fringe field is opposite in polarity from that of the main solenoid, the resulting dispersive rays cancel at the IP; as a result the synchrotron radiation from the two magnetic fields produces only a small dilution of the vertical spot size. The contribution to the spot size from the finite opening angle of the synchrotron flux is found to be comparable to the contribution from solenoidal dispersion, and both are acceptable. We conclude that SR considerations do not rule out use of a flux excluder, and that the range of crossing angles and solenoidal fields available is large.

  20. IGFBP3 Promoter Methylation in Colorectal Cancer: Relationship with Microsatellite Instability, CpG Island Methylator Phenotype, p53

    Directory of Open Access Journals (Sweden)

    Takako Kawasaki

    2007-12-01

    Full Text Available Insulin-like growth factor binding protein 3 (IGFBP3, which is induced by wild-type p53, regulates IGF and interacts with the TGF-β pathway. IGFBP3 promoter methylation may occur in colorectal cancer with or without the CpG island methylator phenotype (CIMP, which is associated with microsatellite instability (MSI and TGFBR2 mutation. We examined the relationship between IGFBP3 methylation, p53 expression, CIMP and MSI in 902 population-based colorectal cancers. Utilizing real-time PCR (MethyLight, we quantified promoter methylation in IGFBP3 and eight other CIMP-high-specific promoters (CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1. IGFBP3 methylation was far more frequent in non-MSI-high CIMP-high tumors (85% = 35/41 than in MSI-high CIMPhigh (49% = 44/90, P < .0001, MSI-high non-CIMP-high (17% = 6/36, P < .0001, non-MSI-high non-CIMP-high tumors (22% = 152/680, P < .0001. Among CIMPhigh tumors, the inverse relationship between MSI and IGFBP3 methylation persisted in p53-negative tumors (P < .0001, but not in p53-positive tumors. IGFBP3 methylation was associated inversely with TGFBR2 mutation in MSI-high non-CIMP-high tumors (P = .02. In conclusion, IGFBP3 methylation is inversely associated with MSI in CIMP-high colorectal cancers, this relationship is limited to p53-negative tumors. Our data suggest complex relationship between global genomic/epigenomic phenomena (such as MSI/ CIMP, single molecular events (e.g., IGFBP3 methylation, TP53 mutation, TGFBR2 mutation, the related pathways.

  1. Aberrant promoter CpG methylation as a molecular marker for disease monitoring in natural killer cell lymphomas.

    Science.gov (United States)

    Siu, Lisa L P; Chan, John K C; Wong, Kit F; Choy, Carolyn; Kwong, Yok L

    2003-07-01

    Natural killer (NK) cell lymphomas lack suitable clonal markers for tumour cell detection, making the monitoring of minimal residual lymphoma difficult. Aberrant promoter CpG methylation occurs frequently in NK cell lymphomas. The objective of this study was to assess the potential of aberrant methylation as a surrogate tumour marker. Twenty-five primary tumours and 105 serial biopsies taken at various time points after treatment were examined using a methylation-specific polymerase chain reaction (MSP) for a panel of genes, comprising p73, p16, hMLH1, RARbeta and p15, previously shown to be methylated in NK cell lymphomas. All samples underwent independent morphological examination, supplemented by immunostaining for CD56 and in-situ hybridization for Epstein-Barr-virus-encoded RNA. Primary tumours showed the frequent methylation of the genes p73 (92%), p16 (71%), hMLH1 (61%), RARbeta (56%) and p15 (48%). MSP results in serial post-treatment biopsies were correlated with clinicopathological findings. Results were concordant in 89 follow-up samples (18 samples, histology positive/MSP positive; 71 samples, histology negative/MSP negative) and discordant in 16. Fifteen samples were histology negative/MSP positive, and tumour involvement was subsequently confirmed (positive re-biopsies or relapses at the same sites), indicating that MSP was more sensitive for minimal lymphoma detection. One sample was histology positive/MSP negative; a subsequent histological review and continuous clinical remission of the patient did not support tumour involvement. Our findings suggest that MSP for aberrantly methylated genes is a potentially valuable molecular marker for detecting either residual or relapsed disease in NK cell lymphoma patients.

  2. Single dose CpG immunization protects against a heterosubtypic challenge and generates antigen specific memory T cells

    Directory of Open Access Journals (Sweden)

    Alexander eVogel

    2015-06-01

    Full Text Available Despite extensive research, influenza A virus (IAV remains a major cause of morbidity, mortality, and healthcare expenditure. Emerging pandemics from highly pathogenic IAV strains such as H5N1 and pandemic H1N1 highlight the need for universal, cross-protective vaccines. Current vaccine formulations generate strain-specific neutralizing antibodies primarily against the outer coat proteins hemagglutinin and neuraminidase. In contrast to these highly mutable proteins, internal proteins of IAV are more conserved and are a favorable target for developing vaccines that induce strong T cell responses in addition to humoral immunity. Here, we found that intranasal administration with a single dose of CpG and inactivated x31 (H3N2 reduced viral titers and partially protected mice from a heterosubtypic challenge with a lethal dose of PR8 (H1N1. Early after immunization, vaccinated mice showed increased innate immune activation with high levels of MHCII and CD86 expression on dendritic cells in both the draining lymph nodes and lungs. Three days after immunization, CD4 and CD8 cells in the lung upregulated CD69, suggesting that activated lymphocytes are present at the site of vaccine administration. The ensuing effector Th1 responses were capable of producing multiple cytokines and were present at least 30 days after immunization. Furthermore, functional memory responses were observed, as antigen specific IFN-γ+ and GrB+ cells were detected early after lethal infection. Together, this work provides evidence for using pattern recognition receptor agonists as a mucosal vaccine platform for inducing robust T cell responses capable of protecting against heterologous IAV challenges.

  3. Induction of anti-glioma natural killer cell response following multiple low-dose intracerebral CpG therapy.

    Science.gov (United States)

    Alizadeh, Darya; Zhang, Leying; Brown, Christine E; Farrukh, Omar; Jensen, Michael C; Badie, Behnam

    2010-07-01

    Stimulation of toll-like receptor-9 by CpG oligodeoxynucleotides (CpG-ODN) has been shown to counteract the immunosuppressive microenvironment and to inhibit tumor growth in glioma models. These studies, however, have used high doses of CpG-ODN, which can induce toxicity in a clinical setting. The goal of this study was to evaluate the antitumor efficacy of multiple low-dose intratumoral CpG-ODN in a glioma model. Mice bearing 4-day-old intracranial GL261 gliomas received a single or multiple (two or four) intratumoral injections of CpG-ODN (3 microg) every 4 days. Tumor growth was measured by bioluminescent imaging, brain histology, and animal survival. Flow cytometry and cytotoxicity assays were used to assess anti-glioma immune response. Two and four intracranial injections of low-dose CpG-ODN, but not a single injection, eradicated gliomas in 70% of mice. Moreover, surviving animals exhibited durable tumor-free remission (> 3 months) and were protected from intracranial rechallenge with GL261 gliomas, showing the capacity for long-term antitumor immunity. Although most inflammatory cells seemed to increase, activated natural killer (NK) cells (i.e., NK(+)CD107a(+)) were more frequent than CD8(+)CD107a(+) in the brains of rechallenged CpG-ODN-treated animals and showed a stronger in vitro cytotoxicity against GL261 target cells. Leukocyte depletion studies confirmed that NK cells played an important role in the initial CpG-ODN antitumor response, but both CD8 and NK cells were equally important in long-term immunity against gliomas. These findings suggest that multiple low-dose intratumoral injections of CpG-ODN can eradicate intracranial gliomas possibly through mechanisms involving NK-mediated effector function.

  4. Transitions at CpG dinucleotides, geographic clustering of TP53 mutations and food availability patterns in colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Fabio Verginelli

    Full Text Available BACKGROUND: Colorectal cancer is mainly attributed to diet, but the role exerted by foods remains unclear because involved factors are extremely complex. Geography substantially impacts on foods. Correlations between international variation in colorectal cancer-associated mutation patterns and food availabilities could highlight the influence of foods on colorectal mutagenesis. METHODOLOGY: To test such hypothesis, we applied techniques based on hierarchical clustering, feature extraction and selection, and statistical pattern recognition to the analysis of 2,572 colorectal cancer-associated TP53 mutations from 12 countries/geographic areas. For food availabilities, we relied on data extracted from the Food Balance Sheets of the Food and Agriculture Organization of the United Nations. Dendrograms for mutation sites, mutation types and food patterns were constructed through Ward's hierarchical clustering algorithm and their stability was assessed evaluating silhouette values. Feature selection used entropy-based measures for similarity between clusterings, combined with principal component analysis by exhaustive and heuristic approaches. CONCLUSION/SIGNIFICANCE: Mutations clustered in two major geographic groups, one including only Western countries, the other Asia and parts of Europe. This was determined by variation in the frequency of transitions at CpGs, the most common mutation type. Higher frequencies of transitions at CpGs in the cluster that included only Western countries mainly reflected higher frequencies of mutations at CpG codons 175, 248 and 273, the three major TP53 hotspots. Pearson's correlation scores, computed between the principal components of the datamatrices for mutation types, food availability and mutation sites, demonstrated statistically significant correlations between transitions at CpGs and both mutation sites and availabilities of meat, milk, sweeteners and animal fats, the energy-dense foods at the basis of

  5. Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression

    Directory of Open Access Journals (Sweden)

    Sakaki Yoshiyuki

    2004-02-01

    Full Text Available Abstract Background Gene expression is regulated mainly by transcription factors (TFs that interact with regulatory cis-elements on DNA sequences. To identify functional regulatory elements, computer searching can predict TF binding sites (TFBS using position weight matrices (PWMs that represent positional base frequencies of collected experimentally determined TFBS. A disadvantage of this approach is the large output of results for genomic DNA. One strategy to identify genuine TFBS is to utilize local concentrations of predicted TFBS. It is unclear whether there is a general tendency for TFBS to cluster at promoter regions, although this is the case for certain TFBS. Also unclear is the identification of TFs that have TFBS concentrated in promoters and to what level this occurs. This study hopes to answer some of these questions. Results We developed the cluster score measure to evaluate the correlation between predicted TFBS clusters and promoter sequences for each PWM. Non-promoter sequences were used as a control. Using the cluster score, we identified a PWM group called PWM-PCP, in which TFBS clusters positively correlate with promoters, and another PWM group called PWM-NCP, in which TFBS clusters negatively correlate with promoters. The PWM-PCP group comprises 47% of the 199 vertebrate PWMs, while the PWM-NCP group occupied 11 percent. After reducing the effect of CpG islands (CGI against the clusters using partial correlation coefficients among three properties (promoter, CGI and predicted TFBS cluster, we identified two PWM groups including those strongly correlated with CGI and those not correlated with CGI. Conclusion Not all PWMs predict TFBS correlated with human promoter sequences. Two main PWM groups were identified: (1 those that show TFBS clustered in promoters associated with CGI, and (2 those that show TFBS clustered in promoters independent of CGI. Assessment of PWM matches will allow more positive interpretation of TFBS in

  6. Caspase 8 and maspin are downregulated in breast cancer cells due to CpG site promoter methylation

    Directory of Open Access Journals (Sweden)

    Koeffler Phillip

    2010-02-01

    Full Text Available Abstract Background Epigenetic changes associated with promoter DNA methylation results in silencing of several tumor suppressor genes that lead to increased risk for tumor formation and for progression of the cancer. Methods Methylation specific PCR (MSP and bisulfite sequencing were used for determination of proapoptotic gene Caspase 8 (CASP8 and the tumor suppressor gene maspin promoter methylation in four breast cancer and two non-tumorigenic breast cell lines. Involvement of histone H3 methylation in those cell lines were examined by CHIP assay. Results The CpG sites in the promoter region of CASP8 and maspin were methylated in all four breast cancer cell lines but not in two non-tumorigenic breast cell lines. Demethylation agent 5-aza-2'-deoxycytidine (5-aza-dc selectively inhibits DNA methyltransferases, DNMT3a and DNMT3b, and restored CASP8 and maspin gene expression in breast cancer cells. 5-aza-dc also reduced histone H3k9me2 occupancy on CASP8 promoter in SKBR3cells, but not in MCF-7 cells. Combination of histone deacetylase inhibitor Trichostatin A (TSA and 5-aza-dc significant decrease in nuclear expression of Di-methyl histone H3-Lys27 and slight increase in acetyl histone H3-Lys9 in MCF-7 cells. CASP8 mRNA and protein level in MCF-7 cells were increased by the 5-aza-dc in combination with TSA. Data from our study also demonstrated that treatment with 5-FU caused a significant increase in unmethylated CASP8 and in CASP8 mRNA in all 3 cancer lines. Conclusions CASP8 and maspin expression were reduced in breast cancer cells due to promoter methylation. Selective application of demethylating agents could offer novel therapeutic opportunities in breast cancer.

  7. Epigenetic silencing of BTB and CNC homology 2 and concerted promoter CpG methylation in gastric cancer.

    Science.gov (United States)

    Haam, Keeok; Kim, Hee-Jin; Lee, Kyung-Tae; Kim, Jeong-Hwan; Kim, Mirang; Kim, Seon-Young; Noh, Seung-Moo; Song, Kyu-Sang; Kim, Yong Sung

    2014-09-01

    BTB and CNC homology 2 (BACH2) is a lymphoid-specific transcription factor with a prominent role in B-cell development. Genetic polymorphisms within a single locus encoding BACH2 are associated with various autoimmune diseases and allergies. In this study, restriction landmark genomic scanning revealed methylation at a NotI site in a CpG island covering the BACH2 promoter in gastric cancer cell lines and primary gastric tumors. Increased methylation of the BACH2 promoter was observed in 52% (43/83) of primary gastric tumors, and BACH2 hypermethylation was significantly associated with decreased gene expression. Treatment with 5-aza-2'-deoxycytidine and/or trichostatin. A restored BACH2 expression in BACH2-silenced gastric cancer cell lines, and knockdown of BACH2 using short hairpin RNA (i.e. RNA interference) increased cell proliferation in gastric cancer cells. Clinicopathologic data showed that decreased BACH2 expression occurred significantly more frequently in intestinal-type (27/44, 61%) compared with diffuse-type (13/50, 26%) gastric cancers (P<0.001). Furthermore, BACH2 promoter methylation paralleled that of previously identified targets, such as LRRC3B, LIMS2, PRKD1 and POPDC3, in a given set of gastric tumors. We propose that concerted methylation in many promoters plays a role in accelerating gastric tumor formation and that methylated promoter loci may be targets for therapeutic treatment, such as the recently introduced technique of epigenetic editing. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  8. Aging of blood can be tracked by DNA methylation changes at just three CpG sites.

    Science.gov (United States)

    Weidner, Carola Ingrid; Lin, Qiong; Koch, Carmen Maike; Eisele, Lewin; Beier, Fabian; Ziegler, Patrick; Bauerschlag, Dirk Olaf; Jöckel, Karl-Heinz; Erbel, Raimund; Mühleisen, Thomas Walter; Zenke, Martin; Brümmendorf, Tim Henrik; Wagner, Wolfgang

    2014-02-03

    Human aging is associated with DNA methylation changes at specific sites in the genome. These epigenetic modifications may be used to track donor age for forensic analysis or to estimate biological age. We perform a comprehensive analysis of methylation profiles to narrow down 102 age-related CpG sites in blood. We demonstrate that most of these age-associated methylation changes are reversed in induced pluripotent stem cells (iPSCs). Methylation levels at three age-related CpGs--located in the genes ITGA2B, ASPA and PDE4C--were subsequently analyzed by bisulfite pyrosequencing of 151 blood samples. This epigenetic aging signature facilitates age predictions with a mean absolute deviation from chronological age of less than 5 years. This precision is higher than age predictions based on telomere length. Variation of age predictions correlates moderately with clinical and lifestyle parameters supporting the notion that age-associated methylation changes are associated more with biological age than with chronological age. Furthermore, patients with acquired aplastic anemia or dyskeratosis congenita--two diseases associated with progressive bone marrow failure and severe telomere attrition--are predicted to be prematurely aged. Our epigenetic aging signature provides a simple biomarker to estimate the state of aging in blood. Age-associated DNA methylation changes are counteracted in iPSCs. On the other hand, over-estimation of chronological age in bone marrow failure syndromes is indicative for exhaustion of the hematopoietic cell pool. Thus, epigenetic changes upon aging seem to reflect biological aging of blood.

  9. Listening to excluded young people’s perspectives on how digital technologies support and challenge their lives

    National Research Council Canada - National Science Library

    Sue Cranmer

    2010-01-01

    Listening to excluded young people’s perspectives on how digital technologies support and challenge their lives This article reports on the perspectives of young people who have been excluded from school on how ICTs support...

  10. Schedules of Controlled Substances: Table of Excluded Nonnarcotic Products: Vicks® VapoInhaler®.

    Science.gov (United States)

    2016-02-08

    This final rule adopts the interim final rule, with a correction to spelling of the manufacturer's name that was published in the Federal Register on October 27, 2015. The Drug Enforcement Administration is amending the table of Excluded Nonnarcotic Products to update the listing for Vicks® VapoInhaler®, containing 50 mg levmetamfetamine in a nasal decongestant inhaler, marketed by The Procter & Gamble Company. This over-the-counter, non-narcotic drug product is excluded from provisions of the Controlled Substances Act.

  11. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.

    Science.gov (United States)

    Greally, John M

    2002-01-08

    To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival.

  12. Cadmium tolerance and accumulation in Excluder Thlaspi arvense and various accessions of hyperaccumulator Noccaea caerulescens

    NARCIS (Netherlands)

    Seregin, I.V.; Kozhevnikova, A.D.; Zhukovskaya, V.; Schat, H.

    2015-01-01

    Cadmium (Cd) accumulation and tolerance were analyzed in hyperaccumulator Noccaea caerulescens F.K. Mey and excluder Thlaspi arvense L. Five accessions of N. caerulescens (La Calamine (LC, Belgium), Saint Félix de Palliéres (SF, France), Col du Mas de l’Aire (CMA, France), Ganges (GA, France) from

  13. 20 CFR 668.650 - Can INA grantees exclude segments of the eligible population?

    Science.gov (United States)

    2010-04-01

    ... eligible population? 668.650 Section 668.650 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION... population? (a) No, INA grantees cannot exclude segments of the eligible population. INA grantees must document in their Two Year Plan that a system is in place to afford all members of the eligible population...

  14. Excluding Ethical Issues from U.S. History Textbooks: 911 and the War on Terror

    Science.gov (United States)

    Romanowski, Michael H.

    2009-01-01

    This research study examined nine secondary American history textbooks regarding their treatment of 9/11 and related events. The analysis centered on both the knowledge included and excluded from the discussion in each book. Particular attention was given to the moral and ethical issues relevant to 9/11. Findings show that textbooks vary in their…

  15. 75 FR 13678 - Schedules of Controlled Substances; Table of Excluded Nonnarcotic Products: Nasal Decongestant...

    Science.gov (United States)

    2010-03-23

    ... Excluded Nonnarcotic Products: Nasal Decongestant Inhalers Manufactured by Classic Pharmaceuticals, LLC... (containing 50 mg Levmetamfetamine) manufactured by Classic Pharmaceuticals, LLC and marketed under various..., which may be lawfully sold over the counter without a prescription under the Federal Food, Drug, and...

  16. Acting on Observed Social Exclusion: Developmental Perspectives on Punishment of Excluders and Compensation of Victims

    Science.gov (United States)

    Will, Geert-Jan; Crone, Eveline A.; van den Bos, Wouter; Güroglu, Berna

    2013-01-01

    This study examined punishment of excluders and compensation of victims after observing an instance of social exclusion at various phases of adolescent development. Participants (n = 183; age 9 to 22 years) were first included in a virtual ball-tossing game, Cyberball, and then "observed" the exclusion of a peer. Subsequently, they…

  17. NGO Provision of Basic Education: Alternative or Complementary Service Delivery to Support Access to the Excluded?

    Science.gov (United States)

    Rose, Pauline

    2009-01-01

    This paper focuses on approaches by non-government organisations (NGOs) to reach primary school-aged children excluded from access to the conventional state education system. It highlights recent shifts in international literature and agency priorities from the portrayal of NGO provision as a (non-formal) "alternative" to (formal) state…

  18. 7 CFR 205.310 - Agricultural products produced on an exempt or excluded operation.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Agricultural products produced on an exempt or excluded operation. 205.310 Section 205.310 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) ORGANIC FOODS PRODUCTION AC...

  19. Walk the Talk? The Effect of Voting and Excludability in Public Goods Experiments

    Directory of Open Access Journals (Sweden)

    Hans J. Czap

    2010-01-01

    Full Text Available The purpose of this paper is to investigate the effect of voting and excludability on individual contributions to group projects. We conducted two experiments on excludable and nonexcludable public goods, which provided several important results. First, contrary to our expectations, subjects are generally contributing more to the non-excludable compared to the excludable public good. Second, participating in a vote to choose a public project per se makes no difference in contributions. However, if the project that the individual voted for also gets selected by the group, they contribute significantly more to that project. Third, empathy and locus of control are important driving forces of participation in common projects. Our results have implications on the procedural design of obtaining funding for public projects. First, the public should get involved and have a say in the determination of which project should be realized. Second, it might well pay off to attempt to develop a consensus among the population and obtain near unanimous votes, because in our experiment, subjects discriminate between the project they voted for and the project chosen by the majority. Third, the policy proposers should stress the other-regarding interest of the public good rather than just pecuniary incentives.

  20. 46 CFR 148.04-13 - Ferrous metal borings, shavings, turnings, or cuttings (excluding stainless steel).

    Science.gov (United States)

    2010-10-01

    ... (excluding stainless steel). 148.04-13 Section 148.04-13 Shipping COAST GUARD, DEPARTMENT OF HOMELAND... stainless steel). (a) This section applies to the stowage and transportation in bulk of hazardous materials... steel). However, unmanned barges on which the article is stowed for or transported on a voyage entirely...

  1. ALTERNATIVE FORMULATIONS TO REDUCE CFC USE IN U.S. EXEMPTED AND EXCLUDED AEROSOL PRODUCTS

    Science.gov (United States)

    The report examines products exempted and excluded from those affected by the 1978 ban on the use of chlorofluorocarbons (CFCs) as aerosol propellants, the present consumption of CFCs still utilized for these products in the U.S., and alternative formulations which may be used to...

  2. 26 CFR 1.401(a)(26)-6 - Excludable employees.

    Science.gov (United States)

    2010-04-01

    ... nonresident aliens) may be treated as an excludable employee. (ii) Special treaty rule. In addition, an...), a plan that uses the elapsed time method of determining years of service may use either 91... general method of crediting service for the employee. If one of the equivalencies set forth in 29 CFR 2530...

  3. 40 CFR 1039.20 - What requirements from this part apply to excluded stationary engines?

    Science.gov (United States)

    2010-07-01

    ... name and trademark of another company you choose to designate. (3) State the engine displacement (in... to excluded stationary engines? 1039.20 Section 1039.20 Protection of Environment ENVIRONMENTAL... COMPRESSION-IGNITION ENGINES Overview and Applicability § 1039.20 What requirements from this part apply to...

  4. Influence of streambank fencing on the environmental quality of cattle-excluded pastures.

    Science.gov (United States)

    Miller, J J; Chanasyk, D S; Curtis, T; Willms, W D

    2010-01-01

    Limited information exists on the effect of streambank fencing on riparian zone pastures. The objective of this study was to test the hypothesis that 4 to 6 yr of streambank fencing would improve the environmental quality of the cattle-excluded pasture compared with the grazed pasture and cause the fenced pasture to act as a buffer or filter strip. Rangeland health, vegetative and soil properties, and rainfall simulation runoff were measured in the cattle-excluded and adjacent grazed native pastures along the fenced reach of the Lower Little Bow River in southern Alberta, Canada, for 3 yr (2005-2007). Rangeland health was improved (health score increase from 55 to 72%); vegetation cover (13-21%) and standing litter (38-742%) were increased; and bare soil (72-93%) and soil bulk density (6-8%) were decreased under cattle exclusion, indicating an improvement in environmental quality from streambank fencing. In contrast, other vegetation (total and live basal area, fallen litter) and soil properties (soil water and soil C, N, and P) were not improved by cattle exclusion. Cattle exclusion significantly (P fenced pasture may act as a buffer for certain runoff variables. In contrast, other runoff variables (turbidity, electrical conductivity, pH, concentrations and loads of total suspended solids, and certain N and P fractions) in the cattle-excluded pasture were generally not improved by streambank fencing. Overall, streambank fencing improved the quality of certain environmental variables within the cattle-excluded pasture.

  5. Unanimous versus partial rejection: How the number of excluders influences the impact of ostracism in children

    NARCIS (Netherlands)

    Sandstrom, M.J.; Deutz, M.H.F.; Lansu, T.A.M.; Noorden, T.H.J. van; Karremans, J.C.T.M.; Cillessen, A.H.N.

    2017-01-01

    Previous research has shown that ostracism - the experience of being ignored and excluded - has negative effects on all of us, young and old. Using a Cyberball paradigm, the present research replicates the effects of ostracism on the moods (anger, anxiety, happiness, and anger) and fundamental needs

  6. Unanimous versus partial rejection : How the number of excluders influences the impact of ostracism in children

    NARCIS (Netherlands)

    Sandstrom, Marlene J.; Deutz, Marike H F; Lansu, Tessa A M; van Noorden, Tirza H J; Karremans, Johan C.; Cillessen, Antonius H N

    Previous research has shown that ostracism-the experience of being ignored and excluded-has negative effects on all of us, young and old. Using a Cyberball paradigm, the present research replicates the effects of ostracism on the moods (anger, anxiety, happiness, and anger) and fundamental needs

  7. Ontario Universities Benefits Survey, 1987-88. Part I: Benefits Excluding Pensions.

    Science.gov (United States)

    University of Western Ontario, London.

    Results of the 1987-1988 survey of benefits, excluding pensions, for 17 Ontario, Canada, universities are presented. Information is provided on the following areas: administration and insurance plans, communication of benefits, proposed changes in benefits, provision of life and dismemberment insurance, maternity leave policy, Ontario health…

  8. Endoscopic findings in the excluded stomach after Roux-en-Y gastric bypass surgery.

    Science.gov (United States)

    Kuga, Rogerio; Safatle-Ribeiro, Adriana V; Faintuch, Joel; Ishida, Robson K; Furuya, Carlos K; Garrido, Arthur B; Cecconello, Ivan; Ishioka, Shinichi; Sakai, Paulo

    2007-10-01

    After gastric bypass surgery performed because of morbid obesity, the excluded stomach can rarely be endoscopically examined. With the advent of a new apparatus and technique, possible mucosal changes can be routinely accessed and monitored, thus preventing potential benign and malignant complications. Prospective observational study in a homogeneous population with nonspecific symptoms. Outpatient clinic of a large public academic hospital. Forty consecutive patients (mean +/- SD age, 44.5 +/- 10.0 y ears; 85.0% women) were seen at a mean +/- SD of 77.3 +/- 19.4 months after Roux-en-Y gastric bypass surgery. Elective double-balloon enteroscopy of the excluded stomach was performed. Rate of successful intubation, endoscopic findings, and complications. The excluded stomach was reached in 35 of 40 patients (87.5%). Mean +/- SD time to enter the organ was 24.9 +/- 14.3 minutes (range, 5-75 minutes). Endoscopic findings were normal in 9 patients (25.7%), whereas in 26 (74.3%), various types of gastritis (erythematous, erosive, hemorrhagic erosive, and atrophic) were identified, primarily in the gastric body and antrum. No cancer was documented in the present series. Tolerance was good, and no complications were recorded during or after the intervention. The double-balloon method is useful and practical for access to the excluded stomach. Although cancer was not noted, most of the studied population had gastritis, including moderate and severe forms. Surveillance of the excluded stomach is recommended after Roux-en-Y gastric bypass surgery performed because of morbid obesity.

  9. Long-Term Outcome of the GORE EXCLUDER AAA Endoprosthesis for Treatment of Infrarenal Aortic Aneurysms.

    Science.gov (United States)

    Poublon, Claire G; Holewijn, Suzanne; van Sterkenburg, Steven M M; Tielliu, Ignace F J; Zeebregts, Clark J; Reijnen, Michel M P J

    2017-05-01

    To evaluate long-term outcome of GORE EXCLUDER AAA Endoprosthesis (W.L. Gore & Associates, Inc, Flagstaff, Arizona) for elective treatment of infrarenal aortic aneurysms and to evaluate performance of different generations of the device. A retrospective analysis was performed of 248 patients undergoing elective endovascular aneurysm repair with the GORE EXCLUDER between January 2000 and December 2015 in 2 hospitals. Primary endpoint was reintervention-free survival. Secondary endpoints were technical success, overall survival, rupture-free survival, endoleaks, sac diameter change (> 5 mm), limb occlusion, and migration (> 5 mm). Median follow-up time was 26 months (range, 1-190 months). Assisted primary technical success was 96.8%. Reintervention-free survival for 5 and 10 years was 85.2% and 75.6%, respectively. Independent risk factors for reintervention were technical success (P < .001), type I endoleak (P < .001), and type II endoleak (P = .003). Late adverse events requiring reintervention included rupture (0.4%), limb occlusion (0.4%), and stent migration (0.4%). Type Ia (4.8%), Ib (2.8%), II (35.9%), and V (6.5%) endoleaks were reported throughout follow-up. Sac growth was more prevalent with the original GORE EXCLUDER compared with the low permeability GORE EXCLUDER (P = .001) and in the presence of type I, II, and V endoleaks (P < .05). Three conversions (1.2%) were performed. Overall survival at 5 and 10 years was 68.4% and 49.0%, with no reported aneurysm-related deaths. Treatment with the GORE EXCLUDER is effective with acceptable reintervention rates in the long-term and few device-related adverse events or ruptures up to 10 years. Observed late adverse events and new-onset endoleaks emphasize the need for long-term surveillance. Copyright © 2017 SIR. Published by Elsevier Inc. All rights reserved.

  10. Addressing dichotomous data for participants excluded from trial analysis: a guide for systematic reviewers.

    Directory of Open Access Journals (Sweden)

    Elie A Akl

    Full Text Available Systematic reviewer authors intending to include all randomized participants in their meta-analyses need to make assumptions about the outcomes of participants with missing data.The objective of this paper is to provide systematic reviewer authors with a relatively simple guidance for addressing dichotomous data for participants excluded from analyses of randomized trials.This guide is based on a review of the Cochrane handbook and published methodological research. The guide deals with participants excluded from the analysis who were considered 'non-adherent to the protocol' but for whom data are available, and participants with missing data.Systematic reviewer authors should include data from 'non-adherent' participants excluded from the primary study authors' analysis but for whom data are available. For missing, unavailable participant data, authors may conduct a complete case analysis (excluding those with missing data as the primary analysis. Alternatively, they may conduct a primary analysis that makes plausible assumptions about the outcomes of participants with missing data. When the primary analysis suggests important benefit, sensitivity meta-analyses using relatively extreme assumptions that may vary in plausibility can inform the extent to which risk of bias impacts the confidence in the results of the primary analysis. The more plausible assumptions draw on the outcome event rates within the trial or in all trials included in the meta-analysis. The proposed guide does not take into account the uncertainty associated with assumed events.This guide proposes methods for handling participants excluded from analyses of randomized trials. These methods can help in establishing the extent to which risk of bias impacts meta-analysis results.

  11. TSH alone is not sufficient to exclude all patients with a functioning thyroid nodule from undergoing testing to exclude thyroid cancer

    Energy Technology Data Exchange (ETDEWEB)

    Hurtado-Lopez, Luis-Mauricio; Monroy-Lozano, Blanca-Estela [General Hospital of Mexico, Mexico City (Mexico); Martinez-Duncker, Carlos [Hospital Infantil de Mexico Federico Gomez, Medicina Nuclear Molecular, Mexico City, DF (Mexico)

    2008-06-15

    The purpose of the study was to analyze whether the thyroid-stimulating hormone (TSH) alone avoids tests to exclude malignancy in all patients with functional thyroid nodules (FTN). Sixty-nine patients with FTN on {sup 99m}Tc scintigraphy, radioiodine uptake test (RIU), {sup 99m}Tc thyroid uptake, TSH assay, T3, and T4 obtained within 48 h were retrospectively identified out of 2,356 thyroid scans performed from January 2000 to April 2007. FTNs were classified as causing total, partial, or no inhibition of the thyroid as group 1, 2, or 3, respectively. TSH was subnormal in 21 of 69 (30.43%) patients. In group 1 (N = 23, 33.3%), TSH was subnormal, normal, and high in eight, nine, and six patients; in group 2 (N = 17, 24.6%), TSH was subnormal, normal, and high in four, six, and seven patients, and in group 3 (N = 29, 42%), TSH was subnormal, normal, and high in 9, 13, and 7 patients, respectively. TSH was significantly lower in group 1. In T3, T4, {sup 99m}Tc thyroid uptake, and RIU, there were no differences between the three groups. Only 30.43% of patients had subnormal TSH. TSH alone cannot avoid tests to exclude malignancy in all patients with FTN. FTN existence can only be accurately assessed by thyroid scintigraphy. The current incidence of FTN may be unknown because scintigraphy is not routinely performed in all patients with thyroid nodules. Thyroid scintigraphy of patients with high TSH can detect diseases such as Hashimoto's thyroiditis and identify patients with FTN in whom no further diagnostic procedures would be needed in patients with normal TSH levels with nondiagnostic fine-needle aspiration results. (orig.)

  12. Efficient in vivo priming by vaccination with recombinant NY-ESO-1 protein and CpG in antigen naive prostate cancer patients.

    Science.gov (United States)

    Karbach, Julia; Neumann, Antje; Atmaca, Akin; Wahle, Claudia; Brand, Kathrin; von Boehmer, Lotta; Knuth, Alexander; Bender, Armin; Ritter, Gerd; Old, Lloyd J; Jäger, Elke

    2011-02-15

    NY-ESO-1, one of the most immunogenic tumor antigens, is expressed in 15% to 25% of metastatic prostate cancers. The immunological and clinical effects of vaccination with recombinant NY-ESO-1 protein combined with CpG as adjuvant were evaluated. In a phase I clinical study, patients with advanced prostate cancer were vaccinated with recombinant NY-ESO-1 protein (100 μg) mixed with CpG 7909 (2.5 mg) every 3 weeks intradermally for 4 doses. Objectives of the study were the safety of the vaccine and changes of specific humoral and cellular immunological responses to NY-ESO-1 in relation to detectable NY-ESO-1 expression in the individual tumor. All 12 baseline sero-negative patients developed high-titer NY-ESO-1 antibody responses. B-cell epitope mapping identified NY-ESO-1 p91-110 to be recognized most frequently by vaccine-induced antibodies. Two patients developed significant antibody titers against the adjuvant CpG. NY-ESO-1-specific CD4+ and/or CD8+ T-cell responses were induced in 9 patients (69%). Five of these 9 patients did not express NY-ESO-1 in the autologous tumor. Postvaccine CD8+ T-cell clones recognized and lyzed HLA-matched tumor cell lines in an antigen-specific manner. Our data provide clear evidence for the capacity of NY-ESO-1 protein/CpG vaccine to induce integrated antigen-specific immune responses in vivo and to efficiently prime CD8+ T-cell responses in NY-ESO-1 antigen-negative patients. Our results may also support further clinical vaccination protocols with NY-ESO-1 protein not only focused on the treatment of existing cancer, but also to prevent further development of NY-ESO-1 positive cancers in vivo. ©2010 AACR.

  13. Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Hye Ryun Woo

    2008-08-01

    Full Text Available Methylcytosine-binding proteins decipher the epigenetic information encoded by DNA methylation and provide a link between DNA methylation, modification of chromatin structure, and gene silencing. VARIANT IN METHYLATION 1 (VIM1 encodes an SRA (SET- and RING-associated domain methylcytosine-binding protein in Arabidopsis thaliana, and loss of VIM1 function causes centromere DNA hypomethylation and centromeric heterochromatin decondensation in interphase. In the Arabidopsis genome, there are five VIM genes that share very high sequence similarity and encode proteins containing a PHD domain, two RING domains, and an SRA domain. To gain further insight into the function and potential redundancy among the VIM proteins, we investigated strains combining different vim mutations and transgenic vim knock-down lines that down-regulate multiple VIM family genes. The vim1 vim3 double mutant and the transgenic vim knock-down lines showed decreased DNA methylation primarily at CpG sites in genic regions, as well as repeated sequences in heterochromatic regions. In addition, transcriptional silencing was released in these plants at most heterochromatin regions examined. Interestingly, the vim1 vim3 mutant and vim knock-down lines gained ectopic CpHpH methylation in the 5S rRNA genes against a background of CpG hypomethylation. The vim1 vim2 vim3 triple mutant displayed abnormal morphological phenotypes including late flowering, which is associated with DNA hypomethylation of the 5' region of FWA and release of FWA gene silencing. Our findings demonstrate that VIM1, VIM2, and VIM3 have overlapping functions in maintenance of global CpG methylation and epigenetic transcriptional silencing.

  14. Immune modulation of T regulatory cells and IgE responses in horses vaccinated with West Nile virus vaccine combined with a CpG ODN.

    Science.gov (United States)

    Behrens, Nicole E; Gershwin, Laurel J

    2015-10-26

    Hypersensitivity reactions, such as hives or fatal anaphylactic shock, in response to vaccination constitute a health hazard for horses that develop allergies to vaccine components. In such horses vaccination with viral vaccines stimulates an IgE response to non-target antigens. Viral vaccines share contaminating non-target proteins, such as bovine serum albumin (BSA); these antigens can stimulate IgE production with each exposure. We hypothesized that the addition of a CpG oligodeoxynucleotide (ODN) administered in conjunction with a West Nile virus vaccine would decrease the IgE response; through up-regulation of T regulatory cells and T helper 1 cells thus decreasing the potential to induce a type 1 hypersensitivity response. Thirty adult horses were injected with either CpG ODN or control GpC ODN with a killed WNV vaccine. T regulatory cell numbers and BSA specific IgE concentrations were determined pre and post vaccination. Multicolor flow cytometry was used to evaluate expression of CD4, CD25, and intracellular Foxp3 on PBMCs. Serum concentrations of BSA specific IgE were determined by ELISA. Cell culture supernatants from BSA re-stimulated lymphocytes were evaluated for concentrations of IL-2, IL-4, IL-10, and IFN-γ. The inclusion of the CpG ODN significantly increased the differentiation of T regulatory cells in response to antigen in vitro and in vivo. A significant inverse correlation was found between T regulatory cell numbers and serum BSA specific IgE concentrations. These results suggest that we can provide a safer alternate vaccination strategy, particularly for horses that have demonstrated a pro-allergic phenotype. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Demethylation by 5-aza-2'-deoxycytidine in colorectal cancer cells targets genomic DNA whilst promoter CpG island methylation persists

    Directory of Open Access Journals (Sweden)

    Kim Kyu-Tae

    2010-07-01

    Full Text Available Abstract Background DNA methylation and histone acetylation are epigenetic modifications that act as regulators of gene expression. Aberrant epigenetic gene silencing in tumours is a frequent event, yet the factors which dictate which genes are targeted for inactivation are unknown. DNA methylation and histone acetylation can be modified with the chemical agents 5-aza-2'-deoxycytidine (5-aza-dC and Trichostatin A (TSA respectively. The aim of this study was to analyse de-methylation and re-methylation and its affect on gene expression in colorectal cancer cell lines treated with 5-aza-dC alone and in combination with TSA. We also sought to identify methylation patterns associated with long term reactivation of previously silenced genes. Method Colorectal cancer cell lines were treated with 5-aza-dC, with and without TSA, to analyse global methylation decreases by High Performance Liquid Chromatography (HPLC. Re-methylation was observed with removal of drug treatments. Expression arrays identified silenced genes with differing patterns of expression after treatment, such as short term reactivation or long term reactivation. Sodium bisulfite sequencing was performed on the CpG island associated with these genes and expression was verified with real time PCR. Results Treatment with 5-aza-dC was found to affect genomic methylation and to a lesser extent gene specific methylation. Reactivated genes which remained expressed 10 days post 5-aza-dC treatment featured hypomethylated CpG sites adjacent to the transcription start site (TSS. In contrast, genes with uniformly hypermethylated CpG islands were only temporarily reactivated. Conclusion These results imply that 5-aza-dC induces strong de-methylation of the genome and initiates reactivation of transcriptionally inactive genes, but this does not require gene associated CpG island de-methylation to occur. In addition, for three of our selected genes, hypomethylation at the TSS of an epigenetically

  16. TLR9 ligand (CpG oligodeoxynucleotide induces CLL B-cells to differentiate into CD20+ antibody-secreting cells

    Directory of Open Access Journals (Sweden)

    Hussein eGhamlouch

    2014-06-01

    Full Text Available B-cell chronic lymphocytic leukemia (CLL is the most frequent adult leukemia in the Western world. It is a heterogeneous disease characterized by clonal proliferation and the accumulation of CD5+ mature B lymphocytes. However, the normal counterpart from which the latter cells arise has not yet been identified. CD27 expression and gene expression profiling data suggest that CLL cells are related to memory B-cells. In vitro, memory B-cells differentiate into plasma cells when stimulated with CpG oligodeoxynucleotide (CpG. The objective of the present study was therefore to investigate the ability of CpG, in the context of CD40 ligation, to induce the differentiation of CLL B-cells into antibody-secreting cells (ASCs. CD20+CD38− CLL B-cells were stimulated with a combination of CpG, CD40 ligand and cytokines (CpG/CD40L/c in a two-step, seven-day culture system. We found that the CpG/CD40L/c culture system prompted CLL B-cells to differentiate into CD19+CD20+CD27+CD38- ASCs. These cells secreted large amounts of IgM and had the same shape as plasma cells. However, only IgMs secreted by ASCs that had differentiated from unmutated CLL B-cells were poly/autoreactive. Class-switch recombination to IgG and IgA was detected in cells expressing the activation-induced cytidine deaminase gene (AICDA. Although these ASCs expressed high levels of the transcription factors PRDM1 (BLIMP1, IRF4 and XBP1s, they did not downregulate expression of PAX5. Our results suggest that CLL B-cells can differentiate into ASCs, undergo class-switch recombination and produce poly/autoreactive antibodies. Furthermore, our findings may be relevant for (i identifying the normal counterpart of CLL B-cells and (ii developing novel treatment strategies in CLL.

  17. The snowball effect: friendship moderates escalations in depressed affect among avoidant and excluded children.

    Science.gov (United States)

    Bukowski, William M; Laursen, Brett; Hoza, Betsy

    2010-11-01

    A three-wave longitudinal study conducted with preadolescent boys and girls (N = 231 at Time 1 [T1]) was used to assess the hypotheses that aspects of social withdrawal would be predictors of a "snowball" cascade of depressed affect, and that friendship experiences would moderate these effects. Consistent with these hypotheses, multilevel modeling showed that measures of avoidance and exclusion at T1 were associated with concurrent levels of depressed affect and were antecedent to escalating trajectories of depressed affect over time. These accelerating growth curves fit a snowball cascade model. The analyses also showed the protective effects of friendship. Specifically, the snowball effect was limited to avoidant and excluded children who were friendless. Depressed affect did not increase among avoidant and excluded children who were friended.

  18. Trust and cooperation in the public sphere: why Roma people should not be excluded?

    Directory of Open Access Journals (Sweden)

    Dragoş DRAGOMAN

    2014-05-01

    Full Text Available The recent political developments in Romania and other Central and East European countries, marked by rising populism and political extremism, shed light on the essential issue of building a free, tolerant and inclusive public sphere, which is willing to let arguments to be decisive instead of power, status, race or wealth. The current tendencies of socially excluding Roma, indiscriminately taken by populists for unjustified social burden and intolerable racial difference, are a warning for more radical political action that could undermine on the long-run the effort to set up a democratic public space. Excluding from start an entire minority would only encourage future exclusions based on ideology, ethnicity or religion, according to the narrow definition populists use to give to the concept of ‘people’.

  19. Using coronary calcification to exclude an ischemic etiology for cardiomyopathy: A validation study and systematic review.

    Science.gov (United States)

    Premaratne, Manuja; Shamsaei, Mohabbat; Chow, Jonathan D H; Haddad, Tony; Erthal, Fernanda; Curran, Helen; Yam, Yeung; Szczotka, Agnieszka; Mielniczuk, Lisa; Wells, George A; Beanlands, Rob S; Hossain, Alomgir; Chow, Benjamin J W

    2017-03-01

    Preliminary data suggests the absence of coronary artery calcification (CAC) excludes ischemic etiologies of cardiomyopathy. We prospectively validate and perform a systematic review to determine the utility of an Agatston score=0 to exclude the diagnosis of ischemic cardiomyopathy. Patients with newly diagnosed LV dysfunction were prospectively enrolled. Patients underwent CAC imaging and were followed until an etiologic diagnosis of cardiomyopathy was made. Eighty-two patients were enrolled in the study and underwent CAC imaging with 81.7% patients having non-ischemic cardiomyopathy. An Agatston score=0 successfully excluded an ischemic etiology for cardiomyopathy with a specificity of 100% (CI: 74.7-100%) and a positive predictive value of 100% (CI: 85.0%-100%). A systematic literature review was performed and studies were deemed suitable for inclusion if: 1) patients with CHF, cardiomyopathy or LV dysfunction were enrolled, 2) underwent CAC imaging and patients were assessed for an Agatston score=0 or the absence of CAC, and 3) the final etiologic diagnosis (ischemic or non-ischemic) was provided. Eight studies provided sufficient information to calculate operating characteristics for an Agatston score=0 and were combined with our validation cohort for a total of 754 patients. An Agatston score=0 excluded ischemic cardiomyopathy with specificity and positive predictive values of 98.4% (CI: 95.6-99.5%), and 98.3% (CI: 95.5-99.5%), respectively. In patients with cardiomyopathy of unknown etiology, an Agatston score=0 appears to rule out an ischemic etiology. A screening CAC may be a simple and cost-effective method of triaging patients, identifying those who do and do not need additional CAD investigations. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  20. Schoolchildren's consumption of competitive foods and beverages, excluding à la carte.

    Science.gov (United States)

    Kakarala, Madhuri; Keast, Debra R; Hoerr, Sharon

    2010-09-01

    Competitive foods/beverages are those in school vending machines, school stores, snack bars, special sales, and items sold à la carte in the school cafeteria that compete with United States Department of Agriculture (USDA) meal program offerings. Grouping à la carte items with less nutritious items allowed in less regulated venues may obfuscate analysis of the school competitive food environment. Excluding à la carte items from competitive foods, the objectives were to: (1) assess competitive food use by gender, ethnicity, eligibility for free or reduced-price meals, and participation in school meals programs, (2) determine differences between grade levels in energy intakes obtained from food sources, (3) determine the nutrient intake derived from competitive foods for students who consumed them, and (4) determine energy-adjusted differences in 24-hour nutrient intakes of protein, calcium, iron, and other selected nutrients between competitive food consumer and nonconsumers. Competitive foods/beverages use, excluding à la carte items, was examined using the third School Nutrition Dietary Assessment Study (SNDA III), a nationally representative sample of 2309 schoolchildren in grades 1 to 12. Mean nutrient intakes were adjusted for energy intake and other covariates, and differences between consumers and nonconsumers of competitive items were determined using analysis of variance and sudaan. Excluding à la carte items, 22% of schoolchildren consumed competitive items in a representative school day and use was highest in high school. Consumers of competitive items other than à la carte had significantly higher mean energy, sugar intakes, and lower sodium, dietary fiber, B vitamins, and iron intakes than nonconsumers. Use of competitive foods/beverages, excluding à la carte, was detrimental to children's diet quality.

  1. Ionic Asymmetry and Solvent Excluded Volume Effects on Spherical Electric Double Layers: A Density Functional Approach

    Energy Technology Data Exchange (ETDEWEB)

    Medasani, Bharat; Ovanesyan, Zaven; Thomas, Dennis G.; Sushko, Maria L.; Marucho, Marcelo

    2014-05-29

    In this article we present a classical density functional theory for electrical double layers of spherical macroions that extends the capabilities of conventional approaches by accounting for electrostatic ion correlations, size asymmetry and excluded volume effects. The approach is based on a recent approximation introduced by Hansen-Goos and Roth for the hard sphere excess free energy of inhomogeneous fluids (J. Chem. Phys. 124, 154506). It accounts for the proper and efficient description of the effects of ionic asymmetry and solvent excluded volume, especially at high ion concentrations and size asymmetry ratios including those observed in experimental studies. Additionally, we utilize a leading functional Taylor expansion approximation of the ion density profiles. In addition, we use the Mean Spherical Approximation for multi-component charged hard sphere fluids to account for the electrostatic ion correlation effects. These approximations are implemented in our theoretical formulation into a suitable decomposition of the excess free energy which plays a key role in capturing the complex interplay between charge correlations and excluded volume effects. We perform Monte Carlo simulations in various scenarios to validate the proposed approach, obtaining a good compromise between accuracy and computational cost. We use the proposed computational approach to study the effects of ion size, ion size asymmetry and solvent excluded volume on the ion profiles, integrated charge, mean electrostatic potential, and ionic coordination number around spherical macroions in various electrolyte mixtures. Our results show that both solvent hard sphere diameter and density play a dominant role in the distribution of ions around spherical macroions, mainly for experimental water molarity and size values where the counterion distribution is characterized by a tight binding to the macroion, similar to that predicted by the Stern model.

  2. Clean Water Act (excluding Section 404). Environmental guidance program reference book: Revision 6

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-15

    This Reference Book contains a current copy of the Clean Water Act (excluding Section 404) and those regulations that implement the statutes and appear to be most relevant to US Department of Energy (DOE) activities. The document is provided to DOE and contractor staff for informational purposes only and should not be interpreted as legal guidance. Updates that include important new requirements will be provided periodically. Questions concerning this Reference Book may be directed to Mark Petts, EH-231 (202/586-2609).

  3. A discrete fibre dispersion method for excluding fibres under compression in the modelling of fibrous tissues.

    Science.gov (United States)

    Li, Kewei; Ogden, Ray W; Holzapfel, Gerhard A

    2018-01-01

    Recently, micro-sphere-based methods derived from the angular integration approach have been used for excluding fibres under compression in the modelling of soft biological tissues. However, recent studies have revealed that many of the widely used numerical integration schemes over the unit sphere are inaccurate for large deformation problems even without excluding fibres under compression. Thus, in this study, we propose a discrete fibre dispersion model based on a systematic method for discretizing a unit hemisphere into a finite number of elementary areas, such as spherical triangles. Over each elementary area, we define a representative fibre direction and a discrete fibre density. Then, the strain energy of all the fibres distributed over each elementary area is approximated based on the deformation of the representative fibre direction weighted by the corresponding discrete fibre density. A summation of fibre contributions over all elementary areas then yields the resultant fibre strain energy. This treatment allows us to exclude fibres under compression in a discrete manner by evaluating the tension-compression status of the representative fibre directions only. We have implemented this model in a finite-element programme and illustrate it with three representative examples, including simple tension and simple shear of a unit cube, and non-homogeneous uniaxial extension of a rectangular strip. The results of all three examples are consistent and accurate compared with the previously developed continuous fibre dispersion model, and that is achieved with a substantial reduction of computational cost. © 2018 The Author(s).

  4. Excluded-Mean-Variance Neural Decision Analyzer for Qualitative Group Decision Making

    Directory of Open Access Journals (Sweden)

    Ki-Young Song

    2012-01-01

    Full Text Available Many qualitative group decisions in professional fields such as law, engineering, economics, psychology, and medicine that appear to be crisp and certain are in reality shrouded in fuzziness as a result of uncertain environments and the nature of human cognition within which the group decisions are made. In this paper we introduce an innovative approach to group decision making in uncertain situations by using a mean-variance neural approach. The key idea of this proposed approach is to compute the excluded mean of individual evaluations and weight it by applying a variance influence function (VIF; this process of weighting the excluded mean by VIF provides an improved result in the group decision making. In this paper, a case study with the proposed excluded-mean-variance approach is also presented. The results of this case study indicate that this proposed approach can improve the effectiveness of qualitative decision making by providing the decision maker with a new cognitive tool to assist in the reasoning process.

  5. A novel emulsion-type adjuvant containing CpG oligodeoxynucleotides enhances CD8+ T-cell-mediated anti-tumor immunity.

    Science.gov (United States)

    Song, Ying-Chyi; Cheng, Han-Yin; Leng, Chih-Hsiang; Chiang, Sheng-Kuo; Lin, Chih-Wei; Chong, Pele; Huang, Ming-Hsi; Liu, Shih-Jen

    2014-01-10

    PELC is a novel emulsion-type adjuvant that contains the bioresorbable polymer poly (ethylene glycol)-block-poly (lactide-co-ε-caprolactone) (PEG-b-PLACL), Span®85 and squalene. To investigate whether PELC is able to enhance CTL responses of antigens for treating tumor, peptides or protein antigens derived from HPV16 E7 were formulated with PELC nanoparticles and CpG oligodeoxynucleotide. We identified that PELC formulation could delay the release of antigens in vitro and in vivo. We assessed the immunogenicity of an H-2D(b)-restricted CTL epitope RAHYNIVTF (RAH) formulated with PELC or PELC/CpG and investigated the ability of these formulations to promote tumor regression. Following a single-dose subcutaneous injection in mice, we found that the RAH peptide formulated with PELC/CpG (RAH/PELC/CpG) resulted in increased numbers of IFN-γ-secreting cells and RAH-specific CD8(+) T cells and an enhanced cytotoxic T cell response compared with RAH formulated with PELC or CpG alone. The tumor-bearing mice received a single-dose injection of RAH/PELC/CpG, which induced complete tumor regression. These results demonstrated that peptide antigen formulated with PELC/CpG nanoparticles is feasible for cancer immunotherapy. © 2013. Published by Elsevier B.V. All rights reserved.

  6. Systematic CpT (ApG) Depletion and CpG Excess Are Unique Genomic Signatures of Large DNA Viruses Infecting Invertebrates

    Science.gov (United States)

    Upadhyay, Mohita; Sharma, Neha; Vivekanandan, Perumal

    2014-01-01

    Differences in the relative abundance of dinucleotides, if any may provide important clues on host-driven evolution of viruses. We studied dinucleotide frequencies of large DNA viruses infecting vertebrates (n = 105; viruses infecting mammals = 99; viruses infecting aves = 6; viruses infecting reptiles = 1) and invertebrates (n = 88; viruses infecting insects = 84; viruses infecting crustaceans = 4). We have identified systematic depletion of CpT(ApG) dinucleotides and over-representation of CpG dinucleotides as the unique genomic signature of large DNA viruses infecting invertebrates. Detailed investigation of this unique genomic signature suggests the existence of invertebrate host-induced pressures specifically targeting CpT(ApG) and CpG dinucleotides. The depletion of CpT dinucleotides among large DNA viruses infecting invertebrates is at least in part, explained by non-canonical DNA methylation by the infected host. Our findings highlight the role of invertebrate host-related factors in shaping virus evolution and they also provide the necessary framework for future studies on evolution, epigenetics and molecular biology of viruses infecting this group of hosts. PMID:25369195

  7. Transcriptionally Repressive Chromatin Remodelling and CpG Methylation in the Presence of Expanded CTG-Repeats at the DM1 Locus.

    Science.gov (United States)

    Brouwer, Judith Rixt; Huguet, Aline; Nicole, Annie; Munnich, Arnold; Gourdon, Geneviève

    2013-01-01

    An expanded CTG-repeat in the 3' UTR of the DMPK gene is responsible for myotonic dystrophy type I (DM1). Somatic and intergenerational instability cause the disease to become more severe during life and in subsequent generations. Evidence is accumulating that trinucleotide repeat instability and disease progression involve aberrant chromatin dynamics. We explored the chromatin environment in relation to expanded CTG-repeat tracts in hearts from transgenic mice carrying the DM1 locus with different repeat lengths. Using bisulfite sequencing we detected abundant CpG methylation in the regions flanking the expanded CTG-repeat. CpG methylation was postulated to affect CTCF binding but we found that CTCF binding is not affected by CTG-repeat length in our transgenic mice. We detected significantly decreased DMPK sense and SIX5 transcript expression levels in mice with expanded CTG-repeats. Expression of the DM1 antisense transcript was barely affected by CTG-repeat expansion. In line with altered gene expression, ChIP studies revealed a locally less active chromatin conformation around the expanded CTG-repeat, namely, decreased enrichment of active histone mark H3K9/14Ac and increased H3K9Me3 enrichment (repressive chromatin mark). We also observed binding of PCNA around the repeats, a candidate that could launch chromatin remodelling cascades at expanded repeats, ultimately affecting gene transcription and repeat instability.

  8. A live Leishmania major vaccine containing CpG motifs induces the de novo generation of Th17 cells in C57BL/6 mice.

    Science.gov (United States)

    Wu, Wenhui; Huang, Lu; Mendez, Susana

    2010-09-01

    Cutaneous leishmaniasis produces open sores that lead to scarring and disfiguration. We have reported that vaccination of C57BL/6 mice with live Leishmania major plus CpG DNA (Lm/CpG) prevents lesion development and provides long-term immunity. Our current study aims to characterize the components of the adaptive immune response that are unique to Lm/CpG. We find that this vaccine enhances the proliferation of CD4(+) Th17 cells, which contrasts with the highly polarized Th1 response caused by L. major alone; the Th17 response is dependent upon release of vaccine-induced IL-6. Neutralization of IFN-gamma and, in particular, IL-17 caused increased parasite burdens in Lm/CpG-vaccinated mice. IL-17R-deficient Lm/CpG-vaccinated mice develop lesions, and display decreased IL-17 and IFN-gamma, despite normal IL-12, production. Neutrophil accumulation is also decreased in the IL-17R-deficient Lm/CpG-vaccinated mice but Treg numbers are augmented. Our data demonstrate that activation of immune cells through CpG DNA, in the presence of live L. major, causes the specific induction of Th17 cells, which enhances the development of a protective cellular immunity against the parasite. Our study also demonstrates that vaccines combining live pathogens with immunomodulatory molecules may strikingly modify the natural immune response to infection in an alternative manner to that induced by killed or subunit vaccines.

  9. Phase 1 study in malaria naïve adults of BSAM2/Alhydrogel®+CPG 7909, a blood stage vaccine against P. falciparum malaria.

    Directory of Open Access Journals (Sweden)

    Ruth D Ellis

    Full Text Available A Phase 1 dose escalating study was conducted in malaria naïve adults to assess the safety, reactogenicity, and immunogenicity of the blood stage malaria vaccine BSAM2/Alhydrogel®+ CPG 7909. BSAM2 is a combination of the FVO and 3D7 alleles of recombinant AMA1 and MSP1(42, with equal amounts by weight of each of the four proteins mixed, bound to Alhydrogel®, and administered with the adjuvant CPG 7909. Thirty (30 volunteers were enrolled in two dose groups, with 15 volunteers receiving up to three doses of 40 µg total protein at Days 0, 56, and 180, and 15 volunteers receiving up to three doses of 160 µg protein on the same schedule. Most related adverse events were mild or moderate, but 4 volunteers experienced severe systemic reactions and two were withdrawn from vaccinations due to adverse events. Geometric mean antibody levels after two vaccinations with the high dose formulation were 136 µg/ml for AMA1 and 78 µg/ml for MSP1(42. Antibody responses were not significantly different in the high dose versus low dose groups and did not further increase after third vaccination. In vitro growth inhibition was demonstrated and was closely correlated with anti-AMA1 antibody responses. A Phase 1b trial in malaria-exposed adults is being conducted.Clinicaltrials.gov NCT00889616.

  10. Environmental stress affects DNA methylation of a CpG rich promoter region of serotonin transporter gene in a nurse cohort.

    Science.gov (United States)

    Alasaari, Jukka S; Lagus, Markus; Ollila, Hanna M; Toivola, Auli; Kivimäki, Mika; Vahtera, Jussi; Kronholm, Erkki; Härmä, Mikko; Puttonen, Sampsa; Paunio, Tiina

    2012-01-01

    Shift-working nurses are exposed to a stressful work environment, which puts them at an increased risk for burnout and depression. We explored the effect of environmental stress on serotonin transporter gene (SLC6A4) promoter methylation among nurses from high and low work stress environments. Using bisulfite sequencing, we investigated the methylation status of five CpG residues of a CpG-rich region in the promoter of SLC6A4 by comparing female shift working nurses from a high work stress environment (n = 24) to low work stress environment (n = 25). We also analyzed the association of 5-HTTLPR polymorphism at 5' end of SLC6A4. Work stress was assessed by the Karasek's Model and possible signs of burnout or depression were measured by the Maslach Burnout Index General Survey and Beck Depression Index. Methylation levels were assessed by bisulfite sequencing of DNA extracted from peripheral blood leucocytes. Restriction enzyme treatment followed by standard PCR was used to identify 5-HTTLPR genotypes. We found that nurses in the high stress environment had significantly lower promoter methylation levels at all five CpG residues compared to nurses in the low stress environment (pburnout was not significantly associated to methylation levels. However, when mutually adjusted for both, burnout and work stress were significant contributors (p = 0.038 and pdepressed mood in long-term stress.

  11. Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences.

    Science.gov (United States)

    Günther, Katharina; Rust, Mareike; Leers, Joerg; Boettger, Thomas; Scharfe, Maren; Jarek, Michael; Bartkuhn, Marek; Renkawitz, Rainer

    2013-03-01

    The heterogeneous collection of nucleosome remodelling and deacetylation (NuRD) complexes can be grouped into the MBD2- or MBD3-containing complexes MBD2-NuRD and MBD3-NuRD. MBD2 is known to bind to methylated CpG sequences in vitro in contrast to MBD3. Although functional differences have been described, a direct comparison of MBD2 and MBD3 in respect to genome-wide binding and function has been lacking. Here, we show that MBD2-NuRD, in contrast to MBD3-NuRD, converts open chromatin with euchromatic histone modifications into tightly compacted chromatin with repressive histone marks. Genome-wide, a strong enrichment for MBD2 at methylated CpG sequences is found, whereas CpGs bound by MBD3 are devoid of methylation. MBD2-bound genes are generally lower expressed as compared with MBD3-bound genes. When depleting cells for MBD2, the MBD2-bound genes increase their activity, whereas MBD2 plus MBD3-bound genes reduce their activity. Most strikingly, MBD3 is enriched at active promoters, whereas MBD2 is bound at methylated promoters and enriched at exon sequences of active genes.

  12. Up-regulation of expression and lack of 5' CpG island hypermethylation of p16 INK4a in HPV-positive cervical carcinomas

    Directory of Open Access Journals (Sweden)

    Frank Georgy A

    2007-03-01

    Full Text Available Abstract Background High risk type human papilloma viruses (HR-HPV induce carcinomas of the uterine cervix by expressing viral oncogenes E6 and E7. Oncogene E7 of HR-HPV disrupts the pRb/E2F interaction, which negatively regulates the S phase entry. Expression of tumor suppressor p16ink4a drastically increases in majority of HR-HPV associated carcinomas due to removal of pRb repression. The p16ink4a overexpression is an indicator of an aberrant expression of viral oncogenes and may serve as a marker for early diagnostic of cervical cancer. On the other hand, in 25–57% of cervical carcinomas hypermethylation of the p16 INK4a promoter has been demonstrated using a methylation-specific PCR, MSP. To evaluate a potential usage of the p16 INK4a 5' CpG island hypermethylation as an indicator of tumor cell along with p16ink4a overexpression, we analyzed the methylation status of p16 INK4a in cervical carcinomas Methods Methylation status of p16 INK4a was analyzed by MSP and by bisulfite-modified DNA sequencing. The expression of p16ink4a was analyzed by RT-PCR and by immunohistochemical technique. Results The extensive methylation within p16 INK4a 5' CpG island was not detected either in 13 primary cervical carcinomas or in 5 cancer cell lines by bisulfite-modified DNA sequencing (including those that were positive by MSP in our hands. The number and distribution of rare partially methylated CpG sites did not differ considerably in tumors and adjacent normal tissues. The levels of the p16 INK4a mRNA were increased in carcinomas compared to the normal tissues independently of the number of partially methylated CpGs within 5'CpG island. The transcriptional activation of p16 INK4a was accompanied by p16ink4a cytoplasmic immunoreactivity in the majority of tumor cells and presence of a varied number of the p16 positive nuclei in different tumors. Conclusion Hypermethylaion of the p16INK4a 5' CpG island is not a frequent event in HR-HPV-positive cervical

  13. The effect of excluding juveniles on apparent adult olive baboons (Papio anubis) social networks

    Science.gov (United States)

    Fedurek, Piotr; Lehmann, Julia

    2017-01-01

    In recent years there has been much interest in investigating the social structure of group living animals using social network analysis. Many studies so far have focused on the social networks of adults, often excluding younger, immature group members. This potentially may lead to a biased view of group social structure as multiple recent studies have shown that younger group members can significantly contribute to group structure. As proof of the concept, we address this issue by investigating social network structure with and without juveniles in wild olive baboons (Papio anubis) at Gashaka Gumti National Park, Nigeria. Two social networks including all independently moving individuals (i.e., excluding dependent juveniles) were created based on aggressive and grooming behaviour. We used knockout simulations based on the random removal of individuals from the network in order to investigate to what extent the exclusion of juveniles affects the resulting network structure and our interpretation of age-sex specific social roles. We found that juvenile social patterns differed from those of adults and that the exclusion of juveniles from the network significantly altered the resulting overall network structure. Moreover, the removal of juveniles from the network affected individuals in specific age-sex classes differently: for example, including juveniles in the grooming network increased network centrality of adult females while decreasing centrality of adult males. These results suggest that excluding juveniles from the analysis may not only result in a distorted picture of the overall social structure but also may mask some of the social roles of individuals belonging to different age-sex classes. PMID:28323851

  14. Method for excluding salt and other soluble materials from produced water

    Science.gov (United States)

    Phelps, Tommy J [Knoxville, TN; Tsouris, Costas [Oak Ridge, TN; Palumbo, Anthony V [Oak Ridge, TN; Riestenberg, David E [Knoxville, TN; McCallum, Scott D [Knoxville, TN

    2009-08-04

    A method for reducing the salinity, as well as the hydrocarbon concentration of produced water to levels sufficient to meet surface water discharge standards. Pressure vessel and coflow injection technology developed at the Oak Ridge National Laboratory is used to mix produced water and a gas hydrate forming fluid to form a solid or semi-solid gas hydrate mixture. Salts and solids are excluded from the water that becomes a part of the hydrate cage. A three-step process of dissociation of the hydrate results in purified water suitable for irrigation.

  15. Chip-excluding in Lathe Cutting 1st. Report : Chip Form Geometry I

    OpenAIRE

    小尾, 誠; 岩里, 茂; 丹沢, 常正

    1981-01-01

    The cfficiency of chip-excluding in lathe cutting is very often determined by chip forms. So, the relation between the chip form and cutting conditions must be explained from the point of view of not only practical experiences but also theoretical studies. Here in the paper, the basic equation for chip forms has been derived analytically and the chip forms are simulated on the basis of an assumption that the chip is formed by certain herahedrons which are piled. By this study the following re...

  16. 5 CFR 919.420 - May I approve a transaction with an excluded or disqualified person at a lower tier?

    Science.gov (United States)

    2010-01-01

    ... excluded or disqualified person at a lower tier? 919.420 Section 919.420 Administrative Personnel OFFICE OF... a transaction with an excluded or disqualified person at a lower tier? If a transaction at a lower tier is subject to your approval, you as an agency official may not approve— (a) A covered transaction...

  17. 31 CFR 19.420 - May I approve a transaction with an excluded or disqualified person at a lower tier?

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false May I approve a transaction with an excluded or disqualified person at a lower tier? 19.420 Section 19.420 Money and Finance: Treasury Office... transaction with an excluded or disqualified person at a lower tier? If a transaction at a lower tier is...

  18. 20 CFR 10.818 - How is a provider notified of OWCP's intent to exclude him or her?

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false How is a provider notified of OWCP's intent to exclude him or her? 10.818 Section 10.818 Employees' Benefits OFFICE OF WORKERS' COMPENSATION... How is a provider notified of OWCP's intent to exclude him or her? The Regional Director shall...

  19. 20 CFR 30.718 - How is a provider notified of OWCP's intent to exclude him or her?

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false How is a provider notified of OWCP's intent to exclude him or her? 30.718 Section 30.718 Employees' Benefits OFFICE OF WORKERS' COMPENSATION... OWCP's intent to exclude him or her? The Regional Director shall initiate the exclusion process by...

  20. 9 CFR 130.16 - User fees for veterinary diagnostic serology tests performed at NVSL (excluding FADDL) or at...

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false User fees for veterinary diagnostic serology tests performed at NVSL (excluding FADDL) or at authorized sites. 130.16 Section 130.16 Animals... USER FEES § 130.16 User fees for veterinary diagnostic serology tests performed at NVSL (excluding...

  1. 9 CFR 130.19 - User fees for other veterinary diagnostic services or materials provided at NVSL (excluding FADDL).

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false User fees for other veterinary... User fees for other veterinary diagnostic services or materials provided at NVSL (excluding FADDL). (a) User fees for other veterinary diagnostic services or materials available from NVSL (excluding FADDL...

  2. Anxiety Associated Increased CpG Methylation in the Promoter of Asb1: A Translational Approach Evidenced by Epidemiological and Clinical Studies and a Murine Model.

    Science.gov (United States)

    Emeny, Rebecca T; Baumert, Jens; Zannas, Anthony S; Kunze, Sonja; Wahl, Simone; Iurato, Stella; Arloth, Janine; Erhardt, Angelika; Balsevich, Georgia; Schmidt, Mathias V; Weber, Peter; Kretschmer, Anja; Pfeiffer, Liliane; Kruse, Johannes; Strauch, Konstantin; Roden, Michael; Herder, Christian; Koenig, Wolfgang; Gieger, Christian; Waldenberger, Melanie; Peters, Annette; Binder, Elisabeth B; Ladwig, Karl-Heinz

    2018-01-01

    Epigenetic regulation in anxiety is suggested, but evidence from large studies is needed. We conducted an epigenome-wide association study (EWAS) on anxiety in a population-based cohort and validated our finding in a clinical cohort as well as a murine model. In the KORA cohort, participants (n=1522, age 32-72 years) were administered the Generalized Anxiety Disorder (GAD-7) instrument, whole blood DNA methylation was measured (Illumina 450K BeadChip), and circulating levels of hs-CRP and IL-18 were assessed in the association between anxiety and methylation. DNA methylation was measured using the same instrument in a study of patients with anxiety disorders recruited at the Max Planck Institute of Psychiatry (MPIP, 131 non-medicated cases and 169 controls). To expand our mechanistic understanding, these findings were reverse translated in a mouse model of acute social defeat stress. In the KORA study, participants were classified according to mild, moderate, or severe levels of anxiety (29.4%/6.0%/1.5%, respectively). Severe anxiety was associated with 48.5% increased methylation at a single CpG site (cg12701571) located in the promoter of the gene encoding Asb1 (β-coefficient=0.56 standard error (SE)=0.10, p (Bonferroni)=0.005), a protein hypothetically involved in regulation of cytokine signaling. An interaction between IL-18 and severe anxiety with methylation of this CpG cite showed a tendency towards significance in the total population (p=0.083) and a significant interaction among women (p=0.014). Methylation of the same CpG was positively associated with Panic and Agoraphobia scale (PAS) scores (β=0.005, SE=0.002, p=0.021, n=131) among cases in the MPIP study. In a murine model of acute social defeat stress, Asb1 gene expression was significantly upregulated in a tissue-specific manner (p=0.006), which correlated with upregulation of the neuroimmunomodulating cytokine interleukin 1 beta. Our findings suggest epigenetic regulation of the stress

  3. Prejudice in practitioners who work with socially excluded people in Andalusia: A dual process approach

    Directory of Open Access Journals (Sweden)

    José-Luis Álvarez-Castillo

    2016-12-01

    Full Text Available It is assumed that the professional profile of those who work with socially excluded people is not compatible with the maintenance of prejudices against the group they help. The current study tested this hypothesis regarding the Dual Process Cognitive-Motivational Model of Duckitt (2001 and Duckitt and Sibley (2010. Data from 565 Andalusian professionals were collected in a cross-sectional survey, using measures of socio-demographics, personality, values, ideological attitudes, political position, and prejudice. The model fitted to data reproduced the basic relations in the hypothesized model, although its explanatory power was limited. Prejudice was significantly explained by both paths (authoritarianism and dominance, leading to the conclusion that the reduced level of prejudice held by professionals corresponds to the perception of socially excluded people as a dissident group. This suggests that professional identity as a broad construct may moderate the variance in prejudice. Finally, these findings also suggest that the professional development of social workers should be promoted.

  4. MRI of the breast in patients with DCIS to exclude the presence of invasive disease

    Energy Technology Data Exchange (ETDEWEB)

    Deurloo, Eline E. [Academic Medical Center, Department of Radiology, Amsterdam (Netherlands); Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital, Department of Radiology, Amsterdam (Netherlands); Sriram, Jincey D.; Rutgers, Emiel J.T. [Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital, Department of Surgery, Amsterdam (Netherlands); Teertstra, Hendrik J.; Loo, Claudette E. [Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital, Department of Radiology, Amsterdam (Netherlands); Wesseling, Jelle [Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital, Department of Pathology, Amsterdam (Netherlands); Gilhuijs, Kenneth G.A. [Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital, Department of Radiology, Amsterdam (Netherlands); University Medical Center Utrecht, Department of Radiology, Image Sciences Institute, Utrecht (Netherlands)

    2012-07-15

    Core biopsy underestimates invasion in more than 20% of patients with preoperatively diagnosed ductal carcinoma in situ (DCIS) without evidence of invasion (pure DCIS). The aim of the current study was to evaluate the efficacy of preoperative magnetic resonance imaging (MRI) to discriminate between patients with DCIS who are at high risk of invasive breast cancer and patients at low risk. One hundred and twenty-five patients, preoperatively diagnosed with pure DCIS (128 lesions; 3 bilateral) by core-needle biopsy, were prospectively included. Clinical, mammographic, histological (core biopsy) and MRI features were assessed. All patients underwent breast surgery. Analyses were performed to identify features associated with presence of invasion. Eighteen lesions (14.1%) showed invasion on final histology. Seventy-three lesions (57%) showed suspicious enhancement on MRI with a type 1 (n = 12, 16.4%), type 2 (n = 19, 26.0%) or type 3 curve, respectively (n = 42, 57.5%). At multivariate analysis, the most predictive features for excluding presence of invasive disease were absence of enhancement or a type 1 curve on MRI (negative predictive value 98.5%; A{sub Z} 0.80, P = 0.00006). Contrast medium uptake kinetics at MRI provide high negative predictive value to exclude presence of invasion and may be useful in primary surgical planning in patients with a preoperative diagnosis of pure DCIS. (orig.)

  5. A comparison of trapping techniques (Coleoptera: Carabidae, Buprestidae, Cerambycidae, and Curculionoidea excluding Scolytinae)

    Science.gov (United States)

    Skvarla, Michael J.; Dowling, Ashley P. G.

    2017-01-01

    Beetles (Coleoptera) are a charismatic group of insects targeted by collectors and often used in biodiversity surveys. As part of a larger project, we surveyed a small (4 hectare) plot in the Boston Mountains of Arkansas using 70 traps of 12 trap types and Berlese–Tullgren extraction of leaf litter and identified all Buprestidae, Carabidae, Cerambycidae, and Curculionoidea (Anthribidae, Attelabidae, Brachyceridae, Brentidae, and Curculionidae excluding Scolytinae) to species. This resulted in the collection of 7,973 specimens representing 242 species arranged in 8 families. In a previous publication, we reported new state records and the number of specimens collected per species. In this publication, we used these data to determine the most effective collection method for four beetle groups: Carabidae, Cerambycidae, Curculionoidea (excluding Scolytinae), and Buprestidae. We found that the combination of pitfall and Malaise traps was most effective for Carabidae, Cerambycidae, and Curculionoidea, but that the combination of Malaise and green Lindgren funnel traps was most effective at collecting Buprestidae. Species accumulation curves did not become asymptotic and extrapolated rarefaction curves did not become asymptotic until 350–1,000 samples, suggesting that much more effort is required to completely inventory even a small site. Additionally, seasonal activity is presented for each species and the similarity and overlap between collecting dates and seasons is discussed for each family. PMID:28042105

  6. Tuberculosis peer educators: personal experiences of working with socially excluded communities in London.

    Science.gov (United States)

    Croft, L A; Hayward, A C; Story, A

    2013-10-01

    Peer education is a relatively unexplored intervention for tuberculosis (TB) control, particularly among socially excluded communities. In London, peer educators are used to raise awareness of TB and promote uptake of radiological screening among people using homeless and/or drug and alcohol treatment services. To understand the motivation and personal impact of being a peer educator on people with experience of anti-tuberculosis treatment, homelessness and addiction. In-depth semi-structured interviews with peer educators were recorded and transcribed, and then analysed using a grounded theory approach to identify themes. Reflexivity and thick description were used to support transparency of findings. Becoming a peer educator supports individuals in making sense of past experiences and renewing their sense of self. The role places value on personal experience and the communication approach this supports. The project environment is an important motivator, providing the peer with structure, social support and respect. Being a peer educator with experience of homelessness and addiction can be beneficial and empowering and help long-term recovery. Peers are an underused resource for strengthening TB control among socially excluded populations. There is a need for further research into the contribution of peers to TB control, including analyses of economic effectiveness.

  7. The Gore Excluder AAA endoprosthesis with C3 delivery system: results in high-volume centers.

    Science.gov (United States)

    Krajcer, Z

    2014-02-01

    The use of endovascular aortic aneurysm repair (EVAR) has increased dramatically, chiefly because of its low perioperative morbidity compared with open surgery. Challenges to the success of EVAR remain, however, with the most important being features of the patient's infrarenal aortic neck anatomy that make optimal placement of the endoprosthesis difficult. These features include a short, wide, severely angulated, or reverse-tapered neck and the presence of calcifications or thrombus. Suboptimal endograft positioning may necessitate use of aortic cuffs, thereby increasing the time and cost of an EVAR procedure, or increase the likelihood of graft migration, which can lead to endoleaks and additional interventions. Efforts to improve outcomes of EVAR and expand its application in patients with challenging aortic neck anatomy have focused on the development of endografts and delivery systems with innovative designs. The low-permeability Gore Excluder AAA endoprosthesis with C3 delivery system, which became available in Europe and the United States in 2010, represents one such design. The C3 system allows the proximal end of the endoprosthesis to be reconstrained after insertion so that the device can, if necessary, be rotated or moved cranially or caudally. Repositioning may facilitate contralateral gate cannulation and placement of the endograft closer to the lowest renal artery (without covering its orifice), thereby possibly decreasing the risk of inadequate sealing and consequent graft migration and endoleaks. Early clinical studies of the Gore Excluder AAA endoprosthesis with C3 delivery system have yielded promising results.

  8. Computer assisted strain-gauge plethysmography is a practical method of excluding deep venous thrombosis

    Energy Technology Data Exchange (ETDEWEB)

    Goddard, A.J.P.; Chakraverty, S.; Wright, J

    2001-01-01

    AIM: To evaluate a computed strain-gauge plethysmograph (CSGP) as a screening tool to exclude above knee deep venous thrombosis (DVT). METHODS: The first phase took place in the Radiology department. One hundred and forty-nine patients had both Doppler ultrasound and CSGP performed. Discordant results were resolved by venography where possible. The second phase took place in an acute medical admissions ward using a modified protocol. A further 173 patients had both studies performed. The results were collated and analysed. RESULTS: Phase 1. The predictive value of a negative CSGP study was 98%. There were two false-negative CSGP results (false-negative rate 5%), including one equivocal CSGP study which had deep venous thrombosis on ultrasound examination. Two patients thought to have thrombus on ultrasound proved not to have acute thrombus on venography. Phase 2. The negative predictive value of CSGP using a modified protocol was 97%. There were two definite and one possible false-negative studies (false-negative rate 4-7%). CONCLUSION: Computer strain-gauge plethysmograph can provide a simple, cheap and effective method of excluding lower limb DVT. However, its use should be rigorously assessed in each hospital in which it is used. Goddard, A.J.P., Chakraverty, S. and Wright, J. (2001)

  9. Stainless-steel wires exclude gulls from a wastewater treatment plant

    Science.gov (United States)

    Clark, Daniel E.; Koenen, Kiana K. G.; MacKenzie, Kenneth G.; Pereira, Jillian W.; DeStefano, Stephen

    2013-01-01

    There is growing concern about the prevalence of pathogens and antibiotic-resistant bacteria in the environment and the role wildlife plays in their transmission and dissemination. Gulls feeding at wastewater treatment plants may provide a route for transmission of pathogens and bacteria to public water supplies or other critical areas. The authors identified gulls routinely feeding at a wastewater treatment plant in Millbury, Mass., and tested the effectiveness of overhead stainless-steel wires in excluding gulls from the plant. The number of gulls in certainstructures was compared before and after wiring and during an experimental approach using simultaneous treatments and controls. Stainless-steel wires spaced at 0.9-3.3 m (3-10 ft) effectively prevented gulls from using treatment structures (p 24 months. Materials costs to wire all structures was about $5,700, and labor costs were $4,020. Overhead stainless-steel wires can provide a long-term, cost-efficient method of excluding ring-billed gulls from wastewater treatment plants.

  10. A systematic review of clinical trials of treatments for the congenital ichthyoses, excluding ichthyosis vulgaris.

    Science.gov (United States)

    Hernández-Martin, Angela; Aranegui, Beatriz; Martin-Santiago, Ana; Garcia-Doval, Ignacio

    2013-10-01

    The ichthyoses comprise a group of inherited disorders of keratinization. Because of the need for lifelong treatment, it is important that therapies are beneficial, safe, and well tolerated. We sought to review the evidence on existing treatments for the congenital ichthyoses, excluding ichthyosis vulgaris. We undertook a systematic review using the methodology of the Cochrane Collaboration. Articles published in MEDLINE, EMBASE, and CENTRAL and registered clinical trials were screened. Randomized controlled trials involving patients with the inherited ichthyoses, either syndromic or nonsyndromic but excluding ichthyosis vulgaris, were considered. Six trials met the inclusion criteria. Topical treatments including 5% urea, 20% propylene glycol alone or in combination with 5% lactic acid, calcipotriol ointment, and liarozole 5% cream showed therapeutic benefit. Oral liarozole, a retinoic acid metabolism blocking agent, showed no advantage over oral acitretin. Most studies were performed on a small sample of patients and lacked methodological and reporting quality. The small number of trials and the nearly constant positive results make publication bias likely. The absence of standardization of outcome measures precluded the comparison of studies. Topical treatments including emollients, calcipotriol ointment, and liarozole cream seem to have therapeutic benefit and a good safety profile, although the use of topical calcipotriol is limited by a maximum weekly dose of 100 g. The advantage of oral liarozole over acitretin is uncertain. Multicenter trials comparing oral and topical interventions and evaluation of long-term outcomes are needed. Copyright © 2013 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

  11. Unanimous versus partial rejection: How the number of excluders influences the impact of ostracism in children.

    Science.gov (United States)

    Sandstrom, Marlene J; Deutz, Marike H F; Lansu, Tessa A M; van Noorden, Tirza H J; Karremans, Johan C; Cillessen, Antonius H N

    2017-04-01

    Previous research has shown that ostracism-the experience of being ignored and excluded-has negative effects on all of us, young and old. Using a Cyberball paradigm, the present research replicates the effects of ostracism on the moods (anger, anxiety, happiness, and anger) and fundamental needs (belongingness, control, meaningful existence, and self-esteem) of children (Study 1) and then extends the literature by examining the role of the number of ostracizers and inclusive members in this process by randomly assigning children to conditions varying in degree of ostracism (Study 2). Results of both studies showed that experiencing ostracism strongly and negatively affected all moods and fundamental needs-with the exception of anxiety. Study 2 in addition showed that the ratio of excluders to inclusive group members had different effects across outcomes. In all cases, complete ostracism produced the worst outcomes, suggesting that the presence of even a single ally reduces children's distress. For sadness, unanimous ostracism seemed particularly toxic. In some cases, facing two ostracizers produced significantly worse outcomes than only one, suggesting that consensual rejection might drive the negative effects on happiness, and sense of belonging, control, and meaningful existence. For self-esteem, only one ostracizer (in the presence of two inclusive members) was sufficient to induce a negative effect. Aggr. Behav. 43:190-203, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. Matching excluded-volume hadron-resonance gas models and perturbative QCD to lattice calculations

    Science.gov (United States)

    Albright, M.; Kapusta, J.; Young, C.

    2014-08-01

    We match three hadronic equations of state at low energy densities to a perturbatively computed equation of state of quarks and gluons at high energy densities. One of them includes all known hadrons treated as point particles, which approximates attractive interactions among hadrons. The other two include, in addition, repulsive interactions in the form of excluded volumes occupied by the hadrons. A switching function is employed to make the crossover transition from one phase to another without introducing a thermodynamic phase transition. A χ2 fit to accurate lattice calculations with temperature 100coupling and the hard core radius of protons and neutrons, which turns out to be 0.62±0.04 fm. The most physically reasonable models include the excluded-volume effect. Not only do they include the effects of attractive and repulsive interactions among hadrons, but they also achieve better agreement with lattice QCD calculations of the equation of state. The equations of state constructed in this paper do not result in a phase transition, at least not for the temperatures and baryon chemical potentials investigated. It remains to be seen how well these equations of state will represent experimental data on high-energy heavy-ion collisions when implemented in hydrodynamic simulations.

  13. Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation

    DEFF Research Database (Denmark)

    Milani, Lili; Lundmark, Anders; Nordlund, Jessica

    2008-01-01

    To identify genes that are regulated by cis-acting functional elements in acute lymphoblastic leukemia (ALL) we determined the allele-specific expression (ASE) levels of 2, 529 genes by genotyping a genome-wide panel of single nucleotide polymorphisms in RNA and DNA from bone marrow and blood...... of these sites. Our results demonstrate that CpG site methylation is one of the factors that regulates gene expression in ALL cells....... overexpression of one allele to apparent monoallelic expression. For genes exhibiting ASE, 55% displayed bidirectional ASE in which overexpression of either of the two SNP alleles occurred. For bidirectional ASE we also observed overall higher levels of ASE and correlation with the methylation level...

  14. Comparison of CpG island methylator phenotype (CIMP frequency in colon cancer using different probe- and gene-specific scoring alternatives on recommended multi-gene panels.

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    Marianne Berg

    Full Text Available BACKGROUND: In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP. However, a consensus of how to score CIMP is not reached, and variation in definition may influence the reported CIMP prevalence in tumours. Thus, we sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer. METHODS: Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA, with subsequent fragment analysis, was used to investigate methylation of tumour samples. In total, 31 CpG sites, located in 8 different genes (RUNX3, MLH1, NEUROG1, CDKN2A, IGF2, CRABP1, SOCS1 and CACNA1G were investigated in 64 distinct colon cancers and 2 colon cancer cell lines. The Ogino gene panel includes all 8 genes, in addition to the Weisenberger panel of which only 5 of the 8 genes included were investigated. In total, 18 alternative combinations of scoring of CIMP positivity on probe-, gene-, and panel-level were analysed and compared. RESULTS: For 47 samples (71%, the CIMP status was constant and independent of criteria used for scoring; 34 samples were constantly scored as CIMP negative, and 13 (20% consistently scored as CIMP positive. Only four of 31 probes (13% investigated showed no difference in the numbers of positive samples using the different cut-offs. Within the panels a trend was observed that increasing the gene-level stringency resulted in a larger difference in CIMP positive samples than increasing the probe-level stringency. A significant difference between positive samples using 'the most stringent' as compared to 'the least stringent' criteria (20% vs 46%, respectively; p<0.005 was demonstrated. CONCLUSIONS: A statistical significant variation in the frequency of CIMP depending on the cut-offs and genes included in a panel was found, with twice as many positives samples by least compared to most stringent definition

  15. Induction of humoral and cellular immune response to hepatitis B virus (HBV) vaccine can be upregulated by CpG oligonucleotides complexed with Dectin-1 ligand.

    Science.gov (United States)

    Ito, H; Ando, T; Nakamura, M; Ishida, H; Kanbe, A; Kobiyama, K; Yamamoto, T; Ishii, K J; Hara, A; Seishima, M; Ishikawa, T

    2017-02-01

    A persistent hepatitis B virus (HBV) infection is characterized by a lack of or a weak immune response to HBV, which may be reflective of tolerance to HBV. Efficient induction of HBV-specific immune response leads to the clearance of HBV in patients with a chronic HBV infection. CpG oligodeoxynucleotides (ODN) has a powerful adjuvant effect in HBV vaccination. A recent report demonstrated that the immunization by B/K CpG ODN (K3) wrapped by the nonagonistic Dectin-1 ligand, schizophyllan (SPG), namely K3-SPG, was more effective in the induction of antigen-specific immune response than that by K3. In this study, we examined the efficacy of K3-SPG as a HBV vaccine adjuvant. Wild-type (WT) mice and HBV transgenic (HBV-Tg) mice were subcutaneously immunized with hepatitis B surface antigen (HBsAg) alone, HBsAg and K3, or HBsAg and K3-SPG. The vaccination with HBsAg and K3-SPG significantly enhanced humoral and cellular immune response to HBV antigen compared to the other vaccinations in WT and HBV-Tg mice. K3-SPG induced the accumulation of dendritic cells (DCs) into draining lymph node and the activation of DCs. The expression of cytokines and chemokines related to Th1 and Th2 responses was upregulated after the vaccination including with K3-SPG. In conclusion, these results indicated that the vaccination using K3-SPG may overcome tolerance even in patients with chronic HBV infection. © 2016 John Wiley & Sons Ltd.

  16. Insertion of core CpG island element into human CMV promoter for enhancing recombinant protein expression stability in CHO cells.

    Science.gov (United States)

    Mariati; Yeo, Jessna H M; Koh, Esther Y C; Ho, Steven C L; Yang, Yuansheng

    2014-01-01

    The human cytomegalovirus promoter (hCMV) is susceptible to gene silencing in CHO cells, most likely due to epigenetic events, such as DNA methylation and histone modifications. The core CpG island element (IE) from the hamster adenine phosphoribosyltransferase gene has been shown to prevent DNA methylation. A set of modified hCMV promoters was developed by inserting one or two copies of IE in either forward or reverse orientations either upstream of the hCMV enhancer, between the enhancer and core promoter (CP), or downstream of the CP. The modified hCMV with one copy of IE inserted between the enhancer and core promoter in reverse orientation (MR1) was most effective at enhancing expression stability without compromising expression level when compared with the wild-type (WT) hCMV. A third of 18 EGFP expressing clones generated using MR1 retained 70% of their starting expression level after 8 weeks of culture in the absence of selection pressure, while none of 18 WT hCMV generated clones had expression above 50%. MR1 also improved antibody expression stability of methotrexate (MTX) amplified CHO cell lines. Stably transfected pools generated using MR1 maintained 62% of their original monoclonal antibody titer after 8 weeks of culture in the absence of MTX, compared to only 37% for WT hCMV pools. Low levels of CpG methylation within both WT hCMV and MR1 were observed in all the analyzed cell lines and the methylation levels did not correlate to the expression stability, suggesting IE enhances expression stability by other mechanisms other than preventing methylation. © 2014 American Institute of Chemical Engineers.

  17. Evaluation of TLR9 expression on PBMCs and CpG ODN-TLR9 ligation on IFN-α production in SLE patients.

    Science.gov (United States)

    Mortezagholi, Sahar; Babaloo, Zohreh; Rahimzadeh, Parisa; Namdari, Haideh; Ghaedi, Mojgan; Gharibdoost, Farhad; Mirzaei, Reza; Bidad, Katayoon; Salehi, Eisa

    2017-02-01

    Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by autoreactive antibodies. Recent findings revealed the importance of innate immune responses, especially Toll-like receptors (TLRs) in the pathogenesis of SLE. In this study, the level of TLR9 expression on peripheral blood mononuclear cells (PBMCs) was analyzed. The levels of produced IFN-α were also measured in supernatant of PBMCs from SLE patients and healthy controls after stimulation with CpG ODN2216 which is a plasmocytoid dendritic cell (pDC)-specific TLR9 ligand. TLR9 expression was analyzed by real-time polymerase chain reaction (PCR) and flow cytometry in 35 SLE patients and 38 healthy controls and IFN-α concentration was measured in supernatants using enzyme-linked immunosorbent assay (ELISA). The results showed that the TLR9 expression in the mRNA and the protein level was significantly higher in PBMCs from SLE patients. However, IFN-α concentration in patients and controls significantly increased in response to CpG stimulation but this increase was significantly higher in healthy controls compared with SLE patients. Our results do not show any association between taking hydroxychloroquine and reduction in IFN-α production in SLE patients. Regarding the findings of the study, there is the possibility that TLR9 has played a role in SLE pathogenesis, and consequently it implies that TLRs can be considered to be the therapeutic targets for systemic autoimmunity. We may conclude that PBMCs in patients are functionally impaired in response to TLR ligation via innate response stimulating pathogen-associated molecular patterns (PAMPs).

  18. Development of TRAIL Resistance by Radiation-Induced Hypermethylation of DR4 CpG Island in Recurrent Laryngeal Squamous Cell Carcinoma

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    Lee, Jong Cheol [Department of Otorhinolaryngology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan (Korea, Republic of); Department of Biomedical Research Center, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan (Korea, Republic of); Lee, Won Hyeok [Department of Biomedical Research Center, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan (Korea, Republic of); Min, Young Joo [Department of Biomedical Research Center, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan (Korea, Republic of); Department of Internal Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan (Korea, Republic of); Cha, Hee Jeong [Department of Pathology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan (Korea, Republic of); Han, Myung Woul [Department of Otorhinolaryngology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan (Korea, Republic of); Chang, Hyo Won [Department of Otolaryngology, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of); Kim, Sun-A [Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of); Choi, Seung-Ho [Department of Otolaryngology, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of); Kim, Seong Who, E-mail: swhokim@gmail.com [Department of Biochemistry and Molecular Biology, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of); Kim, Sang Yoon, E-mail: sykim3715@gmail.com [Department of Otolaryngology, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of); Biomedical Research Institute, Korea Institute of Science and Technology, Seoul (Korea, Republic of)

    2014-04-01

    Purpose: There are limited therapeutic options for patients with recurrent head and neck cancer after radiation therapy failure. To assess the use of tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) as a salvage chemotherapeutic agent for recurrent cancer after radiation failure, we investigated the effect of clinically relevant cumulative irradiation on TRAIL-induced apoptosis. Methods and Materials: Using a previously established HN3 cell line from a laryngeal carcinoma patient, we generated a chronically irradiated HN3R isogenic cell line. Viability and apoptosis in HN3 and HN3R cells treated with TRAIL were analyzed with MTS and PI/annexin V-FITC assays. Western blotting and flow cytometry were used to determine the underlying mechanism of TRAIL resistance. DR4 expression was semiquantitatively scored in a tissue microarray with 107 laryngeal cancer specimens. Methylation-specific polymerase chain reaction and bisulfite sequencing for DR4 were performed for genomic DNA isolated from each cell line. Results: HN3R cells were more resistant than HN3 cells to TRAIL-induced apoptosis because of significantly reduced levels of the DR4 receptor. The DR4 staining score in 37 salvage surgical specimens after radiation failure was lower in 70 surgical specimens without radiation treatment (3.03 ± 2.75 vs 5.46 ± 3.30, respectively; P<.001). HN3R cells had a methylated DR4 CpG island that was partially demethylated by the DNA demethylating agent 5-aza-2′-deoxycytidine. Conclusion: Epigenetic silencing of the TRAIL receptor by hypermethylation of a DR4 CpG island might be an underlying mechanism for TRAIL resistance in recurrent laryngeal carcinoma treated with radiation.

  19. Stable phase-shift despite quasi-rhythmic movements: a CPG-driven dynamic model of active tactile exploration in an insect

    Directory of Open Access Journals (Sweden)

    Nalin eHarischandra

    2015-08-01

    Full Text Available An essential component of autonomous and flexible behaviour in animals is active exploration of the environment, allowing for perception-guided planning and control of actions. An important sensory system involved is active touch. Here, we introduce a general modelling framework of Central Pattern Generators (CPGs for movement generation in active tactile exploration behaviour. The CPG consists of two network levels: (i phase-coupled Hopf oscillators for rhythm generation, and (ii pattern formation networks for capturing the frequency and phase characteristics of individual joint oscillations. The model captured the natural, quasi-rhythmic joint kinematics as observed in coordinated antennal movements of walking stick insects. Moreover, it successfully produced tactile exploration behaviour on a three-dimensional skeletal model of the insect antennal system with physically realistic parameters. The effect of proprioceptor ablations could be simulated by changing the amplitude and offset parameters of the joint oscillators, only. As in the animal, the movement of both antennal joints was coupled with a stable phase difference, despite the quasi-rhythmicity of the joint angle time courses. We found that the phase-lead of the distal scape-pedicel joint relative to the proximal head-scape joint was essential for producing the natural tactile exploration behaviour and, thus, for tactile efficiency. For realistic movement patterns, the phase-lead could vary within a limited range of 10 to 30 degrees only. Tests with artificial movement patterns strongly suggest that this phase sensitivity is not a matter of the frequency composition of the natural movement pattern. Based on our modelling results, we propose that a constant phase difference is coded into the CPG of the antennal motor system and that proprioceptors are acting locally to regulate the joint movement amplitude.

  20. The application of methylation specific electrophoresis (MSE to DNA methylation analysis of the 5' CpG island of mucin in cancer cells

    Directory of Open Access Journals (Sweden)

    Yokoyama Seiya

    2012-02-01

    Full Text Available Abstract Background Methylation of CpG sites in genomic DNA plays an important role in gene regulation and especially in gene silencing. We have reported mechanisms of epigenetic regulation for expression of mucins, which are markers of malignancy potential and early detection of human neoplasms. Epigenetic changes in promoter regions appear to be the first step in expression of mucins. Thus, detection of promoter methylation status is important for early diagnosis of cancer, monitoring of tumor behavior, and evaluating the response of tumors to targeted therapy. However, conventional analytical methods for DNA methylation require a large amount of DNA and have low sensitivity. Methods Here, we report a modified version of the bisulfite-DGGE (denaturing gradient gel electrophoresis using a nested PCR approach. We designated this method as methylation specific electrophoresis (MSE. The MSE method is comprised of the following steps: (a bisulfite treatment of genomic DNA, (b amplification of the target DNA by a nested PCR approach and (c applying to DGGE. To examine whether the MSE method is able to analyze DNA methylation of mucin genes in various samples, we apply it to DNA obtained from state cell lines, ethanol-fixed colonic crypts and human pancreatic juices. Result The MSE method greatly decreases the amount of input DNA. The lower detection limit for distinguishing different methylation status is Conclusions The MSE method can provide a qualitative information of methylated sequence profile. The MSE method allows sensitive and specific analysis of the DNA methylation pattern of almost any block of multiple CpG sites. The MSE method can be applied to analysis of DNA methylation status in many different clinical samples, and this may facilitate identification of new risk markers.

  1. Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains

    DEFF Research Database (Denmark)

    Crowther, P J; Doherty, J P; Linsenmeyer, M E

    1991-01-01

    Efficient recovery of clones from the 5' end of the human L1 dispersed repetitive elements necessitates the use of deletion mcr- host strains since this region contains a CpG island which is hypermethylated in vivo. Clones recovered with conventional mcr+ hosts seem to have been derived preferent...

  2. Negative effects overpower the positive of kelp to exclude invertebrates from the understorey community.

    Science.gov (United States)

    Connell, Sean D

    2003-09-01

    Marine macroalgal forests are one of the most widespread and studied habitats on subtidal coasts, but there remain challenges in understanding why many sessile invertebrates are anomalously absent from understorey communities. In a series of experiments on recruitment of invertebrates, I partitioned the habitat-modifying effects of kelp into their positive and negative effects. Experiments revealed that a reduction of light intensity and removal of sediment by canopies acted to facilitate recruitment, but physical abrasion by the canopy acted as a negative force to overpower these positive effects. Understorey assemblages, therefore, represent biased subsets of taxa from a local pool capable of colonization. On balance, negative effects acted to exclude invertebrates from the understorey community. The asymmetric strength of negative effects not only explains the enigma of exclusion but also indicates that, when it exists, understorey coexistence with canopy plants must reflect a more even match between positive and negative effects.

  3. Dyslexic adults can learn from repeated stimulus presentation but have difficulties in excluding external noise.

    Directory of Open Access Journals (Sweden)

    Rachel L Beattie

    Full Text Available We examined whether the characteristic impairments of dyslexia are due to a deficit in excluding external noise or a deficit in taking advantage of repeated stimulus presentation. We compared non-impaired adults and adults with poor reading performance on a visual letter detection task that varied two aspects: the presence or absence of background visual noise, and a small or large stimulus set. There was no interaction between group and stimulus set size, indicating that the poor readers took advantage of repeated stimulus presentation as well as the non-impaired readers. The poor readers had higher thresholds than non-impaired readers in the presence of high external noise, but not in the absence of external noise. The results support the hypothesis that an external noise exclusion deficit, not a perceptual anchoring deficit, impairs reading for adults.

  4. Excluded and behaving unethically: social exclusion, physiological responses, and unethical behavior.

    Science.gov (United States)

    Kouchaki, Maryam; Wareham, Justin

    2015-03-01

    Across 2 studies, we investigated the ethical consequences of physiological responses to social exclusion. In Study 1, participants who were socially excluded were more likely to engage in unethical behavior to make money and the level of physiological arousal experienced during exclusion--measured using galvanic skin response--mediated the effects of exclusion on unethical behavior. Likewise, in Study 2, results from a sample of supervisor-subordinate dyads revealed a positive relationship between experience of workplace ostracism and unethical behaviors as rated by the immediate supervisors. This relationship was mediated by employees' reports of experienced physiological arousal. Together, the results of these studies demonstrate that physiological arousal accompanies social exclusion and provides an explanatory mechanism for the increased unethical behavior in both samples. Theoretical implications of these findings for research on ethical behavior and social exclusion in the workplace are discussed. PsycINFO Database Record (c) 2015 APA, all rights reserved.

  5. [Immunophenotyping of B chronic lymphoproliferative syndromes (CLL excluded): confrontation with the histology].

    Science.gov (United States)

    El Borgi, Wijden; Ben Salah, Nawel; Ben Lakhal, Fatma; Makni, Lamia; Gouider, Emna; Hafsia, Raouf

    2013-01-01

    Immunophenotyping is a major tool for the diagnosis of the chronic lymphoïd leukaemia (CLL). Its interest remains limited in the classification of the other B chronic lymphoproliférative syndromes (B-CLPS). We evaluate the place of the flow cytometry (CMF) in the diagnosis and classification of the non CLL B-CLPS. The cases with Matutes score of 4 or more are excluded. A confrontation of the results to the histology is made. 28 cases of non CLL B-CLPS are diagnosed. CMF shows a κ monoclonal population in 15 cases and λ in 13 cases. A co-expression CD19+CD5 + is found in 11 cases concording with an atypic CLL or a mantel cell lymphoma in 6 cases with Matutes score of 3. In 5 cases, we concluded to non CLL B-CLPS (Matutesconfrontation of the histology results remains essential.

  6. A simple and fast method to exclude high Plasmodium falciparum parasitaemia in travellers with imported malaria.

    Science.gov (United States)

    van Gool, Tom; van Wolfswinkel, Marlies E; Koelewijn, Rob; van Thiel, Pieter P A M; Jacobs, Jan; van Hellemond, Jaap J; van Genderen, Perry J J

    2011-10-14

    Counts of malaria parasites in peripheral blood are important to assess severity of Plasmodium falciparum malaria. Thin and thick smears are routinely used for this purpose. In this study the Binax NOW Malaria Test, an easy-to-perform rapid diagnostic test, with Histidine Rich Protein-2 (HRP-2) and aldolase as diagnostic markers, was used for semi-quantitative assessment of parasitaemia of P. falciparum. In 257 patients with imported P. falciparum malaria, reactivity of aldolase increased with higher parasitaemia. In all patients with a parasitaemia above 50,000 asexual parasites/μl (> 1%) co-reactivity of HRP-2 and aldolase was observed. Absence of aldolase reactivity in the presence of HRP-2 was a reliable predictive marker to exclude high (> 1%) parasitaemia in P. falciparum malaria. Assessment of HRP-2 and aldolase co-reactivity can be of help in clinical decision making in the acute care setting of returning travellers suspected of having malaria.

  7. Comparing Legal Approaches: Mental Disorders as Grounds for Excluding Criminal Responsibility

    Directory of Open Access Journals (Sweden)

    Carl-Friedrich Stuckenberg

    2016-08-01

    Full Text Available The effect of mental disorders on criminal responsibility seems to be more or less the same in all jurisdictions. However, upon a closer look, the details of the regulatory schemes and the practical effects vary considerably and this discord has increased even more in the past 30 years. This article undertakes a brief comparative survey with a focus on substantive criminal law in order to sketch a normative matrix which shows that there are three basic approaches to deal with mental disorders as grounds for excluding criminal responsibility. While psychiatry has made considerable progress over the past 150 years, in providing more humane treatment to mentally ill persons, it is a disturbing observation that the criminal law appears to be significantly less tolerant towards mentally disturbed offenders in modern times than during the previous two millennia.

  8. Excluded-volume effects for a hadron gas in Yang-Mills theory

    CERN Document Server

    Alba, Paolo; Nada, Alessandro; Panero, Marco; Stöcker, Horst

    2016-01-01

    When the multiplicities of particles produced in heavy-ion collisions are fitted to the hadron-resonance-gas model, excluded-volume effects play a significant role. In this work, we study the impact of such effects onto the equation of state of pure Yang-Mills theory at low temperatures, comparing the predictions of the statistical model with lattice results. In particular, we present a detailed analysis of the SU(2) and SU(3) Yang-Mills theories: we find that, for both of them, the best fits to the equilibrium thermodynamic quantities are obtained when one assumes that the volume of different glueball states is inversely proportional to their mass. The implications of these findings for QCD are discussed.

  9. Excluded and avoided: racial microaggressions targeting Asian international students in Canada.

    Science.gov (United States)

    Houshmand, Sara; Spanierman, Lisa B; Tafarodi, Romin W

    2014-07-01

    This qualitative study explored East and South Asian international students' (N = 12) experiences with racial microaggressions at one Canadian university. Data were collected through unstructured, individual interviews. Using a modified version of the consensual qualitative research method (Hill, Thompson, & Williams, 1997), we identified six racial microaggressions themes: (a) excluded and avoided, (b) ridiculed for accent, (c) rendered invisible, (d) disregarded international values and needs, (e) ascription of intelligence, and (f) environmental microaggressions (structural barriers on campus). In addition, we used the same approach to identify themes pertaining to the ways in which students coped with racial microaggressions: (a) engaging with own racial and cultural groups, (b) withdrawing from academic spheres, and (c) seeking comfort in the surrounding multicultural milieu. Microaggressions and coping themes differed based on country of origin and language proficiency. Implications for research and practice are discussed.

  10. Experience with the GORE EXCLUDER iliac branch endoprosthesis for common iliac artery aneurysms.

    Science.gov (United States)

    van Sterkenburg, Steven M M; Heyligers, Jan M M; van Bladel, Mathijs; Verhagen, Hence J; Eefting, Daniël; van Sambeek, Marc R; Zeebregts, Clark J; Reijnen, Michel M P J

    2016-06-01

    In this study, we analyzed the procedural success and early outcome of endovascular treatment of a multicenter cohort of patients with common iliac artery (CIA) aneurysms treated with the new GORE EXCLUDER (W. L. Gore & Associates, Flagstaff, Ariz) iliac branch endoprosthesis (IBE). A retrospective cohort analysis was performed in 13 sites in The Netherlands. Anatomic, demographic, procedural, and follow-up data were assessed from hospital records. From November 2013 to December 2014, 51 CIA aneurysms were treated with an IBE in 46 patients. The median diameter of the treated aneurysm was 40.5 (range, 25.0-90.0) mm. The mean procedural time was 198 ± 56 minutes. All but one implantation were successful; two type Ib endoleaks were noticed, resulting in a procedural success rate of 93.5%. The two type Ib endoleaks spontaneously disappeared at 30 days. There was no 30-day mortality. Ipsilateral buttock claudication was present in only two cases at 30 days and disappeared during follow-up. The incidence of reported erectile dysfunction was low and severe ischemic complications were absent. After a mean follow-up of 6 months, data on 17 treated aneurysms were available. Two showed a stable diameter, whereas 15 showed a mean decrease of 3.9 ± 2.2 mm (P < .001). Reinterventions were performed in two patients (7.1%). The 6-month primary patency of the internal component of the IBE device was 94%. The use of the GORE EXCLUDER IBE device for CIA aneurysms is related to high procedural success, high patency rates, and low reintervention rates at short-term follow-up. Prospective data with longer follow-up are awaited to establish the role of the device in the treatment algorithm of CIA aneurysms. Copyright © 2016 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

  11. Accountability and the pressures to exclude: A cautionary tale from England.

    Directory of Open Access Journals (Sweden)

    E. Rustique-Forrester

    2005-04-01

    Full Text Available Recent studies have produced conflicting findings about whether test-based rewards and sanctions create incentives that improve student performance, or hurdles that increase dropout and pushout rates from schools. This article reports the findings from a study that examined the impact of England's accountability reforms and investigated whether the confluent pressures associated with increased testing, school ranking systems, and other sanctions contributed to higher levels of student exclusion (expulsion and suspension. The study found that England's high-stakes approach to accountability, combined with the dynamics of school choice and other curriculum and testing pressures led to a narrowing of the curriculum, the marginalization of low-performing students, and a climate perceived by teachers to be less tolerant of students with academic and behavioral difficulties. A comparison of higher- and lower-excluding schools, however, found that these effects were more pronounced in the higher-excluding schools, which lacked strong systems and internal structures for supporting staff communication, teacher collaboration, and students' individual needs. The study offers an international perspective on recent trends toward greater accountability in education, pointing to a complex inter-relationship between the pressures of national policies and the unintended consequences on schools' organizational and teachers' instructional capacities. The study's findings raise particular implications for the United States and show that in the design of accountability systems, attention must be paid to how the pressures from accountability will affect the capacity of schools and teachers to respond to students who are low-performing and struggling academically.

  12. Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy

    Directory of Open Access Journals (Sweden)

    McMillen David R

    2008-09-01

    Full Text Available Abstract Background Simulating the major molecular events inside an Escherichia coli cell can lead to a very large number of reactions that compose its overall behaviour. Not only should the model be accurate, but it is imperative for the experimenter to create an efficient model to obtain the results in a timely fashion. Here, we show that for many parameter regimes, the effect of the host cell genome on the transcription of a gene from a plasmid-borne promoter is negligible, allowing one to simulate the system more efficiently by removing the computational load associated with representing the presence of the rest of the genome. The key parameter is the on-rate of RNAP binding to the promoter (k_on, and we compare the total number of transcripts produced from a plasmid vector generated as a function of this rate constant, for two versions of our gene expression model, one incorporating the host cell genome and one excluding it. By sweeping parameters, we identify the k_on range for which the difference between the genome and no-genome models drops below 5%, over a wide range of doubling times, mRNA degradation rates, plasmid copy numbers, and gene lengths. Results We assess the effect of the simulating the presence of the genome over a four-dimensional parameter space, considering: 24 min Conclusion Exclusion of the genome is shown to yield less than 5% difference in transcript numbers over wide ranges of values, and computational speed is improved by two to 24 times by excluding explicit representation of the genome.

  13. Oral Challenge without Skin Testing Safely Excludes Clinically Significant Delayed-Onset Penicillin Hypersensitivity.

    Science.gov (United States)

    Confino-Cohen, Ronit; Rosman, Yossi; Meir-Shafrir, Keren; Stauber, Tali; Lachover-Roth, Idit; Hershko, Alon; Goldberg, Arnon

    Penicillins are the drug family most commonly associated with hypersensitivity reactions. Current guidelines recommend negative skin tests (ST) before re-administering penicillins to patients with previous nonimmediate reactions (NIR). The objective of this study was to examine whether ST are necessary before re-administering penicillin to patients with NIR. Patients with NIR to penicillins starting longer than 1 hour after last dose administration or starting any time after the first treatment day or patients with vague recollection of their reaction underwent penicillin ST. Disregarding ST results, patients were challenged with the relevant penicillins. One-tenth of the therapeutic dose followed by the full dose was administered at 1-hour interval and patients continued taking the full dose for 5 days. A total of 710 patients with alleged BL allergy were evaluated. Patients with a history of immediate reaction (52, 7.3%) or cephalosporin allergy (16, 2.2%) were excluded. Of the remaining 642 patients, 62.3% had negative ST, 5.3% positive ST, and 32.4% equivocal ST. A total of 617 (96.1%) patients were challenged. Immediate reaction was observed in 9 patients (1.5%): 1-positive ST, 7-negative ST, and 1-equivocal ST (P = .7). Late reaction to the first-day challenge occurred in 24 patients (4%). An at-home challenge was continued by 491 patients. Complete 5-day and partial challenges were well tolerated by 417 (85%) and 44 patients (8.9%), respectively, disregarding ST results. Thirty patients (6.1%) developed mild reactions to the home challenge regardless of their ST results. A 5-day oral challenge without preceding ST is safe and sufficient to exclude penicillin allergy after NIR developing during penicillin treatment. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  14. Template-based automatic breast segmentation on MRI by excluding the chest region.

    Science.gov (United States)

    Lin, Muqing; Chen, Jeon-Hor; Wang, Xiaoyong; Chan, Siwa; Chen, Siping; Su, Min-Ying

    2013-12-01

    Methods for quantification of breast density on MRI using semiautomatic approaches are commonly used. In this study, the authors report on a fully automatic chest template-based method. Nonfat-suppressed breast MR images from 31 healthy women were analyzed. Among them, one case was randomly selected and used as the template, and the remaining 30 cases were used for testing. Unlike most model-based breast segmentation methods that use the breast region as the template, the chest body region on a middle slice was used as the template. Within the chest template, three body landmarks (thoracic spine and bilateral boundary of the pectoral muscle) were identified for performing the initial V-shape cut to determine the posterior lateral boundary of the breast. The chest template was mapped to each subject's image space to obtain a subject-specific chest model for exclusion. On the remaining image, the chest wall muscle was identified and excluded to obtain clean breast segmentation. The chest and muscle boundaries determined on the middle slice were used as the reference for the segmentation of adjacent slices, and the process continued superiorly and inferiorly until all 3D slices were segmented. The segmentation results were evaluated by an experienced radiologist to mark voxels that were wrongly included or excluded for error analysis. The breast volumes measured by the proposed algorithm were very close to the radiologist's corrected volumes, showing a % difference ranging from 0.01% to 3.04% in 30 tested subjects with a mean of 0.86% ± 0.72%. The total error was calculated by adding the inclusion and the exclusion errors (so they did not cancel each other out), which ranged from 0.05% to 6.75% with a mean of 3.05% ± 1.93%. The fibroglandular tissue segmented within the breast region determined by the algorithm and the radiologist were also very close, showing a % difference ranging from 0.02% to 2.52% with a mean of 1.03% ± 1.03%. The total error by adding the

  15. Should children with overweight or obesity be excluded from height references?

    Science.gov (United States)

    Júlíusson, Pétur B; Brannsether, Bente; Kristiansen, Hege; Hoppenbrouwers, Karel; Bjerknes, Robert; Roelants, Mathieu

    2015-11-01

    Growth reference charts are usually based on measurements of children free from a medical condition that affects growth. However, samples collected during the past decades often contain a large proportion of overweight or obese children. Because obesity increases linear growth, the question arises to what extent the percentiles curves for length/height are affected by the presence of children with overweight or obesity. Data from two cross-sectional samples of 2-year-old to 18-year-old children were analysed: 12,252 Belgian children, measured in 2002-2004, and 6159 Norwegian children, measured in 2003-2006. The LMS method was used to estimate height-for-age curves with and without children considered overweight or obese according to the International Obesity Task Force thresholds. The prevalence of overweight (including obesity) and obesity was 13.0% and 2.8% in the Belgian and 13.8% and 2.3% in the Norwegian sample. Children were taller when overweight (+0.49 and 0.43 SD, in the Belgian and Norwegian sample, respectively) or obese (+0.73 and 0.72 SD in the Belgian and Norwegian sample, respectively). Effect sizes were smaller in younger and older children, which points to an advanced age of maturation as a possible cause. Excluding overweight and obese children had only a minor impact on the growth curves with largest difference in mean height SD scores -0.09 in the Belgian and -0.12 in the Norwegian sample with a corresponding increase of up to 0.5% and 1.2% in number of children >+2 SD. Current Belgian and Norwegian growth references for length/height were found to be largely unaffected by the current proportion of overweight and obese children. There is, therefore, no need for revised height charts that exclude overweight or obese children. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  16. Underestimating intraspecific variation: the problem with excluding Sts 19 from Australopithecus africanus.

    Science.gov (United States)

    Ahern, J C

    1998-04-01

    Two analyses conclude that Sts 19 cannot be accommodated within the Australopithecus africanus hypodigm (Kimbel and Rak [1993] In Kimbel and Martin [eds.]: Species, Species Concepts, and Primate Evolution. New York: Plenum, pp. 461-484; Sarmiento [1993] Am. J. Phys. Anthropol. [Suppl.] 16:173). Both studies exclude Sts 19 because it possesses synapomorphies with Homo. Furthermore, according to Kimbel and Rak (1993), including Sts 19 in A. africanus results in an unacceptably high degree of polymorphism. This study aims to refute the null hypothesis that Sts 19 belongs to A. africanus. Twelve basicranial characters, as defined and implemented in Kimbel and Rak's study, were scored for casts of seven A. africanus and seven Homo habilis basicranial specimens. These characters were also examined on specimens from a large (N = 87) sample of African pongids. Contrary to Kimbel and Rak's (1993) findings, the null hypothesis is not refuted. The degree of polymorphism among A. africanus with Sts 19 included is less than that seen in Pan troglodytes. In addition, Sts 19 shares only one apomorphy with Homo. However, when treated metrically, Sts 19's morphology for this character is not significantly divergent from other A. africanus specimens.

  17. Strategies to exclude subjects who conceal and fabricate information when enrolling in clinical trials

    Directory of Open Access Journals (Sweden)

    Eric G. Devine

    2017-03-01

    Full Text Available Clinical trials within the US face an increasing challenge with the recruitment of quality candidates. One readily available group of subjects that have high rates of participation in clinical research are subjects who enroll in multiple trials for the purpose of generating income through study payments. Aside from issues of safety and generalizability, evidence suggests that these subjects employ methods of deception to qualify for the strict entrance criteria of some studies, including concealing information and fabricating information. Including these subjects in research poses a significant risk to the integrity of data quality and study designs. Strategies to limit enrollment of subjects whose motivation is generating income have not been systematically addressed in the literature. The present paper is intended to provide investigators with a range of strategies for developing and implementing a study protocol with protections to minimize the enrollment of subjects whose primary motivation for enrolling is to generate income. This multifaceted approach includes recommendations for advertising strategies, payment strategies, telephone screening strategies, and baseline screening strategies. The approach also includes recommendations for attending to inconsistent study data and subject motivation. Implementing these strategies may be more or less important depending upon the vulnerability of the study design to subject deception. Although these strategies may help researchers exclude subjects with a higher rate of deceptive practices, widespread adoption of subject registries would go a long way to decrease the chances of subjects enrolling in multiple studies or more than once in the same study.

  18. Innovation Chinese rice wine brewing technology by bi-acidification to exclude rice soaking process.

    Science.gov (United States)

    Wei, Xiao Lu; Liu, Shuang Ping; Yu, Jian Shen; Yu, Yong Jian; Zhu, Sheng Hu; Zhou, Zhi Lei; Hu, Jian; Mao, Jian

    2017-04-01

    As a traditional fermented alcoholic beverage of China, Chinese rice wine (CRW) had a long history of more than 5000 years. Rice soaking process was the most crucial step during CRW brewing process, because rice soaking quality directly determined the quality of CRW. However, rice soaking water would cause the eutrophication of water bodies and waste of water. The longer time of rice soaking, the higher the content of biogenic amine, and it would have a huge impact on human health. An innovation brewing technology was carried out to exclude the rice soaking process and the Lactobacillus was added to make up for the total acid. Compared to the traditional brewing technology, the new technology saved water resources and reduced environmental pollution. The concentration of biogenic amine was also decreased by 27.16%, which improving the security of the CRW. The esters increased led to more soft-tasted CRW and less aging time; the quality of CRW would be improved with less alcohol. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  19. CONTRIBUTION TO THE KNOWLEDGE OF THE ARACHNIDS IN THE YUCATAN PENINSULA, MEXICO (EXCLUDING ARANAE AND ACARI

    Directory of Open Access Journals (Sweden)

    Hugo Delfin Gonzalez

    2017-08-01

    Full Text Available The Chelicerata are the second group of arthropods with the highest diversity after insects and they can inhabit almost all types of environments. The most current classification recognizes 11 orders and estimates in the number of species vary from 52,000 to 100,000. We have made an extensive literature review on the diversity of arachnids in the Yucatan Peninsula (YP (excluding spiders and ticks. In Mexico there are 834 known species which represent 6% of the worldwide diversity. In the YP 63 records were found (58 species and 5 genera of arachnids, which represent 6.8% of the Mexican species. According to our research, 28 of the 58 species (48% in the YP were also record in other parts of Mexico, the continent and the world. Undoubtedly, the state of Yucatan is the best represented of the YP. In order to have a better understanding of the diversity of arachnid species is important to promote biological compendiums and sampling programs, which will improve the representation of this group and probably increasing the number of local species.

  20. Excluding the poor from accessing biomedical literature: a rights violation that impedes global health.

    Science.gov (United States)

    Yamey, Gavin

    2008-01-01

    Most biomedical journals charge readers a hefty access toll to read the full text version of a published research article. These tolls bring enormous profits to the traditional corporate publishing industry, but they make it impossible for most people worldwide--particularly in low and middle income countries--to access the biomedical literature. Traditional publishers also insist on owning the copyright on these articles, making it illegal for readers to freely distribute and photocopy papers, translate them, or create derivative educational works. This article argues that excluding the poor from accessing and freely using the biomedical research literature is harming global public health. Health care workers, for example, are prevented from accessing the information they need to practice effective medicine, while policymakers are prevented from accessing the essential knowledge they require to build better health care systems. The author proposes that the biomedical literature should be considered a global public good, basing his arguments upon longstanding and recent international declarations that enshrine access to scientific and medical knowledge as a human right. He presents an emerging alternative publishing model, called open access, and argues that this model is a more socially responsive and equitable approach to knowledge dissemination.

  1. Genome-wide association study of handedness excludes simple genetic models

    Science.gov (United States)

    Armour, J AL; Davison, A; McManus, I C

    2014-01-01

    Handedness is a human behavioural phenotype that appears to be congenital, and is often assumed to be inherited, but for which the developmental origin and underlying causation(s) have been elusive. Models of the genetic basis of variation in handedness have been proposed that fit different features of the observed resemblance between relatives, but none has been decisively tested or a corresponding causative locus identified. In this study, we applied data from well-characterised individuals studied at the London Twin Research Unit. Analysis of genome-wide SNP data from 3940 twins failed to identify any locus associated with handedness at a genome-wide level of significance. The most straightforward interpretation of our analyses is that they exclude the simplest formulations of the ‘right-shift' model of Annett and the ‘dextral/chance' model of McManus, although more complex modifications of those models are still compatible with our observations. For polygenic effects, our study is inadequately powered to reliably detect alleles with effect sizes corresponding to an odds ratio of 1.2, but should have good power to detect effects at an odds ratio of 2 or more. PMID:24065183

  2. Two-year-olds exclude novel objects as potential referents of novel words based on pragmatics.

    Science.gov (United States)

    Grassmann, Susanne; Stracke, Marén; Tomasello, Michael

    2009-09-01

    Many studies have established that children tend to exclude objects for which they already have a name as potential referents of novel words. In the current study we asked whether this exclusion can be triggered by social-pragmatic context alone without pre-existing words as blockers. Two-year-old children watched an adult looking at a novel object while saying a novel word with excitement. In one condition the adult had not seen the object beforehand, and so the children interpreted the adult's utterance as referring to the gazed-at object. In another condition the adult and child had previously played jointly with the gazed-at object. In this case, children less often assumed that the adult was referring to the object but rather they searched for an alternative referent--presumably because they inferred that the gazed-at object was old news in their common ground with the adult and so not worthy of excited labeling. Since this inference based on exclusion is highly similar to that underlying the Principle of Contrast/Mutual Exclusivity, we propose that this principle is not purely lexical but rather is based on children's understanding of how and why people direct one another's attention to things either with or without language.

  3. A simple and fast method to exclude high Plasmodium falciparum parasitaemia in travellers with imported malaria

    Directory of Open Access Journals (Sweden)

    Jacobs Jan

    2011-10-01

    Full Text Available Abstract Background Counts of malaria parasites in peripheral blood are important to assess severity of Plasmodium falciparum malaria. Thin and thick smears are routinely used for this purpose. Methods In this study the Binax NOW® Malaria Test, an easy-to-perform rapid diagnostic test, with Histidine Rich Protein-2 (HRP-2 and aldolase as diagnostic markers, was used for semi-quantitative assessment of parasitaemia of P. faciparum. Results In 257 patients with imported P. falciparum malaria, reactivity of aldolase increased with higher parasitaemia. In all patients with a parasitaemia above 50,000 asexual parasites/μl (> 1% co-reactivity of HRP-2 and aldolase was observed. Absence of aldolase reactivity in the presence of HRP-2 was a reliable predictive marker to exclude high (> 1% parasitaemia in P. falciparum malaria. Conclusions Assessment of HRP-2 and aldolase co-reactivity can be of help in clinical decision making in the acute care setting of returning travellers suspected of having malaria.

  4. The 'empowered client' in vocational rehabilitation: the excluding impact of inclusive strategies.

    Science.gov (United States)

    van Hal, Lineke B E; Meershoek, Agnes; Nijhuis, Frans; Horstman, Klasien

    2012-09-01

    In vocational rehabilitation, empowerment is understood as the notion that people should make an active, autonomous choice to find their way back to the labour process. Following this line of reasoning, the concept of empowerment implicitly points to a specific kind of activation strategy, namely labour participation. This activation approach has received criticism for being paternalistic, disciplining and having a one-sided orientation on labour participation. Although we share this theoretical criticism, we want to go beyond it by paying attention to the practical consequences of understanding empowerment as an activation strategy. Inspired by the field of Science and Technology Studies, we will explore the meaning of empowerment and activation in concrete practices of vocational rehabilitation in the Netherlands. Our analysis is based on the narratives of people with a work disability about their lives and the vocational rehabilitation programmes they participated in. We present five illustrative cases that how empowerment is 'done' in the practice of vocational rehabilitation and its unintended effects. Our analysis demonstrates that activation strategies seem to be caught in a paradox: instead of including people in society, they have excluding consequences. Vocational rehabilitation professionals can go beyond this paradox by learning from the ways in which empowerment is 'done' by clients in vocational rehabilitation programmes.

  5. [Potentially excluded population from health coverage and health impact since Royal Decree 16/2012: The Central Catalonia experience].

    Science.gov (United States)

    Álamo-Junquera, Dolores; Sala, Núria; Millet, Joan-Pau; Ortega-Gutiérrez, Lluïsa; Planas-Giner, Albert; Rovira, Carol; Comet, Dolors

    2015-01-01

    To assess the proportion of population potentially excluded from healthcare coverage since the Royal Decree-Law 16/2012. To describe the use of health services, the distribution of chronic and infectious diseases, and the pharmaceutical costs in 2012 of the persons potentially excluded compared to the those who maintain their coverage. An observational analytical cross-sectional study was designed and conducted on a Primary Care based population in the Central Catalonia Management Area of the Institut Català de la Salut PARTICIPANTS AND MAIN MEASUREMENTS: Individuals potentially excluded since the application of the Royal Decree-Law 16/2012 were selected and compared with individuals who maintained their healthcare coverage, randomly matched by sex, age and Primary Care service. The information obtained included the use of health services, the distribution of chronic and infectious diseases, and the pharmaceutical costs during the year 2012. A total of 1,699 individuals were identified as potentially excluded from healthcare coverage, 0.53% of the total of population (51.4% men), with a median of age of 34years (interquartile range, 28-43). The use of healthcare services, the chronic morbidity recorded, and the pharmaceutical costs during the year 2012 of the excluded individuals was lower than those of the non-excluded ones (P<.001). On the other hand, the infectious morbidity was higher in the excluded individuals (P<.001). The results of the study suggests that this legislative measure does not seem to be justified for medical or economic reasons. It could also cause public health problems and contribute to the risk of social fracture. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

  6. DNA methylation at a bovine alpha satellite I repeat CpG site during development following fertilization and somatic cell nuclear transfer.

    Directory of Open Access Journals (Sweden)

    Christine Couldrey

    Full Text Available Incomplete epigenetic reprogramming is postulated to contribute to the low developmental success following somatic cell nuclear transfer (SCNT. Here, we describe the epigenetic reprogramming of DNA methylation at an alpha satellite I CpG site (αsatI-5 during development of cattle generated either by artificial insemination (AI or in vitro fertilization (IVF and SCNT. Quantitative methylation analysis identified that SCNT donor cells were highly methylated at αsatI-5 and resulting SCNT blastocysts showed significantly more methylation than IVF blastocysts. At implantation, no difference in methylation was observed between SCNT and AI in trophoblast tissue at αsatI-5, however, SCNT embryos were significantly hyper-methylated compared to AI controls at this time point. Following implantation, DNA methylation at αsatI-5 decreased in AI but not SCNT placental tissues. In contrast to placenta, the proportion of methylation at αsatI-5 remained high in adrenal, kidney and muscle tissues during development. Differences in the average proportion of methylation were smaller in somatic tissues than placental tissues but, on average, SCNT somatic tissues were hyper-methylated at αsatI-5. Although sperm from all bulls was less methylated than somatic tissues at αsatI-5, on average this site remained hyper-methylated in sperm from cloned bulls compared with control bulls. This developmental time course confirms that epigenetic reprogramming does occur, at least to some extent, following SCNT. However, the elevated methylation levels observed in SCNT blastocysts and cellular derivatives implies that there is either insufficient time or abundance of appropriate reprogramming factors in oocytes to ensure complete reprogramming. Incomplete reprogramming at this CpG site may be a contributing factor to low SCNT success rates, but more likely represents the tip of the iceberg in terms of incompletely reprogramming. Until protocols ensure the epigenetic

  7. Environmental stress affects DNA methylation of a CpG rich promoter region of serotonin transporter gene in a nurse cohort.

    Directory of Open Access Journals (Sweden)

    Jukka S Alasaari

    Full Text Available Shift-working nurses are exposed to a stressful work environment, which puts them at an increased risk for burnout and depression. We explored the effect of environmental stress on serotonin transporter gene (SLC6A4 promoter methylation among nurses from high and low work stress environments.Using bisulfite sequencing, we investigated the methylation status of five CpG residues of a CpG-rich region in the promoter of SLC6A4 by comparing female shift working nurses from a high work stress environment (n = 24 to low work stress environment (n = 25. We also analyzed the association of 5-HTTLPR polymorphism at 5' end of SLC6A4. Work stress was assessed by the Karasek's Model and possible signs of burnout or depression were measured by the Maslach Burnout Index General Survey and Beck Depression Index. Methylation levels were assessed by bisulfite sequencing of DNA extracted from peripheral blood leucocytes. Restriction enzyme treatment followed by standard PCR was used to identify 5-HTTLPR genotypes.We found that nurses in the high stress environment had significantly lower promoter methylation levels at all five CpG residues compared to nurses in the low stress environment (p<0.01. There was no significant interaction of 5-HTTLPR genotype and work stress with methylation (p = 0.58. In unadjusted (bivariate analysis, burnout was not significantly associated to methylation levels. However, when mutually adjusted for both, burnout and work stress were significant contributors (p = 0.038 and p<0.0001 respectively to methylation levels.Our findings show that environmental stress is concurrent with decreased methylation of the SLC6A4 promoter. This may lead to increased transcriptional activity of the gene, increased reuptake of serotonin from synaptic clefts, and termination of the activity of serotonin. This could present a possible coping mechanism for environmental stress in humans that could eventually increase risk for disturbed functional

  8. Inter-individual differences in CpG methylation at D4Z4 correlate with clinical variability in FSHD1 and FSHD2.

    Science.gov (United States)

    Lemmers, Richard J L F; Goeman, Jelle J; van der Vliet, Patrick J; van Nieuwenhuizen, Merlijn P; Balog, Judit; Vos-Versteeg, Marianne; Camano, Pilar; Ramos Arroyo, Maria Antonia; Jerico, Ivonne; Rogers, Mark T; Miller, Daniel G; Upadhyaya, Meena; Verschuuren, Jan J G M; Lopez de Munain Arregui, Adolfo; van Engelen, Baziel G M; Padberg, George W; Sacconi, Sabrina; Tawil, Rabi; Tapscott, Stephen J; Bakker, Bert; van der Maarel, Silvère M

    2015-02-01

    Facioscapulohumeral muscular dystrophy (FSHD: MIM#158900) is a common myopathy with marked but largely unexplained clinical inter- and intra-familial variability. It is caused by contractions of the D4Z4 repeat array on chromosome 4 to 1-10 units (FSHD1), or by mutations in the D4Z4-binding chromatin modifier SMCHD1 (FSHD2). Both situations lead to a partial opening of the D4Z4 chromatin structure and transcription of D4Z4-encoded polyadenylated DUX4 mRNA in muscle. We measured D4Z4 CpG methylation in control, FSHD1 and FSHD2 individuals and found a significant correlation with the D4Z4 repeat array size. After correction for repeat array size, we show that the variability in clinical severity in FSHD1 and FSHD2 individuals is dependent on individual differences in susceptibility to D4Z4 hypomethylation. In FSHD1, for individuals with D4Z4 repeat arrays of 1-6 units, the clinical severity mainly depends on the size of the D4Z4 repeat. However, in individuals with arrays of 7-10 units, the clinical severity also depends on other factors that regulate D4Z4 methylation because affected individuals, but not non-penetrant mutation carriers, have a greater reduction of D4Z4 CpG methylation than can be expected based on the size of the pathogenic D4Z4 repeat array. In FSHD2, this epigenetic susceptibility depends on the nature of the SMCHD1 mutation in combination with D4Z4 repeat array size with dominant negative mutations being more deleterious than haploinsufficiency mutations. Our study thus identifies an epigenetic basis for the striking variability in onset and disease progression that is considered a clinical hallmark of FSHD. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Template-based automatic breast segmentation on MRI by excluding the chest region

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Muqing [Tu and Yuen Center for Functional Onco-Imaging, Department of Radiological Sciences, University of California, Irvine, California 92697-5020 and National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, 518060 China (China); Chen, Jeon-Hor [Tu and Yuen Center for Functional Onco-Imaging, Department of Radiological Sciences, University of California, Irvine, California 92697-5020 and Department of Radiology, E-Da Hospital and I-Shou University, Kaohsiung 82445, Taiwan (China); Wang, Xiaoyong; Su, Min-Ying, E-mail: msu@uci.edu [Tu and Yuen Center for Functional Onco-Imaging, Department of Radiological Sciences, University of California, Irvine, California 92697-5020 (United States); Chan, Siwa [Department of Radiology, Taichung Veterans General Hospital, Taichung 40407, Taiwan (China); Chen, Siping [National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, 518060 China (China)

    2013-12-15

    Purpose: Methods for quantification of breast density on MRI using semiautomatic approaches are commonly used. In this study, the authors report on a fully automatic chest template-based method. Methods: Nonfat-suppressed breast MR images from 31 healthy women were analyzed. Among them, one case was randomly selected and used as the template, and the remaining 30 cases were used for testing. Unlike most model-based breast segmentation methods that use the breast region as the template, the chest body region on a middle slice was used as the template. Within the chest template, three body landmarks (thoracic spine and bilateral boundary of the pectoral muscle) were identified for performing the initial V-shape cut to determine the posterior lateral boundary of the breast. The chest template was mapped to each subject's image space to obtain a subject-specific chest model for exclusion. On the remaining image, the chest wall muscle was identified and excluded to obtain clean breast segmentation. The chest and muscle boundaries determined on the middle slice were used as the reference for the segmentation of adjacent slices, and the process continued superiorly and inferiorly until all 3D slices were segmented. The segmentation results were evaluated by an experienced radiologist to mark voxels that were wrongly included or excluded for error analysis. Results: The breast volumes measured by the proposed algorithm were very close to the radiologist's corrected volumes, showing a % difference ranging from 0.01% to 3.04% in 30 tested subjects with a mean of 0.86% ± 0.72%. The total error was calculated by adding the inclusion and the exclusion errors (so they did not cancel each other out), which ranged from 0.05% to 6.75% with a mean of 3.05% ± 1.93%. The fibroglandular tissue segmented within the breast region determined by the algorithm and the radiologist were also very close, showing a % difference ranging from 0.02% to 2.52% with a mean of 1.03% ± 1

  10. Limb muscle sound speed estimation by ultrasound computed tomography excluding receivers in bone shadow

    Science.gov (United States)

    Qu, Xiaolei; Azuma, Takashi; Lin, Hongxiang; Takeuchi, Hideki; Itani, Kazunori; Tamano, Satoshi; Takagi, Shu; Sakuma, Ichiro

    2017-03-01

    Sarcopenia is the degenerative loss of skeletal muscle ability associated with aging. One reason is the increasing of adipose ratio of muscle, which can be estimated by the speed of sound (SOS), since SOSs of muscle and adipose are different (about 7%). For SOS imaging, the conventional bent-ray method iteratively finds ray paths and corrects SOS along them by travel-time. However, the iteration is difficult to converge for soft tissue with bone inside, because of large speed variation. In this study, the bent-ray method is modified to produce SOS images for limb muscle with bone inside. The modified method includes three steps. First, travel-time is picked up by a proposed Akaike Information Criterion (AIC) with energy term (AICE) method. The energy term is employed for detecting and abandoning the transmissive wave through bone (low energy wave). It results in failed reconstruction for bone, but makes iteration convergence and gives correct SOS for skeletal muscle. Second, ray paths are traced using Fermat's principle. Finally, simultaneous algebraic reconstruction technique (SART) is employed to correct SOS along ray paths, but excluding paths with low energy wave which may pass through bone. The simulation evaluation was implemented by k-wave toolbox using a model of upper arm. As the result, SOS of muscle was 1572.0+/-7.3 m/s, closing to 1567.0 m/s in the model. For vivo evaluation, a ring transducer prototype was employed to scan the cross sections of lower arm and leg of a healthy volunteer. And the skeletal muscle SOSs were 1564.0+/-14.8 m/s and 1564.1±18.0 m/s, respectively.

  11. Oscillometric casual blood pressure normative standards for Swedish children using ABPM to exclude casual hypertension.

    Science.gov (United States)

    Krmar, Rafael T; Holtbäck, Ulla; Bergh, Anita; Svensson, Eva; Wühl, Elke

    2015-04-01

    Casual blood pressure (CBP) is considered a reliable proxy for cardiovascular health. Although the auscultatory technique is the reference standard method for measuring CBP, oscillometric devices are increasingly being used in children. We sought to establish oscillometric CBP normative standards for Swedish children. Cross-sectional oscillometric CBP readings were obtained by the Welch Allyn Spot Vital Signs 420 monitor and measured according to the International Guidelines' recommendations. Participants with elevated oscillometric CBP levels underwent verification by the auscultatory method. Ambulatory blood pressure monitoring (ABPM) was used to exclude casual hypertension. Data on 1,470 (772 males) apparently healthy Swedish schoolchildren aged 6-16 years were analyzed and sex-specific reference charts normalized to age or height were constructed. Systolic and diastolic CBP values were significantly higher with age, height, height standard deviation score (SDS), body mass index (BMI), and BMI SDS. Gender differences for systolic CBP were present starting from age of 15 years and revealed significantly higher values in boys than in girls, whereas for diastolic CBP, the differences were apparent at the age of 12 years, with higher values in girls. Increased BMI and BMI SDS were positively associated with CBP levels. Positive parental history of hypertension turned out to be a risk factor for higher systolic and diastolic CBP across all ages. Our normative standard for CBP can be used for blood pressure screening and control programs in Swedish children. The use of ABPM should be considered to confirm the diagnosis of casual hypertension. © American Journal of Hypertension, Ltd 2014. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Why are people with mental illness excluded from the rational suicide debate?

    Science.gov (United States)

    Hewitt, Jeanette

    2013-01-01

    The topic of rational suicide is often approached with some trepidation by mental health professionals. Suicide prevention strategies are more likely to be seen as the domain of psychiatry and a wealth of psychiatric literature is devoted to identifying and managing suicide risk. Whether or not suicide can be deemed permissible is ostensibly linked to discussions of autonomy and mental capacity, and UK legislation directs that a patient's wishes must be respected with regard to treatment refusal where decisional capacity is intact. In the context of the care and treatment of those with physical disorders, extreme and untreatable physical suffering is likely to be accepted as rational grounds for suicide, where the person possesses cognitive coherence and an ability to realistically appreciate the consequences of his or her actions. In the case of those with serious mental disorder, the grounds for accepting that suicide is rational are however less clear-cut. Serious mental illness is typically conceived of as a coercive pressure which prevents rational deliberation and as such, the suicides of those with serious mental illness are considered to be substantially non-voluntary acts arising from constitutive irrationality. Therefore, where an appropriate clinician judges that a person with serious mental disorder is non-autonomous, suicide prevention is likely to be thought legally and morally justified. There are arguably, two questionable assumptions in the position that psychiatry adopts: Firstly, that psychogenic pain is in some way less real than physical pain and secondly, that mental illness invariably means that a desire to die is irrational and inauthentic. If it can be shown that some people with serious mental illness can be rational with regard to suicide and that psychological pain is of equal significance as physical suffering, then it may be possible to conclude that some persons with serious mental illness should not by definition be excluded from the

  13. Initial results of the management of aortoiliac aneurysms with GORE® Excluder® Iliac Branched Endoprosthesis.

    Science.gov (United States)

    Schönhofer, S; Mansour, R; Ghotbi, R

    2015-12-01

    We prospectively observed the outcomes of all patients (N.=15) with an aortoiliac and a common iliac artery aneurysm who were electively treated with the GORE® Excluder® Iliac Branched Endoprosthesis (IBE) with regard to clinical, anatomical and radiological results. We evaluated operative mortality, aneurysm rupture rate and aneurysm related mortality as well as conversion to open surgery, incidence of endoleak, rate of aneurysm migration, aneurysm enlargement, graft patency, reintervention rate and the clinical outcome. Postoperative follow-up included a computed tomography angiography (CTA) before discharge, clinical evaluation and Duplex ultrasound or CTA 3 weeks after the intervention and Duplex ultrasound every 3 months afterwards. Mean patient age was 79 years (range 61-83 years); f/m: 1/2; mean follow-up was 9 months; 80% of the patients presented 2 or more major comorbidities and 1/3 were considered to be not eligible for open repair. Mean hospitalization time was 5 days. Technical success rate was 93.3% (intent-to-treat basis). Mortality within 30 days was 0%; there were no ruptures; type II endoleak directly after the procedure occurred in 20%, dropping to 13.3% after 3 months. We defined the initial technical success in absence of type I endoleaks. The initial technical success rate was 100%. No IBE occlusion or type Ia, Ib or III endoleak was observed during the postoperative follow-up (mean follow-up: 9 months). All of the internal iliac side branches remained patent. Reintervention rate, buttock claudication rate and pelvic complication rate were 0%. The GORE® IBE provides a new and safe alternative for the management of complete endovascular repair of an extensive aortoiliac or common iliac aneurysm while maintaining pelvic blood flow in iliac branched devices. Due to the lower complexity if compared to previous endovascular or hybrid methods, it should be performed in every anatomically suitable case.

  14. Normal pancreatic exocrine function does not exclude MRI/MRCP chronic pancreatitis findings.

    Science.gov (United States)

    Alkaade, Samer; Cem Balci, Numan; Momtahen, Amir Javad; Burton, Frank

    2008-09-01

    Abnormal pancreatic function tests have been reported to precede the imaging findings of chronic pancreatitis. Magnetic resonance imaging (MRI) with magnetic resonance cholangiopancreatography (MRCP) is increasingly accepted as the primary imaging modality for the detection of structural changes of early mild chronic pancreatitis. The aim of this study was to evaluate MRI/MRCP findings in patients with symptoms consistent with chronic pancreatitis who have normal Secretin Endoscopic Pancreatic Function test. A retrospective study of 32 patients referred for evaluation of chronic abdominal pain consistent with chronic pancreatitis and reported normal standard abdominal imaging (ultrasound, computed tomography, or MRI). All patients underwent Secretin Endoscopic Pancreatic Function testing and pancreatic MRI/MRCP at our institution. We reviewed the MRI/MRCP images in patients who had normal Secretin Endoscopic Pancreatic Function testing. MRI/MRCP images were assessed for pancreatic duct morphology, gland size, parenchymal signal and morphology, and arterial contrast enhancement. Of the 32 patients, 23 had normal Secretin Endoscopic Pancreatic Function testing, and 8 of them had mild to marked spectrum of abnormal MRI/MRCP findings that were predominantly focal. Frequencies of the findings were as follows: pancreatic duct stricture (n=3), pancreatic duct dilatation (n=3), side branch ectasia (n=4), atrophy (n=5), decreased arterial enhancement (n=5), decreased parenchymal signal (n=1), and cavity formation (n=1). The remaining15 patients had normal pancreatic structure on MRI/MRCP. Normal pancreatic function testing cannot exclude abnormal MRI/MRCP especially focal findings of chronic pancreatitis. Further studies needed to verify significance of these findings and establish MRI/MRCP imaging criteria for the diagnosis of chronic pancreatitis.

  15. Friedreich's ataxia GAA.TTC duplex and GAA.GAA.TTC triplex structures exclude nucleosome assembly.

    Science.gov (United States)

    Ruan, Haihe; Wang, Yuh-Hwa

    2008-11-07

    Both chromatin structure and formation of triplex DNA at expanded GAA TTC repeats have been shown to regulate the FXN gene silencing, which causes Friedreich's ataxia. Recent studies have suggested that the presence of heterochromatin at the long expanded GAA TTC repeats, which is enriched in hypoacetylated histones, deters the transcription of the FXN gene. However, neither direct histone binding nor the effect of histone acetylation on the GAA TTC duplex or the GAA GAA TTC triplex has been measured in vitro. In this study, GAA TTC repeating DNAs derived from the human FXN gene, and the GAA GAA TTC triplex, were examined for their ability to assemble single nucleosomes and nucleosome arrays. Competitive nucleosome reconstitution assays demonstrated that the GAA TTC duplex excludes nucleosomes (53% decrease compared to the pUC control DNA) and that the GAA GAA TTC triplex further lowers the nucleosome assembly efficiency (82% decrease compared to the duplex DNA). The difference in assembly efficiency is amplified more significantly when hypoacetylated histones are used, compared to assembly with hyperacetylated histones. By analyzing the formation of nucleosome arrays on GAA TTC-containing plasmids, the triplex structure was shown to destabilize the ability of adjacent sequences to assemble nucleosomes. These results provide the first direct binding measurements for the GAA TTC duplex and the GAA GAA TTC triplex, and on the effect of histone acetylation, towards dissecting the role of chromatin structure in silencing of the FXN gene. These findings suggest that these sequences could profoundly alter local chromatin structure, and the discrepancy between in vivo and in vitro results supports recent studies showing that, in addition to DNA sequences, other factors such as epigenetic marks could be involved in the mechanism for inhibition of FXN gene expression.

  16. Identification of novel RFLPs in the vicinity of CpG islands in Xq28: Application to the analysis of the pattern of X chromosome inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Camerino, G.; Santachiara-Benerecetti, S. (Univ. di Pavia (Italy)); Rocchi, M. (Univ. di Bari (Italy)); Parolini, O.; Notarangelo, L.D. (Univ. di Brecscia (Italy)); Maestrini, E.; Rivella, S.; Tribioli, C.; Toniolo, D.

    1992-01-01

    Probes of CpG islands were cloned from the distal long arm of the human X chromosome; three of them were found to be polymorphic. A HindIII RFLP was identified by the probe 2-25 (DXS606), and it was mapped to the Xq27-Xq28 boundary. Probes 2-19 (DXS605) and 2-55 (DXS707), which identify EcoRI and MspI polymorphisms, respectively, have been mapped to the distal part of Xq28, in the G6PD-RCP/GCP gene region. Probe 2-19 has been further localized about 16 kb from the 3{prime} end of the G6PD gene. The new RFLPs may be useful for the precise mapping of the many disease genes localized in this part of the human X chromosome. Using the methylation-sensitive rare-cutter enzyme EagI in conjunction with the polymorphic EcoRI site, the authors were able to demonstrate that the RFLP may be used both to study randomness of X chromosome inactivation and for carrier detection in X-linked syndromes where nonrandom X inactivation occurs. It is conceivable that the combined use of 2-19 and of the probes described so far (pSPT-PGK and M27{beta}) will make analysis of X inactivation feasible in virtually every female.

  17. A Built-In CpG Adjuvant in RSV F Protein DNA Vaccine Drives a Th1 Polarized and Enhanced Protective Immune Response

    Directory of Open Access Journals (Sweden)

    Yao Ma

    2018-01-01

    Full Text Available Human respiratory syncytial virus (RSV is the most significant cause of acute lower respiratory infection in children. However, there is no licensed vaccine available. Here, we investigated the effect of five or 20 copies of C-Class of CpG ODN (CpG-C motif incorporated into a plasmid DNA vaccine encoding RSV fusion (F glycoprotein on the vaccine-induced immune response. The addition of CpG-C motif enhanced serum binding and virus-neutralizing antibody responses in BALB/c mice immunized with the DNA vaccines. Moreover, mice vaccinated with CpG-modified vaccines, especially with the higher 20 copies, resulted in an enhanced shift toward a Th1-biased antibody and T-cell response, a decrease in pulmonary pathology and virus replication, and a decrease in weight loss after RSV challenge. This study suggests that CpG-C motif, cloned into the backbone of DNA vaccine encoding RSV F glycoprotein, functions as a built-in adjuvant capable of improving the efficacy of DNA vaccine against RSV infection.

  18. Mucosal Administration of CpG Oligodeoxynucleotide Elicits Strong CC and CXC Chemokine Responses in the Vagina and Serves as a Potent Th1-Tilting Adjuvant for Recombinant gD2 Protein Vaccination against Genital Herpes

    Science.gov (United States)

    Tengvall, Sara; Lundqvist, Annika; Eisenberg, Roselyn J.; Cohen, Gary H.; Harandi, Ali M.

    2006-01-01

    Although sexually transmitted pathogens are capable of inducing pathogen-specific immune responses, vaginal administration of nonreplicating antigens elicits only weak, nondisseminating immune responses. The present study was undertaken to examine the potential of CpG-containing oligodeoxynucleotide (CpG ODN) for induction of chemokine responses in the genital tract mucosa and also as a vaginal adjuvant in combination with glycoprotein D of herpes simplex virus type 2 (HSV-2) for induction of antigen-specific immune responses. We found that a single intravaginal administration of CpG ODN in mice stimulates a rapid and potent response of CC chemokines macrophage inflammatory protein 1α (MIP-1α), MIP-1β, and RANTES as well as of CXC chemokines MIP-2 and IP-10 in the vagina and/or the genital lymph nodes. Importantly, intravaginal vaccination with recombinant gD2 in combination with CpG ODN gave rise to a strong antigen-specific Th1-like immune response in the genital lymph nodes as well as the spleens of the vaccinated mice. Further, such an immunization scheme conferred both systemic and mucosal immunoglobulin G antibody responses as well as protection against an otherwise lethal vaginal challenge with HSV-2. These results illustrate the potential of CpG ODN for induction of potent chemokine responses in the genital tract and also as a vaginal adjuvant for generation of Th1-type mucosal and systemic immune responses towards a nonreplicating antigen derived from a sexually transmitted pathogen. These data have implications for the development of a mucosal vaccine against genital herpes and possibly other sexually transmitted diseases. PMID:16699008

  19. The development and preliminary evaluation of a new Mycobacterium tuberculosis vaccine comprising Ag85b, HspX and CFP-10:ESAT-6 fusion protein with CpG DNA and aluminum hydroxide adjuvants.

    Science.gov (United States)

    Chen, Lei; Xu, Miao; Wang, Zhi-Yu; Chen, Bao-Wen; Du, Wei-Xin; Su, Cheng; Shen, Xiao-Bing; Zhao, Ai-Hua; Dong, Na; Wang, Ya-Jun; Wang, Guo-Zhi

    2010-06-01

    Ag85b and HspX of Mycobacterium tuberculosis (Mtb) (H37Rv) were expressed and purified in this study. These two proteins were combined with another fusion protein CFP-10:ESAT-6 (C/E) (Ag), then mixed with the adjuvants CpG DNA and aluminum hydroxide and used to vaccinate mice and guinea pigs challenged with Mtb (H37Rv). The number of spleen lymphocytes secreting Ag85b, HspX and C/E-specific interferon-gamma were significantly higher in the Ag+Al+CpG group than in the Ag and CpG groups. The combination of Ag, Al and CpG induced the highest concentrations of anti-Ag85b, anti-HspX and anti-C/E immunoglobulin G in mouse serum. Mouse peritoneal macrophages from the Ag+Al+CpG group secreted significantly higher levels of interleukin-12 compared with macrophages from the other groups. The total mean liver, lung and spleen lesion scores and bacterial loads in the spleen in guinea pigs vaccinated with Ag+Al+CpG were lower than those of the other groups, but no significant difference was found. These results show that the mixture of Ag85b, HspX and C/E with a combination of CpG and aluminum adjuvants can induce both humoral and cellular immune responses in mice, whereas it plays only a small role in the control of disease progression in guinea pigs challenged with Mtb.

  20. The "Methyl-CpG Binding Domain protein 2" plays a repressive role in relation to the promoter CpG content in the normal human cell line MRC5.

    Science.gov (United States)

    Perriaud, Laury; Lachuer, Joel; Dante, Robert

    2014-01-01

    In cancer cells, methylation-dependent gene silencing is at least partly mediated by the "Methyl-CpG-Binding Domain protein 2" (MBD2 protein), via the recruitment of chromatin remodeling complexes. However this repressive role was poorly investigated in normal cells. To identify the genes repressed by MBD2 in these cells, we have determined the impact of MBD2 depletion on gene expression in human embryonic MRC5 fibroblasts, using RNA inference combined with microarray analysis. The up-regulation of some randomly selected genes was confirmed and a direct association between gene repression and MBD2 binding on methylated promoters associated to these genes was subsequently established. This control of gene expression appears to depend on the CpG content of promoters as MBD2 depletion was not sufficient to induce the expression of silent genes associated with High-CpG promoters, but it was required to achieve the methyl-dependent transcriptional locking of the genes associated with promoters exhibiting intermediate CpG content. Therefore, MBD2 seems to play a selective role in gene repression depending on the CpG content of the promoter regions.

  1. Effects of excluding a set of random effects on prediction error variance of breeding value.

    Science.gov (United States)

    Cantet, R J

    1997-01-12

    The effects of excluding a set of random effects (U-effects) uncorrelated to breeding values (BV) on prediction error variance (PEV) is studied analytically. Two situations are considered for model comparison: (a) existence of a 'true' model, (b) uncertainty about which of the competing models is 'true'. Models compared are the 'long' one, which includes BV + U-effects, and the 'short' one which includes BV's as the only random systematic effect. Expressions for PEV(BV) were obtained for the long model (PEVL); the short model (PEVS); and the short model assuming the long model is the correct one (PEVSI). It is shown that in general PEVS ≤ PEVL ≤ PEVSI. Results are exemplified by means of an example including a computer simulation. RESUMEN: En este trabajo se estudia analiticamente el efecto de excluir una variable aleatoria (efecto U) no correlacionada con el valor de cría (BV), sobre la varianza del error de predicción de este último (PEV(BV)). Para ello se utilizan dos enfoques de comparación de modelos: (a) existencia de un modelo 'verdadero', (b) incertidumbre respecto de cuál de ambos modelos alternativos es el correcto. Los modelos que se comparan son: el 'largo', que incluye BV+U, y el 'corto', el cuál solo incluye BV. Se obtienen las expresiones para PEV(BV) en las siguientes situaciones: (1) en el modelo largo (PEVL), (2) en el modelo corto (PEVS), y (3) en el modelo corto pero asumiendo que el largo es el verdadero (PEVSI). Se demuestra que en general PEVS ≤ PEVL ≤ PEVSI. Los resultados obtenidos son ilustrados mediante un ejemplo que incluye una simulación estocástica. ZUSAMMENFASSUNG: Veränderung der Fehlervarianz der Zuchtwertvoraussage durch Vernachlässigung einer Gruppe zufäliger Wirkungen. Es wird die Auswirkung der Ausschaltung einer Gruppe zufälliger Wirkungen (U-effects), die mit Zuchtwerten (BV) nicht korreliert sind, auf die Varianz des Voraussage-Fehlers (PEV) analytisch untersucht. Zwei Modelle werden betrachtet: (a

  2. 28 CFR 74.4 - Individuals excluded from compensation pursuant to section 108(B) of the Act.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Individuals excluded from compensation pursuant to section 108(B) of the Act. 74.4 Section 74.4 Judicial Administration DEPARTMENT OF JUSTICE... emancipated minors, on the date they departed the United States for Japan are subject to an irrebuttable...

  3. 21 CFR 1.327 - Who is excluded from all or part of the regulations in this subpart?

    Science.gov (United States)

    2010-04-01

    ... products to all other buyers. (4) A “retail food establishment” includes grocery stores, convenience stores... establishment and not the entire business, which may own numerous retail stores. (g) Persons who manufacture... from all of the requirements in this subpart. A restaurant/retail facility is excluded from all of the...

  4. 34 CFR 85.420 - May I approve a transaction with an excluded or disqualified person at a lower tier?

    Science.gov (United States)

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false May I approve a transaction with an excluded or disqualified person at a lower tier? 85.420 Section 85.420 Education Office of the Secretary, Department of... lower tier? If a transaction at a lower tier is subject to your approval, you as an agency official may...

  5. 2 CFR 180.420 - May I approve a transaction with an excluded or disqualified person at a lower tier?

    Science.gov (United States)

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false May I approve a transaction with an excluded or disqualified person at a lower tier? 180.420 Section 180.420 Grants and Agreements OFFICE OF... person at a lower tier? If a transaction at a lower tier is subject to your approval, you as a Federal...

  6. 22 CFR 208.420 - May I approve a transaction with an excluded or disqualified person at a lower tier?

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false May I approve a transaction with an excluded or disqualified person at a lower tier? 208.420 Section 208.420 Foreign Relations AGENCY FOR INTERNATIONAL... lower tier? If a transaction at a lower tier is subject to your approval, you as an agency official may...

  7. 45 CFR 2506.5 - If a debt is not excluded from these regulations, may it be compromised, suspended, terminated...

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false If a debt is not excluded from these regulations, may it be compromised, suspended, terminated, or waived? 2506.5 Section 2506.5 Public Welfare Regulations Relating to Public Welfare (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE COLLECTION...

  8. Mortality of patients excluded from the Danish Verapamil Infarction Trail II. The DAVIT-II Study Group

    DEFF Research Database (Denmark)

    Madsen, J K; Hansen, J F

    1993-01-01

    The 18 month mortality rate in 2180 patients excluded from the Danish Verapamil Infarction Trail II (DAVIT II) was 25.6%. In non-consenters (n = 368) this was 15.0% compared with 13.85 in 897 placebo-treated patients (hazard ratio 1.09 [P = 0.60] when adjusting for sex and age). The increased...

  9. 9 CFR 130.17 - User fees for other veterinary diagnostic laboratory tests performed at NVSL (excluding FADDL) or...

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false User fees for other veterinary... FEES USER FEES § 130.17 User fees for other veterinary diagnostic laboratory tests performed at NVSL (excluding FADDL) or at authorized sites. (a) User fees for veterinary diagnostics tests performed at the...

  10. 9 CFR 130.18 - User fees for veterinary diagnostic reagents produced at NVSL or other authorized site (excluding...

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false User fees for veterinary diagnostic reagents produced at NVSL or other authorized site (excluding FADDL). 130.18 Section 130.18 Animals and... § 130.18 User fees for veterinary diagnostic reagents produced at NVSL or other authorized site...

  11. Data, Data Everywhere--But Not All the Numbers that Count? Mapping Alternative Provisions for Students Excluded from School

    Science.gov (United States)

    Thomson, Pat; Russell, Lisa

    2009-01-01

    It is now mandatory for English schools to ensure that young people, under 16 years of age, who are excluded from school are placed in an education and training programme within 12 days. The programme must be at least half time, and should offer a meaningful and balanced curriculum. The "Every Child Matters" agenda also suggests that…

  12. Model Misspecification When Excluding Instrumental Variables From PS Models in Settings Where Instruments Modify the Effects of Covariates on Treatment

    Science.gov (United States)

    Wyss, Richard; Ellis, Alan R.; Lunt, Mark; Brookhart, M. Alan; Glynn, Robert J.; Stürmer, Til

    2014-01-01

    Theory and simulations show that variables affecting the outcome only through exposure, known as instrumental variables (IVs), should be excluded from propensity score (PS) models. In pharmacoepidemiologic studies based on automated healthcare databases, researchers will sometimes use a single PS model to control for confounding when evaluating the effect of a treatment on multiple outcomes. Because these “full” models are not constructed with a specific outcome in mind, they will usually contain a large number of IVs for any individual study or outcome. If researchers subsequently decide to evaluate a subset of the outcomes in more detail, they can construct reduced “outcome-specific” models that exclude IVs for the particular study. Accurate estimates of PSs that do not condition on IVs, however, can be compromised when simply excluding instruments from the full PS model. This misspecification may have a negligible impact on effect estimates in many settings, but is likely to be more pronounced for situations where instruments modify the effects of covariates on treatment (instrument-confounder interactions). In studies evaluating drugs during early dissemination, the effects of covariates on treatment are likely modified over calendar time and IV-confounder interaction effects on treatment are likely to exist. In these settings, refitting more flexible PS models after excluding IVs and IV-confounder interactions can work well. The authors propose an alternative method based on the concept of marginalization that can be used to remove the negative effects of controlling for IVs and IV-confounder interactions without having to refit the full PS model. This method fits the full PS model, including IVs and IV-confounder interactions, but marginalizes over values of the instruments. Fitting more flexible PS models after excluding IVs or using the full model to marginalize over IVs can prevent model misspecification along with the negative effects of balancing

  13. Clarifying the use of aggregated exposures in multilevel models: self-included vs. self-excluded measures.

    Directory of Open Access Journals (Sweden)

    Etsuji Suzuki

    Full Text Available Multilevel analyses are ideally suited to assess the effects of ecological (higher level and individual (lower level exposure variables simultaneously. In applying such analyses to measures of ecologies in epidemiological studies, individual variables are usually aggregated into the higher level unit. Typically, the aggregated measure includes responses of every individual belonging to that group (i.e. it constitutes a self-included measure. More recently, researchers have developed an aggregate measure which excludes the response of the individual to whom the aggregate measure is linked (i.e. a self-excluded measure. In this study, we clarify the substantive and technical properties of these two measures when they are used as exposures in multilevel models.Although the differences between the two aggregated measures are mathematically subtle, distinguishing between them is important in terms of the specific scientific questions to be addressed. We then show how these measures can be used in two distinct types of multilevel models-self-included model and self-excluded model-and interpret the parameters in each model by imposing hypothetical interventions. The concept is tested on empirical data of workplace social capital and employees' systolic blood pressure.Researchers assume group-level interventions when using a self-included model, and individual-level interventions when using a self-excluded model. Analytical re-parameterizations of these two models highlight their differences in parameter interpretation. Cluster-mean centered self-included models enable researchers to decompose the collective effect into its within- and between-group components. The benefit of cluster-mean centering procedure is further discussed in terms of hypothetical interventions.When investigating the potential roles of aggregated variables, researchers should carefully explore which type of model-self-included or self-excluded-is suitable for a given situation

  14. Putative regulation mechanism for the MSTN gene by a CpG island generated by the SINE marker Ins227bp.

    Science.gov (United States)

    van den Hoven, René; Gür, Emre; Schlamanig, Manuela; Hofer, Martin; Onmaz, Ali Cesur; Steinborn, Ralf

    2015-06-23

    and for the SINE-free genotype was 1812 to 1854 m. Other performance parameters were not significantly different between the genotypes, except of the relative success score (RSS). The RSS was significantly slightly better on a distance of ≤ 1300 m for all carriers of the C allele and the Ins227bp compared to homozygous T genotypes and SINE-negative horses (p = 0.037 to 0.046). For distances of more than 1300 m the RSS was not significantly different between genotypes. In silico assessment indicated that the Ins227bp promoter insertion might have generated a CpG island and a few novel putative binding sites for transcription factors. All three target polymorphisms (Ins227bp, g.66493737 T ≻ C, BIEC2-417495) are suitable markers to assess the ability of non-elite Thoroughbreds to race at short or longer distances. The CpG island generated by Ins227bp may cause training-induced silencing of MSTN expression.

  15. Lead exposure induces changes in 5-hydroxymethylcytosine clusters in CpG islands in human embryonic stem cells and umbilical cord blood

    Science.gov (United States)

    Sen, Arko; Cingolani, Pablo; Senut, Marie-Claude; Land, Susan; Mercado-Garcia, Adriana; Tellez-Rojo, Martha M; Baccarelli, Andrea A; Wright, Robert O; Ruden, Douglas M

    2015-01-01

    Prenatal exposure to neurotoxicants such as lead (Pb) may cause stable changes in the DNA methylation (5mC) profile of the fetal genome. However, few studies have examined its effect on the DNA de-methylation pathway, specifically the dynamic changes of the 5-hydroxymethylcytosine (5hmC) profile. Therefore, in this study, we investigate the relationship between Pb exposure and 5mC and 5hmC modifications during early development. To study the changes in the 5hmC profile, we use a novel modification of the Infinium™ HumanMethylation450 assay (Illumina, Inc.), which we named HMeDIP-450K assay, in an in vitro human embryonic stem cell model of Pb exposure. We model Pb exposure-associated 5hmC changes as clusters of correlated, adjacent CpG sites, which are co-responding to Pb. We further extend our study to look at Pb-dependent changes in high density 5hmC regions in umbilical cord blood DNA from 48 mother-infant pairs from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) cohort. For our study, we randomly selected umbilical cord blood from 24 male and 24 female children from the 1st and 4th quartiles of Pb levels. Our data show that Pb-associated changes in the 5hmC and 5mC profiles can be divided into sex-dependent and sex-independent categories. Interestingly, differential 5mC sites are better markers of Pb-associated sex-dependent changes compared to differential 5hmC sites. In this study we identified several 5hmC and 5mC genomic loci, which we believe might have some potential as early biomarkers of prenatal Pb exposure. PMID:26046694

  16. A 1. 8-Mb YAC contig in Xp11. 23: Identification of Cpg islands and physical mapping of CA repeats in a region of high gene density

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, M.P.; Nemeth, A.H.; Campbell, L.; Raut, C.P.; Davies, K.E. (Institute of Molecular Medicine, Oxford (United Kingdom)); Weissenbach, J. (Unite de Genetique Moleculaire Humaine, Paris (France))

    1994-05-15

    The genes ARAF1, SYN1, TIMP, and PFC are clustered within 70 kb of one another, and, as reported in the accompanying paper, at least four more genes map within 400 kb: a cluster of Krueppel-type zinc finger genes (including ZNF21, ZNF41, and ZNF81) and ELK-1, a member of the ets oncogene superfamily. This gene-rich region is of particular interest because of the large number of disease genes mapping to Xp11.23: At least three eye diseases (retinitis pigmentosa type 2, congenital stationary night blindness CSNB1, and Aland Island eye disease), Wiskott-Aldrich syndrome, X-linked nephrolithiasis, and a translocation breakpoint associated with synovial sarcoma. The authors have constructed a 1.8-Mb YAC contig in this region, confirming the link between TIMP and OATL1 reported by Knight et al. (1994) and extending the map in the distal direction. To investigate the likelihood that more genes are located within this region, they have carried out detailed mapping of rare-cutter restriction sites in these YACs and identified seven CpG islands. At least six of these islands are located over 50 kb from any known gene locations, suggesting that the region contains at least this many as yet unidentified genes. They have also mapped the physical locations of six highly polymorphic CA repeats within the contig, thus integrating the physical, genetic, and transcriptional maps of the region and facilitating the mapping and identification of disease genes. Together with the report by Knight et al., these data indicate the following order of loci: Xpter-DXS1264-DXS1055-DXS1003-DXS1146-DXS1266-(ZNF41, ARAF1)-SYN1 CA repeat-SYN1 (3[prime] end)-TIMP-SYN1 (5[prime] end)-PFC CA repeat-PFC-(DXS426, ELK1)-(DXS1265, ZNF81)-ZNF21-DXS1267-OATL1-Xcen. 40 refs., 4 figs., 3 tabs.

  17. Impact on malaria parasite multiplication rates in infected volunteers of the protein-in-adjuvant vaccine AMA1-C1/Alhydrogel+CPG 7909.

    Directory of Open Access Journals (Sweden)

    Christopher J A Duncan

    Full Text Available Inhibition of parasite growth is a major objective of blood-stage malaria vaccines. The in vitro assay of parasite growth inhibitory activity (GIA is widely used as a surrogate marker for malaria vaccine efficacy in the down-selection of candidate blood-stage vaccines. Here we report the first study to examine the relationship between in vivo Plasmodium falciparum growth rates and in vitro GIA in humans experimentally infected with blood-stage malaria.In this phase I/IIa open-label clinical trial five healthy malaria-naive volunteers were immunised with AMA1/C1-Alhydrogel+CPG 7909, and together with three unvaccinated controls were challenged by intravenous inoculation of P. falciparum infected erythrocytes.A significant correlation was observed between parasite multiplication rate in 48 hours (PMR and both vaccine-induced growth-inhibitory activity (Pearson r = -0.93 [95% CI: -1.0, -0.27] P = 0.02 and AMA1 antibody titres in the vaccine group (Pearson r = -0.93 [95% CI: -0.99, -0.25] P = 0.02. However immunisation failed to reduce overall mean PMR in the vaccine group in comparison to the controls (vaccinee 16 fold [95% CI: 12, 22], control 17 fold [CI: 0, 65] P = 0.70. Therefore no impact on pre-patent period was observed (vaccine group median 8.5 days [range 7.5-9], control group median 9 days [range 7-9].Despite the first observation in human experimental malaria infection of a significant association between vaccine-induced in vitro growth inhibitory activity and in vivo parasite multiplication rate, this did not translate into any observable clinically relevant vaccine effect in this small group of volunteers.ClinicalTrials.gov [NCT00984763].

  18. Generation of Locomotor-Like Activity in the Isolated Rat Spinal Cord Using Intraspinal Electrical Microstimulation Driven by a Digital Neuromorphic CPG

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    Sebastien eJoucla

    2016-03-01

    Full Text Available Neural prostheses based on electrical microstimulation offer promising perspectives to restore functions following lesions of the central nervous system (CNS. They require the identification of appropriate stimulation sites and the coordination of their activation to achieve the restoration of functional activity. On the long term, a challenging perspective is to control microstimulation by artificial neural networks hybridized to the living tissue. Regarding the use of this strategy to restore locomotor activity in the spinal cord, to date, there has been no proof of principle of such hybrid approach driving intraspinal microstimulation. Here, we address a first step toward this goal in the neonatal rat spinal cord isolated ex vivo, which can display locomotor-like activity while offering an easy access to intraspinal circuitry. Microelectrode arrays were inserted in the lumbar region to determine appropriate stimulation sites to elicit elementary bursting patterns on bilateral L2/L5 ventral roots. Two intraspinal sites were identified at L1 level, one on each side of the spinal cord laterally from the midline and approximately at a median position dorso-ventrally. An artificial CPG implemented on digital integrated circuit (FPGA was built to generate alternating activity and was hybridized to the living spinal cord to drive electrical microstimulation on these two identified sites. Using this strategy, sustained left-right and flexor-extensor alternating activity on bilateral L2/L5 ventral roots could be generated in either whole or thoracically transected spinal cords. These results are a first step toward hybrid artificial/biological solutions based on electrical microstimulation for the restoration of lost function in the injured CNS.

  19. Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas.

    Science.gov (United States)

    Furuta, Junichi; Nobeyama, Yoshimasa; Umebayashi, Yoshihiro; Otsuka, Fujio; Kikuchi, Kanako; Ushijima, Toshikazu

    2006-06-15

    Aberrant methylation of promoter CpG islands (CGI) is involved in silencing of tumor suppressor genes and is also a potential cancer biomarker. Here, to identify CGIs aberrantly methylated in human melanomas, we did a genome-wide search using methylation-sensitive representational difference analysis. CGIs in putative promoter regions of 34 genes (ABHD9, BARHL1, CLIC5, CNNM1, COL2A1, CPT1C, DDIT4L, DERL3, DHRS3, DPYS, EFEMP2, FAM62C, FAM78A, FLJ33790, GBX2, GPR10, GPRASP1, HOXA9, HOXD11, HOXD12, HOXD13, p14ARF, PAX6, PRDX2, PTPRG, RASD1, RAX, REC8L1, SLC27A3, TGFB2, TLX2, TMEM22, TMEM30B, and UNC5C) were found to be methylated in at least 1 of 13 melanoma cell lines but not in two cultured normal melanocytes. Among these genes, Peroxiredoxin 2 (PRDX2) was expressed in normal melanocytes, and its expression was lost in melanomas with methylation. The loss of expression was restored by treatment of melanomas with a demethylating agent 5-aza-2'-deoxycytidine. In surgical melanoma specimens, methylation of PRDX2 was detected in 3 of 36 (8%). Furthermore, immunohistochemical analysis of PRDX2 showed that disappearance of immunoreactivity tends to associate with its methylation. PRDX2 was recently reported to be a negative regulator of platelet-derived growth factor signaling, and its silencing was suggested to be involved in melanomas. On the other hand, 12 CGIs were methylated in >or=9 of the 13 melanoma cell lines and are considered as candidate melanoma biomarkers.

  20. A downstream CpG island controls transcript initiation and elongation and the methylation state of the imprinted Airn macro ncRNA promoter.

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    Martha V Koerner

    Full Text Available A CpG island (CGI lies at the 5' end of the Airn macro non-protein-coding (nc RNA that represses the flanking Igf2r promoter in cis on paternally inherited chromosomes. In addition to being modified on maternally inherited chromosomes by a DNA methylation imprint, the Airn CGI shows two unusual organization features: its position immediately downstream of the Airn promoter and transcription start site and a series of tandem direct repeats (TDRs occupying its second half. The physical separation of the Airn promoter from the CGI provides a model to investigate if the CGI plays distinct transcriptional and epigenetic roles. We used homologous recombination to generate embryonic stem cells carrying deletions at the endogenous locus of the entire CGI or just the TDRs. The deleted Airn alleles were analyzed by using an ES cell imprinting model that recapitulates the onset of Igf2r imprinted expression in embryonic development or by using knock-out mice. The results show that the CGI is required for efficient Airn initiation and to maintain the unmethylated state of the Airn promoter, which are both necessary for Igf2r repression on the paternal chromosome. The TDRs occupying the second half of the CGI play a minor role in Airn transcriptional elongation or processivity, but are essential for methylation on the maternal Airn promoter that is necessary for Igf2r to be expressed from this chromosome. Together the data indicate the existence of a class of regulatory CGIs in the mammalian genome that act downstream of the promoter and transcription start.

  1. Using peripheral blood circulating DNAs to detect CpG global methylation status and genetic mutations in patients with myelodysplastic syndrome.

    Science.gov (United States)

    Iriyama, Chisako; Tomita, Akihiro; Hoshino, Hideaki; Adachi-Shirahata, Mizuho; Furukawa-Hibi, Yoko; Yamada, Kiyofumi; Kiyoi, Hitoshi; Naoe, Tomoki

    2012-03-23

    Myelodysplastic syndrome (MDS) is a hematopoietic stem cell disorder. Several genetic/epigenetic abnormalities are deeply associated with the pathogenesis of MDS. Although bone marrow (BM) aspiration is a common strategy to obtain MDS cells for evaluating their genetic/epigenetic abnormalities, BM aspiration is difficult to perform repeatedly to obtain serial samples because of pain and safety concerns. Here, we report that circulating cell-free DNAs from plasma and serum of patients with MDS can be used to detect genetic/epigenetic abnormalities. The plasma DNA concentration was found to be relatively high in patients with higher blast cell counts in BM, and accumulation of DNA fragments from mono-/di-nucleosomes was confirmed. Using serial peripheral blood (PB) samples from patients treated with hypomethylating agents, global methylation analysis using bisulfite pyrosequencing was performed at the specific CpG sites of the LINE-1 promoter. The results confirmed a decrease of the methylation percentage after treatment with azacitidine (days 3-9) using DNAs from plasma, serum, and PB mono-nuclear cells (PBMNC). Plasma DNA tends to show more rapid change at days 3 and 6 compared with serum DNA and PBMNC. Furthermore, the TET2 gene mutation in DNAs from plasma, serum, and BM cells was quantitated by pyrosequencing analysis. The existence ratio of mutated genes in plasma and serum DNA showed almost equivalent level with that in the CD34+/38- stem cell population in BM. These data suggest that genetic/epigenetic analyses using PB circulating DNA can be a safer and painless alternative to using BM cells. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. Impact on Malaria Parasite Multiplication Rates in Infected Volunteers of the Protein-in-Adjuvant Vaccine AMA1-C1/Alhydrogel+CPG 7909

    Science.gov (United States)

    Duncan, Christopher J. A.; Sheehy, Susanne H.; Ewer, Katie J.; Douglas, Alexander D.; Collins, Katharine A.; Halstead, Fenella D.; Elias, Sean C.; Lillie, Patrick J.; Rausch, Kelly; Aebig, Joan; Miura, Kazutoyo; Edwards, Nick J.; Poulton, Ian D.; Hunt-Cooke, Angela; Porter, David W.; Thompson, Fiona M.; Rowland, Ros; Draper, Simon J.; Gilbert, Sarah C.; Fay, Michael P.; Long, Carole A.; Zhu, Daming; Wu, Yimin; Martin, Laura B.; Anderson, Charles F.; Lawrie, Alison M.; Hill, Adrian V. S.; Ellis, Ruth D.

    2011-01-01

    Background Inhibition of parasite growth is a major objective of blood-stage malaria vaccines. The in vitro assay of parasite growth inhibitory activity (GIA) is widely used as a surrogate marker for malaria vaccine efficacy in the down-selection of candidate blood-stage vaccines. Here we report the first study to examine the relationship between in vivo Plasmodium falciparum growth rates and in vitro GIA in humans experimentally infected with blood-stage malaria. Methods In this phase I/IIa open-label clinical trial five healthy malaria-naive volunteers were immunised with AMA1/C1-Alhydrogel+CPG 7909, and together with three unvaccinated controls were challenged by intravenous inoculation of P. falciparum infected erythrocytes. Results A significant correlation was observed between parasite multiplication rate in 48 hours (PMR) and both vaccine-induced growth-inhibitory activity (Pearson r = −0.93 [95% CI: −1.0, −0.27] P = 0.02) and AMA1 antibody titres in the vaccine group (Pearson r = −0.93 [95% CI: −0.99, −0.25] P = 0.02). However immunisation failed to reduce overall mean PMR in the vaccine group in comparison to the controls (vaccinee 16 fold [95% CI: 12, 22], control 17 fold [CI: 0, 65] P = 0.70). Therefore no impact on pre-patent period was observed (vaccine group median 8.5 days [range 7.5–9], control group median 9 days [range 7–9]). Conclusions Despite the first observation in human experimental malaria infection of a significant association between vaccine-induced in vitro growth inhibitory activity and in vivo parasite multiplication rate, this did not translate into any observable clinically relevant vaccine effect in this small group of volunteers. Trial Registration ClinicalTrials.gov [NCT00984763] PMID:21799809

  3. JC Virus T-Antigen in Colorectal Cancer Is Associated with p53 Expression and Chromosomal Instability, Independent of CpG Island Methylator Phenotype

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    Katsuhiko Nosho

    2009-01-01

    Full Text Available JC virus has a transforming gene encoding JC virus T-antigen (JCVT. JCVT may inactivate wild-type p53, cause chromosomal instability (CIN, and stabilize β-catenin. A link between JCVT and CpG island methylator phenotype (CIMP has been suggested. However, no large-scale study has examined the relations of JCVT with molecular alterations, clinical outcome, or prognosis in colon cancer. We detected JCVT expression (by immunohistochemistry in 271 (35% of 766 colorectal cancers. We quantified DNA methylation in eight CIMP-specific promoters (CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1 and eight other loci (CHFR, HIC1, IGFBP3, MGMT, MINT1, MINT31, p14, WRN by MethyLight. We examined loss of heterozygosity in 2p, 5q, 17q, and 18q. JCVT was significantly associated with p53 expression (P < .0001, p21 loss (P < .0001, CIN (≥2 chromosomal segments with LOH; P < .0001, nuclear β-catenin (P = .006, LINE-1 hypomethylation (P = .002, and inversely with CIMP-high (P = .0005 and microsatellite instability (MSI (P < .0001, but not with PIK3CA mutation. In multivariate logistic regression analysis, the associations of JCVT with p53 [adjusted odds ratio (OR, 8.45; P < .0001], CIN (adjusted OR, 2.53; P = .003, cyclin D1 (adjusted OR, 1.57; P = .02, LINE-1 hypomethylation (adjusted OR, 1.97 for a 30% decline as a unit; P = .03, BRAF mutation (adjusted OR, 2.20; P = .04, and family history of colorectal cancer (adjusted OR, 0.64; P = .04 remained statistically significant. However, JCVT was no longer significantly associated with CIMP, MSI, β-catenin, or cyclooxygenase-2 expression in multivariate analysis. JCVT was unrelated with patient survival. In conclusion, JCVT expression in colorectal cancer is independently associated with p53 expression and CIN, which may lead to uncontrolled cell proliferation.

  4. Combined Analysis of COX-2 and p53 Expressions Reveals Synergistic Inverse Correlations with Microsatellite Instability and CpG Island Methylator Phenotype in Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Shuji Ogino

    2006-06-01

    Full Text Available Cyclooxygenase-2 (COX-2 overexpression and mutations of p53 (a known COX-2 regulator are inversely associated with microsatellite instability—high (MSI-H and CpG island methylator phenotype (CIMP, characterized by extensive promoter methylation, is associated with MSI-H. However, no studies have comprehensively examined interrelations between COX-2, p53, MSI, and CIMP. Using MethyLight, we measured DNA methylation in five CIMP-specific gene promoters [CACNA1G, CDKN2A (p16/INK4A, CRABP1, MLH1, and NEUROG1] in relatively unbiased samples of 751 colorectal cancer cases obtained from two large prospective cohorts; 115 (15% tumors were CIMP-high (≥ 4 of 5 methylated promoters, 251 (33% were CIMP-low (1 to 3 methylated promoters, and the remaining 385 (51% were CIMP-0 (no methylated promoters. CIMP-high tumors were much less frequent in COX-2+/p53+ tumors (4.6% than in COX-2+/p53- tumors (19%; P < .0001, COX-2-/p53+ tumors (17%; P = .04, and COX-2-/p53- tumors (28%; P < .0001. In addition, COX-2+/p53+ tumors were significantly less common in MSI-H CIMP-high tumors (9.7% than in non-MSI-H CIMP-low/CIMP-0 tumors (44–47%; P < .0001. In conclusion, COX-2 and p53 alterations were synergistically inversely correlated with both MSI-H and CIMP-high. Our data suggest that a combined analysis of COX-2 and p53 may be more useful for the molecular classification of colorectal cancer than either COX-2 or p53 analysis alone.

  5. Should Controls With Respiratory Symptoms Be Excluded From Case-Control Studies of Pneumonia Etiology? Reflections From the PERCH Study.

    Science.gov (United States)

    Higdon, Melissa M; Hammitt, Laura L; Deloria Knoll, Maria; Baggett, Henry C; Brooks, W Abdullah; Howie, Stephen R C; Kotloff, Karen L; Levine, Orin S; Madhi, Shabir A; Murdoch, David R; Scott, J Anthony G; Thea, Donald M; Driscoll, Amanda J; Karron, Ruth A; Park, Daniel E; Prosperi, Christine; Zeger, Scott L; O'Brien, Katherine L; Feikin, Daniel R

    2017-06-15

    Many pneumonia etiology case-control studies exclude controls with respiratory illness from enrollment or analyses. Herein we argue that selecting controls regardless of respiratory symptoms provides the least biased estimates of pneumonia etiology. We review 3 reasons investigators may choose to exclude controls with respiratory symptoms in light of epidemiologic principles of control selection and present data from the Pneumonia Etiology Research for Child Health (PERCH) study where relevant to assess their validity. We conclude that exclusion of controls with respiratory symptoms will result in biased estimates of etiology. Randomly selected community controls, with or without respiratory symptoms, as long as they do not meet the criteria for case-defining pneumonia, are most representative of the general population from which cases arose and the least subject to selection bias. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

  6. CpG Island Methylator Phenotype is Associated With Response to Adjuvant Irinotecan-Based Therapy for Stage 3 Colon Cancer

    Science.gov (United States)

    Shiovitz, Stacey; Bertagnolli, Monica M.; Renfro, Lindsay A.; Nam, Eunmi; Foster, Nathan R.; Dzieciatkowski, Slavomir; Luo, Yanxin; Lao, Victoria Valinluck; Monnat, Raymond J.; Emond, Mary J.; Maizels, Nancy; Niedzwiecki, Donna; Goldberg, Richard M.; Saltz, Leonard B.; Venook, Alan; Warren, Robert S.; Grady, William M.

    2014-01-01

    BACKGROUND & AIMS The CpG island methylator phenotype (CIMP), defined by a high frequency of aberrantly methylated genes, is a characteristic of a subclass of colon tumors with distinct clinical and molecular features. Cohort studies have produced conflicting results on responses of CIMP-positive tumors to chemotherapy. We assessed the association between tumor CIMP status and survival of patients receiving adjuvant fluorouracil and leucovorin alone or with irinotecan (IFL) METHODS We analyzed data from patients with stage 3 colon adenocarcinoma randomly assigned to groups given fluorouracil and leucovorin or IFL following surgery, from April 1999 through April 2001. The primary endpoint of the trial was overall survival and the secondary endpoint was disease-free survival. DNA isolated from available tumor samples (n=615) was used to determine CIMP status based on methylation patterns at the CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1 loci. The effects of CIMP on survival were modeled using Kaplan-Meier and Cox proportional hazards; interactions with treatment and BRAF, KRAS, and mismatch repair (MMR) status were also investigated. RESULTS Of the tumor samples characterized for CIMP status, 145 were CIMP positive (23%). Patients with CIMP-positive tumors had shorter overall survival times than patients with CIMP-negative tumors (hazard ratio [HR]=1.36; 95% confidence interval [CI], 1.01–1.84). Treatment with IFL showed a trend toward increased overall survival for patients with CIMP-positive tumors, compared to treatment with fluorouracil and leucovorin (HR=0.62; 95% CI, 0.37–1.05; P=.07), but not for patients with CIMP-negative tumors (HR=1.38; 95% CI, 1.00–1.89; P=.049). In a 3-way interaction analysis, patients with CIMP-positive, MMR-intact tumors benefited most from the addition of irinotecan to fluorouracil and leucovorin therapy (for the interaction, P=.01). CIMP was more strongly associated with response to IFL than MMR status. Results for disease

  7. A single, low dose oral antigen exposure in newborn piglets primes mucosal immunity if administered with CpG oligodeoxynucleotides and polyphosphazene adjuvants.

    Science.gov (United States)

    Pasternak, J Alex; Ng, Siew Hon; Wilson, Heather L

    2014-10-15

    By definition, soluble antigens ingested orally trigger mucosal tolerance such that any subsequent re-exposure by a systemic route results in suppression of immunity. We propose that antigens introduced in extreme early life can readily traverse the gut wall and therefore circumvent induction of mucosal tolerance and instead induce immunity. Piglets were drenched with low-doses of ovalbumin (OVA; 5mg or 0.05 mg) alone, OVA plus adjuvants (CpG oligodeoxynucleotides and PCEP polyphosphazene) or saline within 6h of birth. At 28 days of age, they were administered 10mg OVA plus 1:1 Montanide adjuvant (or saline) via the intraperitoneal (i.p.) route or via the oral route. Serum was obtained on day 28 and day 49 to measure OVA-specific antibodies titres. All piglets boosted orally with OVA plus Montanide, regardless of prior OVA exposure, failed to induce immunity. As expected, piglets drenched with saline but boosted via the i.p. route with OVA plus Montanide showed significant induction of anti-OVA IgA, IgG, IgG1 and IgG2 relative to saline control piglets. Newborn animals drenched with 5mg or 0.05 mg OVA failed to induce oral immunity. A second intramuscular injection in adulthood triggered immunity in the piglets that were drenched with 0.05 mg OVA and boosted initially by the i.p. route suggesting that some systemic lymphocytes were primed despite initial lack of induction of humoral immunity. In contrast, piglets orally immunized with 5mg or 0.05 mg OVA plus adjuvants resulted in significant induction of anti-OVA IgA (5mg only), IgM, IgG, IgG1 and IgG2 in serum relative to saline control piglets as well as significant induction of anti-OVA IgA, IgM (5mg only) IgG, IgG1 (5mg only) or IgG2 relative to piglets drenched with OVA alone. These data clearly show that the response was sensitive to the oral vaccine components and was not simply a response to the i.p. immunization at day 28. This work demonstrates that newborn piglets respond to oral antigens with immunity

  8. Tobacco smoking differently influences cell types of the innate and adaptive immune system-indications from CpG site methylation.

    Science.gov (United States)

    Bauer, Mario; Fink, Beate; Thürmann, Loreen; Eszlinger, Markus; Herberth, Gunda; Lehmann, Irina

    2015-01-01

    Tobacco smoke is worldwide one of the main preventable lifestyle inhalative pollutants causing severe adverse health effects. Epidemiological studies revealed association of tobacco smoking with epigenetic changes at single CpGs in blood. However, the biological relevance of the often only marginal methylation changes remains unclear. Comparing genome-wide changes in CpG methylation of three recently reported epidemiological datasets, two obtained on whole blood and one on peripheral blood mononuclear cells (PBMCs), it becomes evident that the majority of methylation changes (86.7 and 93.3 %) in whole blood account for changes in granulocytes. Analyzing, in more detail, seven highly significant reported smoking-induced methylation changes at single CpGs in different blood cell types of healthy volunteers (n = 32), we confirmatively found a strong cell-type specificity. Two CpGs in GFI1 and F2RL3 were significantly hypomethylated in granulocytes (-11.3 %, p = 0.001; -8.7 %, p = 0.001, respectively) but not in PBMCs of smokers while two CpGs in CPOX and GPR15 were found to be hypomethylated in PBMC (-4.3 %, p = 0.003; -4.2 %, P = 0.009, respectively) and their subtypes of GPR15 non-expressing (-3.2 %, p = 0.027; -2.5 %, p = 0.032, respectively) and smoking-evoked GPR15 expressing T cells (-15.8 %, p smoking behavior at individual level and could therefore serve as valuable biomarkers indicating a disturbed homeostasis in smokers. In contrast to the reported long-term persistent methylation changes in adult smokers after cessation, the hypomethylation at cg05575921 in prenatally tobacco smoke-exposed children (n = 13) from our LINA cohort was less stable and disappeared already within 2 years after birth. Studying cell type-specific methylation changes provides helpful information regarding the biological relevance of epigenetic modifications. Here, we could show that smoking differently affects both cells of the innate and

  9. [Immunostimulatory CpG oligodeoxynucleotides (CpG-ODN) in an orthotopic murine transitional cell carcinoma (TCC) model. Effect on local cytokine expression].

    Science.gov (United States)

    Olbert, P J; Schrader, A J; Hofmann, R; Hegele, A

    2008-09-01

    CpG-oligodeoxynucleotides (CpG-ODN) are potent stimulators of the innate immune system. They promote a Th1-biased immune response with antineoplastic potential. We recently demonstrated antitumoral effects of CpG-ODN in murine transitional cell carcinoma (TCC) models. The purpose of the present work was to more precisely define the immunological nature of this immunotherapeutic approach to TCC.MB-49 TCC was established in female C57/Bl6 mice by intravesical tumor cell instillation after poly-L-lysine conditioning of the bladder (day 0) as described previously. Three groups of six mice were treated: intravesical instillation of 50 microl PBS on days 1, 3, 5, and 7 (group 1, untreated control); 10 nmol CpG 1668 on days 1, 3, 5, and 7 (group 2); and 10 nmol GpC 1668 on days 1, 3, 5, and 7 (group 3). Six native bladders served as no-treatment/no-tumor controls (group 4). Mice were sacrificed on day 11; bladders and draining lymph nodes were removed, and mRNA was prepared for quantitative real-time polymerase chain reaction. Samples were analyzed on a Bio-Rad iCycler for IL 10, TGF-beta, IL 12, and IFNgamma expression; threshold values were compared to beta-actin as housekeeping gene.Tumor take was 100%. Three animals in group 1 had to be sacrificed in advance due to rapid tumor progression. Relative cytokine expression was comparable in groups 1 and 4. IL-10, IL-12, TGF-beta, and IFNgamma were overexpressed in groups 2 and 3. CpG-ODN treatment of murine TCC results in overexpression of both classic Th1 cytokines (IL 12 and IFNgamma) and the Th2 marker IL 10. TGF-beta expression is increased as well. These phenomena are not induced by the growing TCC but by CpG-ODN therapy. They are accompanied by an objective clinical response, as we were able to show recently. Immunostimulatory DNA holds promise to be a novel therapeutic agent in TCC.

  10. Association of two synonymous splicing-associated CpG single nucleotide polymorphisms in calpain 10 and solute carrier family 2 member 2 with type 2 diabetes.

    Science.gov (United States)

    Karambataki, Maria; Malousi, Andigoni; Tzimagiorgis, Georgios; Haitoglou, Constantinos; Fragou, Aikaterini; Georgiou, Elisavet; Papadopoulou, Foteini; Krassas, Gerasimos E; Kouidou, Sofia

    2017-02-01

    Coding synonymous single nucleotide polymorphisms (SNPs) have attracted little attention until recently. However, such SNPs located in epigenetic, CpG sites modifying exonic splicing enhancers (ESEs) can be informative with regards to the recently verified association of intragenic methylation and splicing. The present study describes the association of type 2 diabetes (T2D) with the exonic, synonymous, epigenetic SNPs, rs3749166 in calpain 10 (CAPN10) glucose transporter (GLUT4) translocator and rs5404 in solute carrier family 2, member 2 (SLC2A2), also termed GLUT2, which, according to prior bioinformatic analysis, strongly modify the splicing potential of glucose transport-associated genes. Previous association studies reveal that only rs5404 exhibits a strong negative T2D association, while data on the CAPN10 polymorphism are contradictory. In the present study DNA from blood samples of 99 Greek non-diabetic control subjects and 71 T2D patients was analyzed. In addition, relevant publicly available cases (40) resulting from examination of 110 Personal Genome Project data files were analyzed. The frequency of the rs3749166 A allele, was similar in the patients and non-diabetic control subjects. However, AG heterozygotes were more frequent among patients (73.24% for Greek patients and 54.55% for corresponding non-diabetic control subjects; P=0.0262; total cases, 52.99 and 75.00%, respectively; P=0.0039). The rs5404 T allele was only observed in CT heterozygotes (Greek non-diabetic control subjects, 39.39% and Greek patients, 22.54%; P=0.0205; total cases, 34.69 and 21.28%, respectively; P=0.0258). Notably, only one genotype, heterozygous AG/CC, was T2D-associated (Greek non-diabetic control subjects, 29.29% and Greek patients, 56.33%; P=0.004; total cases, 32.84 and 56.58%, respectively; P=0.0008). Furthermore, AG/CC was strongly associated with very high (≥8.5%) glycosylated plasma hemoglobin levels among patients (P=0.0002 for all cases). These results reveal

  11. Deletion hotspots in AMACR promoter CpG island are cis-regulatory elements controlling the gene expression in the colon.

    Directory of Open Access Journals (Sweden)

    Xiang Zhang

    2009-01-01

    Full Text Available Alpha-methylacyl-coenzyme A racemase (AMACR regulates peroxisomal beta-oxidation of phytol-derived, branched-chain fatty acids from red meat and dairy products -- suspected risk factors for colon carcinoma (CCa. AMACR was first found overexpressed in prostate cancer but not in benign glands and is now an established diagnostic marker for prostate cancer. Aberrant expression of AMACR was recently reported in Cca; however, little is known about how this gene is abnormally activated in cancer. By using a panel of immunostained-laser-capture-microdissected clinical samples comprising the entire colon adenoma-carcinoma sequence, we show that deregulation of AMACR during colon carcinogenesis involves two nonrandom events, resulting in the mutually exclusive existence of double-deletion at CG3 and CG10 and deletion of CG12-16 in a newly identified CpG island within the core promoter of AMACR. The double-deletion at CG3 and CG10 was found to be a somatic lesion. It existed in histologically normal colonic glands and tubular adenomas with low AMACR expression and was absent in villous adenomas and all CCas expressing variable levels of AMACR. In contrast, deletion of CG12-16 was shown to be a constitutional allele with a frequency of 43% in a general population. Its prevalence reached 89% in moderately differentiated CCas strongly expressing AMACR but only existed at 14% in poorly differentiated CCas expressing little or no AMACR. The DNA sequences housing these deletions were found to be putative cis-regulatory elements for Sp1 at CG3 and CG10, and ZNF202 at CG12-16. Chromatin immunoprecipitation, siRNA knockdown, gel shift assay, ectopic expression, and promoter analyses supported the regulation by Sp1 and ZNF202 of AMACR gene expression in an opposite manner. Our findings identified key in vivo events and novel transcription factors responsible for AMACR regulation in CCas and suggested these AMACR deletions may have diagnostic/prognostic value for

  12. Custom-Designed MLPA Using Multiple Short Synthetic Probes Application to Methylation Analysis of Five Promoter CpG Islands in Tumor and Urine Specimens from Patients with Bladder Cancer

    DEFF Research Database (Denmark)

    Serizawa, R.R.; Ralfkiaer, U.; Dahl, C.

    2010-01-01

    will form a single amplifiable template whose length is defined by the number and lengths of the individual probes. We have used this principle to establish a methylation-specific MLPA (MS-MLPA) assay that simultaneously determines the methylation status of five promoter CpG islands, and we have used...... this assay to analyze DNA from tumor tissue and corresponding urine samples from patients with bladder cancer. Our data show that the use of multiple short synthetic probes provides a simple means for custom-designed MS-MLPA analysis....

  13. Custom-Designed MLPA Using Multiple Short Synthetic Probes Application to Methylation Analysis of Five Promoter CpG Islands in Tumor and Urine Specimens from Patients with Bladder Cancer

    DEFF Research Database (Denmark)

    Serizawa, R.R.; Ralfkiaer, U.; Dahl, C.

    2010-01-01

    will form a single amplifiable template whose length is defined by the number and lengths of the individual probes. We have used this principle to establish a methylation-specific MLPA (MS-MLPA) assay that simultaneously determines the methylation status of five promoter CpG islands, and we have used...... this assay to analyze DNA from tumor tissue and corresponding urine samples from patients with bladder cancer. Our data show that the use of multiple short synthetic probes provides a simple means for custom-designed MS-MLPA analysis. (J Mol Diagn 2010, 12:402-408; DOI: 10.2353/jmoldx.2010.090152)...

  14. Linkage analysis of primary open-angle glaucoma excludes the juvenile glaucoma region on chromosome 1q

    Energy Technology Data Exchange (ETDEWEB)

    Wirtz, M.K.; Acott, T.S.; Samples, J.R. [Casey Eye Institute, Portland, OR (United States)]|[Oregon Health Sciences Univ., Portland, OR (United States)] [and others

    1994-09-01

    The gene for one form of juvenile glaucoma has been mapped to chromosome 1q21-q31. This raises the possibility of primary open-angle glaucoma (POAG) also mapping to this region if the same defective gene causes both diseases. To ask this question linkage analysis was performed on a large POAG kindred. Blood samples or skin biopsies were obtained from 40 members of this family. Individuals were diagnosed as having POAG if they met two or more of the following criteria: (1) Visual field defects compatible with glaucoma on automated perimetry; (2) Optic nerve head and/or nerve fiber layer analysis compatible with glaucomatous damage; (3) high intraocular pressures (> 20 mm Hg). Patients were considered glaucoma suspects if they only met one criterion. These individuals were excluded from the analysis. Of the 40 members, seven were diagnosed with POAG; four were termed suspects. The earliest age of onset was 38 years old, while the average age of onset was 65 years old. We performed two-point and multipoint linkage analysis, using five markers which encompass the region 1q21-q31; specifically, D1S194, D1S210, D1S212, D1S191 and LAMB2. Two-point lod scores excluded tight linkage with all markers except D1S212 (maximum lod score of 1.07 at theta = 0.0). In the multipoint analysis, including D1S210-D1S212-LAMB2 and POAG, the entire 11 cM region spanned by these markers was excluded for linkage with POAG; that is, lod scores were < -2.0. In conclusion, POAG in this family does not map to chromosome 1q21-q31 and, thus, they carry a gene that is distinct from the juvenile glaucoma gene.

  15. Diagnostic accuracy of plasma NT-proBNP levels for excluding cardiac abnormalities in the very elderly

    Directory of Open Access Journals (Sweden)

    Westendorp Rudi GJ

    2010-11-01

    Full Text Available Abstract Background In the elderly the diagnosis of chronic heart failure is often challenging and the availability of echocardiography can be limited. Plasma levels of NT-proBNP are valuable tools to diagnose patients with heart failure. However, the performance of this biomarker to detect cardiac abnormalities in the very elderly remains unclear. The aims of this study were to investigate the relation between NT-proBNP and cardiac abnormalities and to evaluate the use of NT-proBNP to exclude structural and functional cardiac abnormalities in a community-based sample of "well-functioning" nonagenarians. Methods A diagnostic cross-sectional study embedded within the Leiden 85-plus Study in the municipality of Leiden, the Netherlands. Plasma NT-proBNP levels were measured and 2-dimensional echocardiography was performed in a subgroup of 80 well-functioning nonagenarians. Linear regression analysis was used to explore the relation between NT-proBNP and cardiac abnormalities and ROC curve analysis was used to assess the performance of NT-proBNP to exclude cardiac abnormalities. The upper limit of the lowest tertile of NT-proBNP was used as a cut-off value. Results NT-proBNP levels were associated with abnormal left ventricular (LV dimensions, LV systolic and diastolic function, left atrial enlargement and valvular heart disease. LV mass, E/A ratio and degree of aortic regurgitation were identified as independent predictors of NT-proBNP. NT-proBNP levels were higher with greater number of echocardiographic abnormalities (P Conclusions In this convenience sample of well-functioning nonagenarians NT-proBNP was related to a wide variety of functional and structural echocardiographic abnormalities. Moreover, NT-proBNP could be used to exclude echocardiographic abnormalities in well-functioning nonagenarians and might be used to indicate who needs to be referred for further cardiovascular examination.

  16. A pragmatic randomized controlled trial of computerized CBT (SPARX) for symptoms of depression among adolescents excluded from mainstream education.

    Science.gov (United States)

    Fleming, Theresa; Dixon, Robyn; Frampton, Christopher; Merry, Sally

    2012-10-01

    Adolescents excluded from mainstream education have high mental health needs. The use of computerized Cognitive Behavioural Therapy (cCBT) has not been investigated with this group. To test the efficacy of the SPARX cCBT programme for symptoms of depression among adolescents in programmes for students excluded or alienated from mainstream education. Adolescents (32; 34% Maori, 38% Pacific Island, 56% male) aged 13-16 with Child Depression Rating Scale Revised (CDRS-R) scores indicating possible through to almost certain depressive disorder were randomized to SPARX to be completed over the following 5 weeks (n = 20) or to waitlist control (n = 12). Assessments were at baseline, 5 weeks and 10 weeks. Those in the wait condition were invited to complete SPARX after the 5 week assessment. Most participants (n = 26, 81%) completed at least 4 levels of SPARX and 22 (69%) completed all 7 levels. Among the 30 (94%) participants who began treatment as randomized and provided 5-week data, significant differences were found between cCBT and wait groups on the CDRS-R (baseline to 5-week mean change -14.7 versus -1.1, pDepression Scale (-4.6 vs. +3.2 p = .05) but not on other self-rating psychological functioning scales. In intent-to-treat analyses CDRS-R changes and remission remained significant. Gains were maintained at 10-week follow-up. SPARX appears to be a promising treatment for students with symptoms of depression who are in alternative schooling programmes for those excluded from mainstream education.

  17. How does the use of mobile phones by 16-24 year old socially excluded women affect their capabilities?

    OpenAIRE

    Faith, Rebecca

    2016-01-01

    This research looks at the impact of mobile phone use on the lives and opportunities of 16-24 year-old socially excluded women, using a novel, cross-disciplinary framework of the capability approach and affordances. \\ud \\ud Fieldwork took the form of semi-structured interviews in 2013-14 with 30 women between the ages of 16-24, and four youth workers. The instrumental affordances of mobile phones are examined to understand whether they provide a means to address issues relating to work, healt...

  18. Type specimens of Hymenoptera deposited in the Museu de Zoologia da Universidade de São Paulo, Brazil (excluding Aculeata

    Directory of Open Access Journals (Sweden)

    Helena C. Onody

    2014-01-01

    Full Text Available The present paper lists the type specimens of Hymenoptera, excluding Aculeata, deposited in the Museu de Zoologia da Universidade de São Paulo, Brazil. We record all labels contents and also additional information from MZSP registers, published material, and other available sources. High resolution photographs of holotypes, lectotypes and syntypes are available through links to Specimage - the image database of The Ohio State University, where they are archived. The collection comprises a total of 332 type-specimens (32 holotypes, 266 paratypes, 12 syntypes, 20 paralectotypes and two lectotypes of eight superfamilies, 18 families, 31 subfamilies, 43 genera and 83 species.

  19. 2 CFR 801.137 - Who in the Department of Veterans Affairs may grant an exception to allow an excluded person to...

    Science.gov (United States)

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false Who in the Department of Veterans Affairs may grant an exception to allow an excluded person to participate in a covered transaction? 801.137... Veterans Affairs may grant an exception to allow an excluded person to participate in a covered transaction...

  20. Routine screening for postnatal depression in a public health family service unit: a retrospective study of self-excluding women.

    Science.gov (United States)

    Grussu, Pietro; Quatraro, Rosa Maria

    2015-01-01

    At this time, there is limited scientific knowledge about women who exclude themselves from screening programs for postnatal depression. In this retrospective descriptive study, we have sought to investigate the socio-demographic and psycho-social factors of women who withdraw from PND screening of their own accord. Study participants were 525 women attending antenatal classes who later took part in institutional routine screening for PND at the Consultorio Familiare Service of the National Health Service, Italy. The PND screening program consisted of the completion of the postpartum depression predictors inventory-revised and psychological well-being (PWB) questionnaires within eight to nine months of pregnancy, and Edinburgh Postnatal Depression Scale, GHQ-12 and PWB within six to eight weeks after childbirth. The Responders group was made up of 346 subjects - 65.9% of the total sample - who completed the entire program of screening for PND. The Non-Responders group, on the other hand, consisted of 179 subjects - 34.1% of the total sample - who, after childbirth, withdrew from the screening program. Compared to the Responders group, the Non-Responders group showed a greater number of subjects with marital dissatisfaction, and with unemployment as a stressful event. Health professionals who detect marital dissatisfaction and/or unemployment as a stressful event in pregnant women should bear in mind that these individuals, besides being at high risk for depression after delivery, will also tend to exclude themselves from screening for PND.

  1. Excluding the typical patient

    DEFF Research Database (Denmark)

    Odlaug, Brian Lawrence; Weinhandl, Eric; Mancebo, Maria C

    2014-01-01

    Over the past 30 years, clinical trials have resulted in several successful pharmacotherapies for obsessive-compulsive disorder (OCD), yet patients in clinical settings often report inadequate response. This study compares clinical characteristics of treatment-seeking OCD patients to the inclusion...

  2. Preliminary Experience with the GORE(®) EXCLUDER(®) Iliac Branch Endoprosthesis for Common Iliac Aneurysm Endovascular Treatment.

    Science.gov (United States)

    Millon, Antoine; Della Schiava, Nellie; Arsicot, Matthieu; De Lambert, Alberic; Feugier, Patrick; Magne, Jean Luc; Lermusiaux, Patrick

    2016-05-01

    The aim of this study is to assess the safety and the short-term results of endovascular treatment of common iliac artery (CIA) aneurysms using the new GORE EXCLUDER iliac branch endoprosthesis (IBE) device. The study is a retrospective with prospective follow-up nonrandomized, single-arm evaluation. Patients with a CIA aneurysm (diameter >30 mm) extending to the iliac bifurcation underwent endovascular treatment with the Gore IBE. Anatomic and procedural data were collected. Computed tomography angiography (CTA) was performed within the 30 days after the procedure and every 6 month. Thirty-day and at least 6-months outcomes were investigated. From February 2014 to December 2014, 10 male patients with aneurysmal CIA (mean age 75 years old) underwent consecutive endovascular treatment with the Gore IBE. The CIA aneurysm (mean diameter 43.2 mm, range 32-49) treated with the Gore IBE was associated with an abdominal aortic aneurysm (AAA) in 5 patients. One patient had a previous AAA open repair. CIA aneurysm was bilateral in 5 patients. Preliminary procedure of internal iliac artery embolization was performed in 3 patients. Technical success rate of the Gore IBE implantation was 100% with a median fluoroscopy time of 35 min (range 12-64, ±16) and median contrast load of 150 mL (range 100-250, ±45). No perioperative complications were observed. Median length of stay was 4 days (range 3-7, ±2). One aortic type Ia endoleak was observed on the postoperative CT scan requiring an aortic extension at day 3. Branch patency was observed in all 10 patients at 1 month and 9 patients at 6 month. All CIA aneurysms were excluded without type Ib or type III endoleak. The technical success and short-term results demonstrate encouraging results and clinical benefits of the new GORE EXCLUDER IBE. A longer follow-up is needed to assess midterm and long-term results. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Oral health of children from rural excluded villages (Trancas and Calchaqui valleys. Tucumán, Argentina).

    Science.gov (United States)

    Delgado, A M; Molina, N; Totongi, M; Bordoni, N; Fernandez, C

    1999-01-01

    The general hypothesis of the study was to evaluate strategically important rural areas to confirm their characteristics of "excluded population" and identify the priorities to allocate human and financial resources of the international co-operation project. The aim of this study was to establish the degree of development of villages in the Trancas and Calchaqui valleys, and the oral health of children living in areas involved in an integral study on excluded villages in the northwest of Argentina. These villages are considered a priority in the UNIR Project; they are thus strategically important as a link with countries of the MERCOSUR. Data on living conditions were obtained through direct inquiries (Project UNIR, W. K. Kellogg Foundation/University of Tucumán) and from data supplied by the Ministry of Economy, by the Ministry of Culture and Education and by the SIEMPRO project of the Secretariat of Social Development of the Ministry of Health. The Human Development Index (HDI) was calculated as World Bank criteria (1995), The studies on dental conditions were carried out in all the children between 12 and 14 years old, that is a total of 58 in the Trancas Valley and 212 in the Calchaqui Valley. (1) The HDI was 0.731 for the province, 0.56 for the Trancas Valley and 0.51 for Calchaqui valley. (2) The results are above the values for the country in the first case, and below the average country values for the valleys. (3) The percentage of BNN families reached 92%. The results for oral health show: (4) the DMFT were 6.34 +/- 0.07 in the Trancas Valley and 7.47 +/- 0.276 in the Calchaquí valley. (5) Carious teeth (CT) were the most important component of this index. (6) The absence of a specific and preventive assistance. (a) Children between 12 and 14 living in the Valleys of Trancas and Calchaqui (Tucumán, Argentina) are affected by severe levels of caries, with values above the national and province means. (b) The human development index is below that of the

  4. Linkage analysis excludes the glaucoma locus on 1q from involvement in autosomal dominant glaucoma with iris hypoplasia

    Energy Technology Data Exchange (ETDEWEB)

    Heon, E.; Sheth, B.P.; Kalenak, J.W. [and others

    1994-09-01

    Genetic factors have been implicated in a variety of types of glaucoma including primary open-angle glaucoma, infantile glaucoma, pigmentary glaucoma, and juvenile open-angle glaucoma. We previously mapped the disease-causing gene for one type of juvenile open angle glaucoma to chromosome 1q21-31. Weatherill and Hart (1969) and Pearce (1983) each noted the association of iris hypoplasia and early-onset autosomal dominant glaucoma. We recently had the opportunity to study a large family (12 affected members) with this phenotype. Affected individuals developed glaucoma at an average age of 30 years. These patients also have a strikingly underdeveloped iris stroma which causes a peculiar eye color. Linkage analysis was able to completely exclude the 1q glaucoma locus from involvement in the disorder that affects this family. A complete clinical description of the family and linkage results at additional candidate loci will be presented.

  5. Race, treatment preferences, and hospice enrollment. Eligibility criteria may exclude patients with the greatest needs for care

    Science.gov (United States)

    Fishman, Jessica; O'Dwyer, Peter; Lu, Hien L.; Henderson, Hope; Asch, David A.; Casarett, David J.

    2009-01-01

    Background The requirement that patients give up curative treatment makes hospice enrollment unappealing for some patients, and may particularly limit use among African American patients. Objectives To determine whether African-American patients with cancer are more likely than white patients are to have preferences for cancer treatment that exclude them from hospice, and whether they are less likely to want specific hospice services. Methods 283 patients receiving treatment for cancer at six oncology clinics within the University of Pennsylvania Cancer Network completed conjoint interviews measuring their perceived need for five hospice services and their preferences for continuing cancer treatment. Patients were followed for six months or until death. Results African American patients had stronger preferences for continuing their cancer treatments on a 7-point scale even after adjusting for age, sex, finances, education, ECOG performance status, quality of life, and physical and psychological symptom burden (adjusted means 4.75 vs. 3.96; β coefficient 0.82; 95% confidence interval 0.22-1.41; p=0.007). African-American patients also had greater perceived needs for hospice services after adjusting for these characteristics (adjusted means 2.31 vs. 1.83) (β coefficient 0.51; 95% confidence interval 0.11-0.92; p=0.01). However, this effect disappeared after adjusting for household finances. Conclusions Hospice eligibility criteria may exclude African-American patients disproportionately despite greater perceived needs for hospice services in this population. The mechanisms driving this health disparity likely include both cultural differences and economic characteristics, and consideration should be given to redesigning hospice eligibility criteria. PMID:19107761

  6. Race, treatment preferences, and hospice enrollment: eligibility criteria may exclude patients with the greatest needs for care.

    Science.gov (United States)

    Fishman, Jessica; O'Dwyer, Peter; Lu, Hien L; Henderson, Hope R; Henderson, Hope; Asch, David A; Casarett, David J

    2009-02-01

    The requirement that patients give up curative treatment makes hospice enrollment unappealing for some patients and may particularly limit use among African-American patients. The current study was conducted to determine whether African-American patients with cancer are more likely than white patients to have preferences for cancer treatment that exclude them from hospice and whether they are less likely to want specific hospice services. Two hundred eighty-three patients who were receiving treatment for cancer at 6 oncology clinics within the University of Pennsylvania Cancer Network completed conjoint interviews measuring their perceived need for 5 hospice services and their preferences for continuing cancer treatment. Patients were followed for 6 months or until death. African-American patients had stronger preferences for continuing their cancer treatments on a 7-point scale even after adjusting for age, sex, finances, education, Eastern Cooperative Oncology Group performance status, quality of life, and physical and psychologic symptom burden (adjusted mean score, 4.75 vs 3.96; beta coefficient, 0.82; 95% confidence interval, 0.22-1.41 [P = .007]). African-American patients also had greater perceived needs for hospice services after adjusting for these characteristics (adjusted mean score, 2.31 vs 1.83; beta coefficient, 0.51; 95% confidence interval, 0.11-0.92 [P = .01]). However, this effect disappeared after adjusting for household finances. Hospice eligibility criteria may exclude African-American patients disproportionately despite greater perceived needs for hospice services in this population. The mechanisms driving this health disparity likely include both cultural differences and economic characteristics, and consideration should be given to redesigning hospice eligibility criteria. (c) 2008 American Cancer Society.

  7. The accuracy of transcranial Doppler in excluding intracranial hypertension following acute brain injury: a multicenter prospective pilot study.

    Science.gov (United States)

    Rasulo, Frank A; Bertuetti, Rita; Robba, Chiara; Lusenti, Francesco; Cantoni, Alfredo; Bernini, Marta; Girardini, Alan; Calza, Stefano; Piva, Simone; Fagoni, Nazzareno; Latronico, Nicola

    2017-02-27

    Untimely diagnosis of intracranial hypertension may lead to delays in therapy and worsening of outcome. Transcranial Doppler (TCD) detects variations in cerebral blood flow velocity which may correlate with intracranial pressure (ICP). We investigated if intracranial hypertension can be accurately excluded through use of TCD. This was a multicenter prospective pilot study in patients with acute brain injury requiring invasive ICP (ICPi) monitoring. ICP estimated with TCD (ICPtcd) was compared with ICPi in three separate time frames: immediately before ICPi placement, immediately after ICPi placement, and 3 hours following ICPi positioning. Sensitivity and specificity, and concordance correlation coefficient between ICPi and ICPtcd were calculated. Receiver operating curve (ROC) and the area under the curve (AUC) analyses were estimated after measurement averaging over time. A total of 38 patients were enrolled, and of these 12 (31.6%) had at least one episode of intracranial hypertension. One hundred fourteen paired measurements of ICPi and ICPtcd were gathered for analysis. With dichotomized ICPi (≤20 mmHg vs >20 mmHg), the sensitivity of ICPtcd was 100%; all measurements with high ICPi (>20 mmHg) also had a high ICPtcd values. Bland-Altman plot showed an overestimation of 6.2 mmHg (95% CI 5.08-7.30 mmHg) for ICPtcd compared to ICPi. AUC was 96.0% (95% CI 89.8-100%) and the estimated best threshold was at ICPi of 24.8 mmHg corresponding to a sensitivity 100% and a specificity of 91.2%. This study provides preliminary evidence that ICPtcd may accurately exclude intracranial hypertension in patients with acute brain injury. Future studies with adequate power are needed to confirm this result.

  8. Infection with Strains of Citrus Tristeza Virus Does Not Exclude Superinfection by Other Strains of the Virus▿

    Science.gov (United States)

    Folimonova, Svetlana Y.; Robertson, Cecile J.; Shilts, Turksen; Folimonov, Alexey S.; Hilf, Mark E.; Garnsey, Stephen M.; Dawson, William O.

    2010-01-01

    Superinfection exclusion or homologous interference, a phenomenon in which a primary viral infection prevents a secondary infection with the same or closely related virus, has been observed commonly for viruses in various systems, including viruses of bacteria, plants, and animals. With plant viruses, homologous interference initially was used as a test of virus relatedness to define whether two virus isolates were “strains” of the same virus or represented different viruses, and subsequently purposeful infection with a mild isolate was implemented as a protective measure against isolates of the virus causing severe disease. In this study we examined superinfection exclusion of Citrus tristeza virus (CTV), a positive-sense RNA closterovirus. Thirteen naturally occurring isolates of CTV representing five different virus strains and a set of isolates originated from virus constructs engineered based on an infectious cDNA clone of T36 isolate of CTV, including hybrids containing sequences from different isolates, were examined for their ability to prevent superinfection by another isolate of the virus. We show that superinfection exclusion occurred only between isolates of the same strain and not between isolates of different strains. When isolates of the same strain were used for sequential plant inoculation, the primary infection provided complete exclusion of the challenge isolate, whereas isolates from heterologous strains appeared to have no effect on replication, movement or systemic infection by the challenge virus. Surprisingly, substitution of extended cognate sequences from isolates of the T68 or T30 strains into T36 did not confer the ability of resulting hybrid viruses to exclude superinfection by those donor strains. Overall, these results do not appear to be explained by mechanisms proposed previously for other viruses. Moreover, these observations bring an understanding of some previously unexplained fundamental features of CTV biology and, most

  9. Infection with strains of Citrus tristeza virus does not exclude superinfection by other strains of the virus.

    Science.gov (United States)

    Folimonova, Svetlana Y; Robertson, Cecile J; Shilts, Turksen; Folimonov, Alexey S; Hilf, Mark E; Garnsey, Stephen M; Dawson, William O

    2010-02-01

    Superinfection exclusion or homologous interference, a phenomenon in which a primary viral infection prevents a secondary infection with the same or closely related virus, has been observed commonly for viruses in various systems, including viruses of bacteria, plants, and animals. With plant viruses, homologous interference initially was used as a test of virus relatedness to define whether two virus isolates were "strains" of the same virus or represented different viruses, and subsequently purposeful infection with a mild isolate was implemented as a protective measure against isolates of the virus causing severe disease. In this study we examined superinfection exclusion of Citrus tristeza virus (CTV), a positive-sense RNA closterovirus. Thirteen naturally occurring isolates of CTV representing five different virus strains and a set of isolates originated from virus constructs engineered based on an infectious cDNA clone of T36 isolate of CTV, including hybrids containing sequences from different isolates, were examined for their ability to prevent superinfection by another isolate of the virus. We show that superinfection exclusion occurred only between isolates of the same strain and not between isolates of different strains. When isolates of the same strain were used for sequential plant inoculation, the primary infection provided complete exclusion of the challenge isolate, whereas isolates from heterologous strains appeared to have no effect on replication, movement or systemic infection by the challenge virus. Surprisingly, substitution of extended cognate sequences from isolates of the T68 or T30 strains into T36 did not confer the ability of resulting hybrid viruses to exclude superinfection by those donor strains. Overall, these results do not appear to be explained by mechanisms proposed previously for other viruses. Moreover, these observations bring an understanding of some previously unexplained fundamental features of CTV biology and, most

  10. The Leishmania donovani lipophosphoglycan excludes the vesicular proton-ATPase from phagosomes by impairing the recruitment of synaptotagmin V.

    Directory of Open Access Journals (Sweden)

    Adrien F Vinet

    2009-10-01

    Full Text Available We recently showed that the exocytosis regulator Synaptotagmin (Syt V is recruited to the nascent phagosome and remains associated throughout the maturation process. In this study, we investigated the possibility that Syt V plays a role in regulating interactions between the phagosome and the endocytic organelles. Silencing of Syt V by RNA interference revealed that Syt V contributes to phagolysosome biogenesis by regulating the acquisition of cathepsin D and the vesicular proton-ATPase. In contrast, recruitment of cathepsin B, the early endosomal marker EEA1 and the lysosomal marker LAMP1 to phagosomes was normal in the absence of Syt V. As Leishmania donovani promastigotes inhibit phagosome maturation, we investigated their potential impact on the phagosomal association of Syt V. This inhibition of phagolysosome biogenesis is mediated by the virulence glycolipid lipophosphoglycan, a polymer of the repeating Galbeta1,4Manalpha1-PO(4 units attached to the promastigote surface via an unusual glycosylphosphatidylinositol anchor. Our results showed that insertion of lipophosphoglycan into ganglioside GM1-containing microdomains excluded or caused dissociation of Syt V from phagosome membranes. As a consequence, L. donovani promatigotes established infection in a phagosome from which the vesicular proton-ATPase was excluded and which failed to acidify. Collectively, these results reveal a novel function for Syt V in phagolysosome biogenesis and provide novel insight into the mechanism of vesicular proton-ATPase recruitment to maturing phagosomes. We also provide novel findings into the mechanism of Leishmania pathogenesis, whereby targeting of Syt V is part of the strategy used by L. donovani promastigotes to prevent phagosome acidification.

  11. Negative D-dimer testing excludes pulmonary embolism in non-high risk patients in the emergency department.

    Science.gov (United States)

    Harringa, John B; Bracken, Rebecca L; Nagle, Scott K; Schiebler, Mark L; Pulia, Michael S; Svenson, James E; Repplinger, Michael D

    2017-06-01

    The purpose of this study was to assess the ability of d-dimer testing to obviate the need for cross-sectional imaging for patients at "non-high risk" for pulmonary embolism (PE). This is a retrospective study of emergency department patients at an academic medical center who underwent cross-sectional imaging (MRA or CTA) to evaluate for PE from 2008 to 2013. The primary outcome was the NPV of d-dimer testing when used in conjunction with clinical decision instruments (CDIs = Wells', Revised Geneva, and Simplified Revised Geneva Scores). The reference standard for PE status included image test results and a 6-month chart review follow-up for venous thromboembolism as a proxy for false negative imaging. Secondary analyses included ROC curves for each CDI and calculation of PE prevalence in each risk stratum. Of 459 patients, 41 (8.9%) had PE. None of the 76 patients (16.6%) with negative d-dimer results had PE. Thus, d-dimer testing had 100% sensitivity and NPV, and there were no differences in CDI performance. Similarly, when evaluated independently of d-dimer results, no CDI outperformed the others (areas under the ROC curves ranged 0.53-0.55). There was a significantly higher PE prevalence in the high versus "non-high risk" groups when stratified by the Wells' Score (p = 0.03). Negative d-dimer testing excluded PE in our retrospective cohort. Each CDI had similar NPVs, whether analyzed in conjunction with or independently of d-dimer results. Our results confirm that PE can be safely excluded in patients with "non-high risk" CDI scores and a negative d-dimer.

  12. HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA

    Science.gov (United States)

    Ajamian, Lara; Abel, Karen; Rao, Shringar; Vyboh, Kishanda; García-de-Gracia, Francisco; Soto-Rifo, Ricardo; Kulozik, Andreas E.; Gehring, Niels H.; Mouland, Andrew J.

    2015-01-01

    Unspliced, genomic HIV-1 RNA (vRNA) is a component of several ribonucleoprotein complexes (RNP) during the viral replication cycle. In earlier work, we demonstrated that the host upframeshift protein 1 (UPF1), a key factor in nonsense-mediated mRNA decay (NMD), colocalized and associated to the viral structural protein Gag during viral egress. In this work, we demonstrate a new function for UPF1 in the regulation of vRNA nuclear export. We establish that the nucleocytoplasmic shuttling of UPF1 is required for this function and demonstrate that UPF1 exists in two essential viral RNPs during the late phase of HIV-1 replication: the first, in a nuclear export RNP that contains Rev, CRM1, DDX3 and the nucleoporin p62, and the second, which excludes these nuclear export markers but contains Gag in the cytoplasm. Interestingly, we observed that both UPF2 and the long isoform of UPF3a, UPF3aL, but not the shorter isoforms UPF3aS and UPF3b, are excluded from the UPF1-Rev-CRM1-DDX3 complex as they are negative regulators of vRNA nuclear export. In silico protein-protein docking analyses suggest that Rev binds UPF1 in a region that overlaps the UPF2 binding site, thus explaining the exclusion of this negative regulatory factor by HIV-1 that is necessary for vRNA trafficking. This work uncovers a novel and unique regulatory circuit involving several UPF proteins that ultimately regulate vRNA nuclear export and trafficking. PMID:26492277

  13. Ion-ion correlation, solvent excluded volume and pH effects on physicochemical properties of spherical oxide nanoparticles.

    Science.gov (United States)

    Ovanesyan, Zaven; Aljzmi, Amal; Almusaynid, Manal; Khan, Asrar; Valderrama, Esteban; Nash, Kelly L; Marucho, Marcelo

    2016-01-15

    One major source of complexity in the implementation of nanoparticles in aqueous electrolytes arises from the strong influence that biological environments has on their physicochemical properties. A key parameter for understanding the molecular mechanisms governing the physicochemical properties of nanoparticles is the formation of the surface charge density. In this article, we present an efficient and accurate approach that combines a recently introduced classical solvation density functional theory for spherical electrical double layers with a surface complexation model to account for ion-ion correlation and excluded volume effects on the surface titration of spherical nanoparticles. We apply the proposed computational approach to account for the charge-regulated mechanisms on the surface chemistry of spherical silica (SiO2) nanoparticles. We analyze the effects of the nanoparticle size, as well as pH level and electrolyte concentration of the aqueous solution on the nanoparticle's surface charge density and Zeta potential. We validate our predictions for 580Å and 200Å nanoparticles immersed in acid, neutral and alkaline mono-valent aqueous electrolyte solutions against experimental data. Our results on mono-valent electrolyte show that the excluded volume and ion-ion correlations contribute significantly to the surface charge density and Zeta potential of the nanoparticle at high electrolyte concentration and pH levels, where the solvent crowding effects and electrostatic screening have shown a profound influence on the protonation/deprotonation reactions at the liquid/solute interface. The success of this approach in describing physicochemical properties of silica nanoparticles supports its broader application to study other spherical metal oxide nanoparticles. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Two CpG mutational hot spots in the X-linked interleukin-2 receptor gamma chain gene (IL2RG) may cause 15% of all human severe combined immunodeficiency

    Energy Technology Data Exchange (ETDEWEB)

    Pepper, A.E.; Puck, J.M. [National Center for Human Genome Research, Bethseda, MD (United States); Liu, X. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States)

    1994-09-01

    Severe combined immunodeficiency (SCID), a syndrome of profoundly impaired cellular and humoral immune function, is caused by various autosomal gene defects, including adenosine deaminase (ADA) deficiency, as well as mutations in the X-linked IL2RG gene encoding the gamma chain of the lymphocyte receptor for IL-2. Mutational analysis of IL2RG was performed using genomic DNA from males with SCID referred from genetics and immunology centers. Single strand conformation polymorphisms (SSCP) were sought by PCR amplification of each of the 8 IL2RG exons using labelled flanking primers. Sequence of exons with aberrant SSCP detected a majority of unique deleterious IL2RG mutations in 30 unrelated SCID patients. However, multiple mutations were seen at CpG dinucleotides, known to be C{yields}T transversion sites. cDNA 690-691 in exon 5 was mutated in 4 patients, 1 patient with each of the C{sub 690}{yields}T causing an Arg{yields}Cys substitution, and 1 with G{sub 691}{yields}A causing Arg{yields}His. Two other patients had SCID caused by a single mutation in IL2RG exon 7. This C{sub 879}{yields}T, also in a CpG, changed an Arg to STOP, resulting in loss of the SH2-related intracellular domain. In addition to our patients, 1 patient with each of the C{sub 690} and the C{sub 879} mutations have been reported by others, giving an overall incidence of 20% from our lab and 21% from all reported IL2RG SCID mutations. While ADA defects account for approximately 15% of SCID, a striking male SCID predominance suggest up to 70% of the cases are X-linked, due to IL2RG mutation. Thus, screening for mutations at the 2 CpG hot spots we have found in IL2RG can identify the genotype of as many SCID cases as are found by ADA testing.

  15. Diagnosis and prognostication of ductal adenocarcinomas of the pancreas based on genome-wide DNA methylation profiling by bacterial artificial chromosome array-based methylated CpG island amplification.

    Science.gov (United States)

    Gotoh, Masahiro; Arai, Eri; Wakai-Ushijima, Saori; Hiraoka, Nobuyoshi; Kosuge, Tomoo; Hosoda, Fumie; Shibata, Tatsuhiro; Kondo, Tadashi; Yokoi, Sana; Imoto, Issei; Inazawa, Johji; Kanai, Yae

    2011-01-01

    To establish diagnostic criteria for ductal adenocarcinomas of the pancreas (PCs), bacterial artificial chromosome (BAC) array-based methylated CpG island amplification was performed using 139 tissue samples. Twelve BAC clones, for which DNA methylation status was able to discriminate cancerous tissue (T) from noncancerous pancreatic tissue in the learning cohort with a specificity of 100%, were identified. Using criteria that combined the 12 BAC clones, T-samples were diagnosed as cancers with 100% sensitivity and specificity in both the learning and validation cohorts. DNA methylation status on 11 of the BAC clones, which was able to discriminate patients showing early relapse from those with no relapse in the learning cohort with 100% specificity, was correlated with the recurrence-free and overall survival rates in the validation cohort and was an independent prognostic factor by multivariate analysis. Genome-wide DNA methylation profiling may provide optimal diagnostic markers and prognostic indicators for patients with PCs.

  16. Diagnosis and Prognostication of Ductal Adenocarcinomas of the Pancreas Based on Genome-Wide DNA Methylation Profiling by Bacterial Artificial Chromosome Array-Based Methylated CpG Island Amplification

    Directory of Open Access Journals (Sweden)

    Masahiro Gotoh

    2011-01-01

    Full Text Available To establish diagnostic criteria for ductal adenocarcinomas of the pancreas (PCs, bacterial artificial chromosome (BAC array-based methylated CpG island amplification was performed using 139 tissue samples. Twelve BAC clones, for which DNA methylation status was able to discriminate cancerous tissue (T from noncancerous pancreatic tissue in the learning cohort with a specificity of 100%, were identified. Using criteria that combined the 12 BAC clones, T-samples were diagnosed as cancers with 100% sensitivity and specificity in both the learning and validation cohorts. DNA methylation status on 11 of the BAC clones, which was able to discriminate patients showing early relapse from those with no relapse in the learning cohort with 100% specificity, was correlated with the recurrence-free and overall survival rates in the validation cohort and was an independent prognostic factor by multivariate analysis. Genome-wide DNA methylation profiling may provide optimal diagnostic markers and prognostic indicators for patients with PCs.

  17. Hypermethylation of the 5′ CpG island of the p14ARF flanking exon 1β in human colorectal cancer displaying a restricted pattern of p53 overexpression concomitant with increased MDM2 expression

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    Nyiraneza Christine

    2012-06-01

    Full Text Available Abstract Background It has been suggested that inactivation of p14ARF, a tumor suppressor central to regulating p53 protein stability through interaction with the MDM2 oncoprotein, abrogates p53 activity in human tumors retaining the wild-type TP53 gene. Differences in expression of tumor suppressor genes are frequently associated with cancer. We previously reported on a pattern of restricted p53 immunohistochemical overexpression significantly associated with microsatellite instability (MSI, low TP53 mutation frequency, and MDM2 overexpression in colorectal cancers (CRCs. In this study, we investigated whether p14ARF alterations could be a mechanism for disabling the p53 pathway in this subgroup of CRCs. Results Detailed maps of the alterations in the p14ARF gene were determined in a cohort of 98 CRCs to detect both nucleotide and copy-number changes. Methylation-specific PCR combined with bisulfite sequencing was used to evaluate the prevalence and distribution of p14ARF methylation. p14ARF alterations were then correlated with MSI status, TP53 mutations, and immunohistochemical expression of p53 and MDM2. The frequency of p14ARF mutations was extremely low (1/98; 1%, whereas coexistence of methylated and unmethylated alleles in both tumors and normal colon mucosa was common (91/98; 93%. Only seven of ninety-eight tumors (7% had a distinct pattern of methylation compared with normal colon mucosa. Evaluation of the prevalence and distribution of p14ARF promoter methylation in a region containing 27 CpG sites in 35 patients showed a range of methylated CpG sites in tumors (0 to 25 (95% CI 1 to 13 versus 0 to 17 (95% CI 0 to 2 in adjacent colon mucosa (P = 0.004. Hypermethylation of the p14ARF promoter was significantly correlated with the restricted p53 overexpression pattern (P = 0.03, and MDM2 overexpression (P = 0.02, independently of MSI phenotype. Although no significant correlation between p14ARF methylation and TP53 mutational

  18. Cost-effectiveness analysis of therapies for chronic kidney disease patients on dialysis: a case for excluding dialysis costs.

    Science.gov (United States)

    Grima, Daniel T; Bernard, Lisa M; Dunn, Elizabeth S; McFarlane, Philip A; Mendelssohn, David C

    2012-11-01

    In many jurisdictions, cost-effectiveness analysis (CEA) plays an important role in determining drug coverage and reimbursement and, therefore, has the potential to impact patient access. Health economic guidelines recommend the inclusion of future costs related to the intervention of interest within CEAs but provide little guidance regarding the definition of 'related'. In the case of CEAs of therapies that extend the lives of patients with chronic kidney disease (CKD) on dialysis but do not impact the need for or the intensity of dialysis, the determination of the relatedness of future dialysis costs to the therapy of interest is particularly ambiguous. The uncertainty as to whether dialysis costs are related or unrelated in these circumstances has led to inconsistencies in the conduct of CEAs for such products, with dialysis costs included in some analyses while excluded in others. Due to the magnitude of the cost of dialysis, whether or not dialysis costs are included in CEAs of such therapies has substantial implications for the results of such analyses, often meaning the difference between a therapy being deemed cost effective (in instances where dialysis costs are excluded) or not cost effective (in instances where dialysis costs are included). This paper explores the issues and implications surrounding the inclusion of dialysis costs in CEAs of therapies that extend the lives of dialysis patients but do not impact the need for dialysis. Relevant case studies clearly demonstrate that, regardless of the clinical benefits of a life-extending intervention for dialysis patients, and due to the high cost of dialysis, the inclusion of dialysis costs in the analysis essentially eliminates the possibility of obtaining a favourable cost-effectiveness ratio. This raises the significant risk that dialysis patients may be denied access to interventions that are cost effective in other populations due solely to the high background cost of dialysis itself. Finally, the

  19. Modulation of single-cell IgG secretion frequency and rates in human memory B cells by CpG DNA, CD40L, IL-21, and cell division.

    Science.gov (United States)

    Henn, Alicia D; Rebhahn, Jonathan; Brown, Miguel A; Murphy, Alison J; Coca, Mircea N; Hyrien, Ollivier; Pellegrin, Tina; Mosmann, Tim; Zand, Martin S

    2009-09-01

    During the recall response by CD27(+) IgG class-switched human memory B cells, total IgG secreted is a function of the following: 1) the number of IgG-secreting cells (IgG-SC), and 2) the secretion rate of each cell. In this study, we report the quantitative ELISPOT method for simultaneous estimation of single-cell IgG secretion rates and secreting cell frequencies in human B cell populations. We found that CD27(+) IgM(-) memory B cells activated with CpG and cytokines had considerable heterogeneity in the IgG secretion rates, with two major secretion rate subpopulations. BCR cross-linking reduced the frequency of cells with high per-cell IgG secretion rates, with a parallel decrease in CD27(high) B cell blasts. Increased cell death may account for the BCR-stimulated reduction in high-rate IgG-SC CD27(high) B cell blasts. In contrast, the addition of IL-21 to CD40L plus IL-4-activated human memory B cells induced a high-rate IgG-SC population in B cells with otherwise low per-cell IgG secretion rates. The profiles of human B cell IgG secretion rates followed the same biphasic distribution and range irrespective of division class. This, along with the presence of non-IgG-producing, dividing B cells in CpG plus cytokine-activated B memory B cell populations, is suggestive of an on/off switch regulating IgG secretion. Finally, these data support a mixture model of IgG secretion in which IgG secreted over time is modulated by the frequency of IgG-SC and the distribution of their IgG secretion rates.

  20. Ubiquitous expression of the rtTA2S-M2 inducible system in transgenic mice driven by the human hnRNPA2B1/CBX3 CpG island

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    Antoniou Michael

    2007-09-01

    Full Text Available Abstract Background A sensitive, ubiquitously expressed tetracycline inducible system would be a valuable tool in mouse transgenesis. However, this has been difficult to obtain due to position effects observed at different chromosomal sites of transgene integration, which negatively affect expression in many tissues. The aim of this study was to test the utility of a mammalian methylation-free CpG island to drive ubiquitous expression of the sensitive doxycycline (Dox inducible rtTA2S-M2 Tet-transactivator in transgenic mice. Results An 8 kb genomic fragment from the methylation-free CpG island of the human hnRNPA2B1-CBX3 housekeeping gene locus was tested. In a number of transgenic mouse lines obtained, rtTA2S-M2 expression was detected in many tissues examined. Characterisation of the highest expressing rtTA2S-M2 transgenic mouse line demonstrated Dox-inducible GFP transgene expression in many tissues. Using this line we also show highly sensitive quantitative induction with low doses of Dox of an assayable plasma protein transgene under the control of a Tet Responsive Element (TRE. The utility of this rtTA2S-M2 line for inducible expression in mouse embryos was also demonstrated using a GATA-6 Tet-inducible transgene to show specific phenotypes in the embryonic lung, as well as broader effects resulting from the inducible widespread overexpression of the transgene. Conclusion The ubiquitously expressing rtTA2S-M2 transgenic mouse line described here provides a very useful tool for studying the effects of the widespread, inducible overexpression of genes during embryonic development and in adult mice.

  1. Percepção e processamento visual da forma em humanos: filtros de freqüências radiais de 1 e 4 cpg Perception and visual processing of form in humans: radial frequency filters of 1 and 4 cpd

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    Natanael Antonio dos Santos

    2002-01-01

    Full Text Available O objetivo deste trabalho foi mensurar curvas de resposta ao contraste para os filtros de freqüências radiais de banda estreita de 1 e 4 cpg para padrões espaciais modulados pela função cilíndrica de Bessel (J0. Foram estimadas 15 curvas para cada filtro com o paradigma psicofísico de somação de resposta de supra-limiar aliado ao procedimento da escolha forçada. Participaram deste experimento 5 voluntários adultos com acuidade visual normal ou corrigida. Os resultados demonstraram somações máximas de limiar de contraste na freqüência de teste dos filtros de 1 e 4 cpg circundadas por inibições nas freqüências vizinhas às freqüências radiais de teste de cada filtro. Estes resultados são consistentes com a existência de filtros de freqüências radiais de banda estreita operando no sistema visual humano através do processo de somação ou inibição em faixa de freqüências específicas.The aim of this work was to measure narrow-band frequency response curves for two radial frequency filters, spatial stimuli modulated by cylindrical Bessel profiles, J0, whose test frequencies were 1 and 4 cpd. Five humans observers with normal or corrected visual acuity measured 15 curves for each filter with a supra-threshold response summation psychophysics method allied within a forced-choice paradigm. The results showed maximum summation effects at test frequency for filters 1 and 4 cpd surrounded on both sides by strong inhibition. These results are consistent with the existence of narrow-band radial frequency filters operating in human visual system either through summation or inhibition of specific frequency ranges.

  2. Relatively high rates of G:C → A:T transitions at CpG sites were observed in certain epithelial tissues including pancreas and submaxillary gland of adult big blue® mice.

    Science.gov (United States)

    Prtenjaca, Anita; Tarnowski, Heather E; Marr, Alison M; Heney, Melanie A; Creamer, Laura; Sathiamoorthy, Sarmitha; Hill, Kathleen A

    2014-01-01

    With few exceptions, spontaneous mutation frequency and pattern are similar across tissue types and relatively constant in young to middle adulthood in wild type mice. Underrepresented in surveys of spontaneous mutations across murine tissues is the diversity of epithelial tissues. For the first time, spontaneous mutations were detected in pancreas and submaxillary gland and compared with kidney, lung, and male germ cells from five adult male Big Blue® mice. Mutation load was assessed quantitatively through measurement of mutant and mutation frequency and qualitatively through identification of mutations and characterization of recurrent mutations, multiple mutations, mutation pattern, and mutation spectrum. A total of 9.6 million plaque forming units were screened, 226 mutants were collected, and 196 independent mutations were identified. Four novel mutations were discovered. Spontaneous mutation frequency was low in pancreas and high in the submaxillary gland. The submaxillary gland had multiple recurrent mutations in each of the mice and one mutant had two independent mutations. Mutation patterns for epithelial tissues differed from that observed in male germ cells with a striking bias for G:C to A:T transitions at CpG sites. A comprehensive review of lacI spontaneous mutation patterns in young adult mice and rats identified additional examples of this mutational bias. An overarching observation about spontaneous mutation frequency in adult tissues of the mouse remains one of stability. A repeated observation in certain epithelial tissues is a higher rate of G:C to A:T transitions at CpG sites and the underlying mechanisms for this bias are not known. Copyright © 2013 Wiley Periodicals, Inc.

  3. “Not Designed for Us”: How Science Museums and Science Centers Socially Exclude Low-Income, Minority Ethnic Groups

    Science.gov (United States)

    Dawson, Emily

    2014-01-01

    This paper explores how people from low-income, minority ethnic groups perceive and experience exclusion from informal science education (ISE) institutions, such as museums and science centers. Drawing on qualitative data from four focus groups, 32 interviews, four accompanied visits to ISE institutions, and field notes, this paper presents an analysis of exclusion from science learning opportunities during visits alongside participants’ attitudes, expectations, and conclusions about participation in ISE. Participants came from four community groups in central London: a Sierra Leonean group (n = 21), a Latin American group (n = 18), a Somali group (n = 6), and an Asian group (n = 13). Using a theoretical framework based on the work of Bourdieu, the analysis suggests ISE practices were grounded in expectations about visitors’ scientific knowledge, language skills, and finances in ways that were problematic for participants and excluded them from science learning opportunities. It is argued that ISE practices reinforced participants preexisting sense that museums and science centers were “not for us.” The paper concludes with a discussion of the findings in relation to previous research on participation in ISE and the potential for developing more inclusive informal science learning opportunities. PMID:25574059

  4. Fragmented red blood cells automated measurement is a useful parameter to exclude schistocytes on the blood film.

    Science.gov (United States)

    Lesesve, J-F; Asnafi, V; Braun, F; Zini, G

    2012-12-01

      The diagnosis of thrombotic microangiopathies (TMA) or disorders that may mimic their features remains difficult. Mechanical hemolytic anemia with the detection of shistocytes on the blood smear is a cornerstone finding to assess the diagnosis, but microscopic evaluation of shistocytes is still problematic with wide interobserver variations. Some of the latest generation automated blood cell counters (ABCC) propose an original quantitative approach of fragmented red cells (FRC), aiming to be equivalent to the microscopic count. This parameter has been poorly evaluated.   To assess the predictive value (PV) of this test, we conducted studies comparing automated and microscopic counts of FRC/schistocytes, based on the analysis of thousands samples in four university hospitals and using the 2 ABCC currently available (Siemens ADVIA series, Sysmex XE-2100). Reference range for FRC was blood smear, but in relationship with a poor PV value. Our study validated the utility of the immediately available FRC parameter on ABCC to exclude schistocytes and the diagnosis of TMA. © 2012 Blackwell Publishing Ltd.

  5. Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: Theory, simulations, and experiments

    Energy Technology Data Exchange (ETDEWEB)

    Ovanesyan, Zaven; Marucho, Marcelo, E-mail: marcelo.marucho@utsa.edu [Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas 78249-5003 (United States); Medasani, Bharat [Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas 78249-5003 (United States); Computational Research Division, Lawrence Berkeley National Lab, Berkeley, California 94700 (United States); Fenley, Marcia O. [Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306 (United States); Guerrero-García, Guillermo Iván [Instituto de Física, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000 San Luis Potosí, San Luis Potosí (Mexico); Department of Chemistry and Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Olvera de la Cruz, Mónica [Department of Chemistry and Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States)

    2014-12-14

    The ionic atmosphere around a nucleic acid regulates its stability in aqueous salt solutions. One major source of complexity in biological activities involving nucleic acids arises from the strong influence of the surrounding ions and water molecules on their structural and thermodynamic properties. Here, we implement a classical density functional theory for cylindrical polyelectrolytes embedded in aqueous electrolytes containing explicit (neutral hard sphere) water molecules at experimental solvent concentrations. Our approach allows us to include ion correlations as well as solvent and ion excluded volume effects for studying the structural and thermodynamic properties of highly charged cylindrical polyelectrolytes. Several models of size and charge asymmetric mixtures of aqueous electrolytes at physiological concentrations are studied. Our results are in good agreement with Monte Carlo simulations. Our numerical calculations display significant differences in the ion density profiles for the different aqueous electrolyte models studied. However, similar results regarding the excess number of ions adsorbed to the B-DNA molecule are predicted by our theoretical approach for different aqueous electrolyte models. These findings suggest that ion counting experimental data should not be used alone to validate the performance of aqueous DNA-electrolyte models.

  6. Rejected and excluded forevermore, but even more devoted: irrevocable ostracism intensifies loyalty to the group among identity-fused persons.

    Science.gov (United States)

    Gómez, Angel; Morales, J Francisco; Hart, Sonia; Vázquez, Alexandra; Swann, William B

    2011-12-01

    When people are ostrasized (i.e., rejected and excluded) by either an outgroup or an ingroup, they may either withdraw or engage in compensatory activities designed to reaffirm their social identity as a group member. The authors proposed here that individual differences in identity fusion (an index of familial orientation toward the group) would moderate the tendency for people to display such compensatory activity. Consistent with this reasoning, the results of four experiments showed that irrevocable ostracism increased endorsement of extreme, pro-group actions (fighting and dying for the ingroup) among fused persons but not among nonfused persons. This effect emerged when an outgroup ostracized fused individuals due either to their nationality (Experiment 1) or their personal preferences (Experiment 2). Similarly, ostracism by the ingroup amplified the tendency for fused persons to both endorse extreme pro-group actions, refuse to leave the group (Experiment 3), and donate money to an ingroup member (Experiment 4). Finally, compensatory activities emerged even when ostracism was based on being "too good" for the group, suggesting that a desire for self-enhancement does not mediate such activities (Experiment 4).

  7. [Diagnosis and management of acquired immune haemolytic anaemia excluding neoplasia. Adequacy with the current guidelines published in 2009].

    Science.gov (United States)

    Lauda-Maillen, M; Catroux, M; Roy-Peaud, F; Souchaud-Debouverie, O; El Masmouhi, B; Roblot, P

    2017-10-01

    Describe the management of Acquired Immune Haemolytic Anaemia (AIHA) and correlate with the current guidelines published in 2009. The secondary objective was to calculate the positive predictive value of the Direct Antiglobulin Test (DAT) for the diagnosis of AIHA. A retrospective and monocentric study was performed from 2010 to 2015 based on positive DATs, identified in the French Blood Agency database or in medical files. All patients managed for initial diagnosis or relapse of AIHA were included, excluding neoplasia. Six hundred and twenty-three patients had a positive DAT, 42 had non-neoplastic AIHA. Thirty-nine patients were included, 32 had warm antibodies, 5 had a negative DAT and 2 had cold antibodies. No cause was found for 46% (17/37) of the warm antibody and negative DATs AIHAs. Autoimmune disease was found in 11 cases (30%), infection in 4 cases (11%). The etiologic investigations were consistent with the guidelines in 49% of cases. Corticosteroids were first prescribed, as recommended. Second-line treatments were rituximab in 9 cases, splenectomy in 4 cases and azathioprine in 3 cases. The management of cold antibody AIHA complied with the guidelines. The positive predictive value of DATs in hospitalized population was of 14% (85/610). AIHA guidelines seem insufficiently applied in our center. Copyright © 2017 Société Nationale Française de Médecine Interne (SNFMI). Published by Elsevier SAS. All rights reserved.

  8. Commentary: is totipotency of a human cell a sufficient reason to exclude its patentability under the European law?

    Science.gov (United States)

    Vrtovec, Katja Triller; Vrtovec, Bojan

    2007-12-01

    This article argues that totipotent character of human totipotent cells--defined as the capacity of a cell "to differentiate into all somatic lineages (ectoderm, mesoderm, endoderm), the germ line and extra-embryonic tissues such as the placenta"--is not a sufficient reason to exclude their patentability on the basis of Article 5(1) of the Directive 98/44/EC on the Legal Protection of Biotechnological Inventions (Biopatent Directive), which maintains that "the human body, at the various stages of its formation and development, [...] cannot constitute patentable inventions." Since human totipotent cells have both the potential to generate an entire new organism or to generate only different tissues or organs of an organism, they simultaneously fit the definition of the unpatentable human body at the earliest stage of its formation as well as of an element of the human body, which "may constitute a patentable invention" pursuant to Article 5(2) of the Biopatent Directive, whether that element is isolated from the human body or otherwise produced by means of a technical process. Therefore, this article suggests that, when evaluating patentability of human totipotent cells, they should be further evaluated according to their location and their method of derivation (i.e., whether human totipotent cells are located in the human body, whether they are isolated from the human body, or whether they are produced otherwise by means of a technical process). Disclosure of potential conflicts of interest is found at the end of this article.

  9. In a long-term experimental demography study, excluding ungulates reversed invader's explosive population growth rate and restored natives

    Science.gov (United States)

    Kalisz, Susan; Spigler, Rachel B.; Horvitz, Carol C.

    2014-01-01

    A major goal in ecology is to understand mechanisms that increase invasion success of exotic species. A recent hypothesis implicates altered species interactions resulting from ungulate herbivore overabundance as a key cause of exotic plant domination. To test this hypothesis, we maintained an experimental demography deer exclusion study for 6 y in a forest where the native ungulate Odocoileus virginianus (white-tailed deer) is overabundant and Alliaria petiolata (garlic mustard) is aggressively invading. Because population growth is multiplicative across time, we introduce metrics that correctly integrate experimental effects across treatment years, the cumulative population growth rate, λc, and its geometric mean, λper-year, the time-averaged annual population growth rate. We determined λc and λper-year of the invader and of a common native, Trillium erectum. Our results conclusively demonstrate that deer are required for the success of Alliaria; its projected population trajectory shifted from explosive growth in the presence of deer (λper-year = 1.33) to decline toward extinction where deer are excluded (λper-year = 0.88). In contrast, Trillium’s λper-year was suppressed in the presence of deer relative to deer exclusion (λper-year = 1.04 vs. 1.20, respectively). Retrospective sensitivity analyses revealed that the largest negative effect of deer exclusion on Alliaria came from rosette transitions, whereas the largest positive effect on Trillium came from reproductive transitions. Deer exclusion lowered Alliaria density while increasing Trillium density. Our results provide definitive experimental support that interactions with overabundant ungulates enhance demographic success of invaders and depress natives’ success, with broad implications for biodiversity and ecosystem function worldwide. PMID:24616522

  10. How accurate is ultrasound of the optic nerve sheath diameter performed by inexperienced operators to exclude raised intracranial pressure?

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    G. J. du Toit

    2015-03-01

    Full Text Available Background: It has been well documented that ultrasound measurement of the optic nerve sheath diameter performed by an experienced operator shows good correlation with raised intracranial pressure, irrespective of the cause. Objective: To establish the accuracy of this technique performed by inexperienced operators.Method: A prospective analytical cross-sectional study was conducted. All patients ≥18 years of age who presented at our medical casualty and emergency departments with suspected meningitis were enrolled in the study. All patients were evaluated with the use of optic nerve sheath diameter ultrasound with or without computed tomography brain scan prior to lumbar puncture. Lumbar puncture opening pressure measurements were compared with the ultrasound measurements.Results: A total of 73 patients were enrolled in the study, of whom 14 had raised intracranial pressure. The study had a sensitivity of 50% (95% confidence interval (CI 26.8%–73.2% and specificity of 89.8% (95% CI 79.5%–95.3% with a positive predictive value of 54.8% (95% CI 29.1%–76.8% and negative predictive value of 88.3% (95% CI 77.8%–94.2%. The likelihood ratio of a positive test was 4.92 (95% CI 1.95–11.89 and that of a negative test 0.56 (95% CI 0.29–0.83. Cohen’s kappa value was 0.41 which indicates a moderate agreement. The receiver operating characteristic (ROC curve had an area under the curve (AUC of 0.73 (95% CI 0.51–0.95. Conclusion: Ultrasound measurement of the optic nerve sheath diameter can be used to exclude raised intracranial pressure, even in the hands of inexperienced operators.

  11. Alternative preparation of inclusion bodies excludes interfering non-protein contaminants and improves the yield of recombinant proinsulin.

    Science.gov (United States)

    Mackin, Robert B

    2014-01-01

    The goal of simple, high-yield expression and purification of recombinant human proinsulin has proven to be a considerable challenge. First, proinsulin forms inclusion bodies during bacterial expression. While this phenomenon can be exploited as a capture step, conventionally prepared inclusion bodies contain significant amounts of non-protein contaminants that interfere with subsequent chromatographic purification. Second, the proinsulin molecules within the inclusion bodies are incorrectly folded, and likely cross-linked to one another, making it difficult to quantify the amount of expressed proinsulin. Third, proinsulin is an intermediate between the initial product of ribosomal translation (preproinsulin) and the final product secreted by pancreatic beta cells (insulin). Therefore, to be efficiently produced in bacteria, it must be produced as an N-terminally extended fusion protein, which has to be converted to authentic proinsulin during the purification scheme. To address all three of these problems, while simultaneously streamlining the procedure and increasing the yield of recombinant proinsulin, we have made three substantive modifications to our previous method for producing proinsulin:.•Conditions for the preparation of inclusion bodies have been altered so contaminants that interfere with semi-preparative reversed-phase chromatography are excluded while the proinsulin fusion protein is retained at high yield.•Aliquots are taken following important steps in the procedure and the quantity of proinsulin-related polypeptide in the sample is compared to the amount present prior to that step.•Final purification is performed using a silica-based reversed-phase matrix in place of a polystyrene-divinylbenzene-based matrix.

  12. Aspects concerning the lengths of the excluded shareholder’s liability towards third parties in the case of limited liability companies in Romania

    Directory of Open Access Journals (Sweden)

    Andreea Stoican

    2016-06-01

    Full Text Available In the current context of reinventing the trading company law, at the end of a lengthy and extremely difficult economic crisis, when every participant in the economic life tried to find their own way to adapt and make their activity survive the new social and commercial realities, not few were the cases when some of the Shareholders were excluded and their liability was drawn onto the legal person itself. Nevertheless, there is a type of legal liability of the former Shareholders, excluded from the Company, that still is quite deficiently regulated and, despite the sound argumentation and comprehensive regulation of Law no. 31/1990, it fails to provide a clear and detailed explanation of the consequences, namely, of the consequences the exclusion of a Shareholder has over the Third Parties of good-faith that the legal person (the Company had or continues to have legal relations with. This paper thus aims at analysing one of the main effects of excluding Shareholders from the company, namely the extent of their liability towards the Third Parties, and it is structured in five parts, as follows: 1 Introduction, 2 About the Shareholders’ exclusion, 3 The effects of excluding a Shareholder from the Limited Liability Company, 4 The excluded Shareholder’s liability towards the Third Parties and 5 Conclusions.

  13. National review of use of extracorporeal membrane oxygenation as respiratory support in thoracic surgery excluding lung transplantation.

    Science.gov (United States)

    Rinieri, Philippe; Peillon, Christophe; Bessou, Jean-Paul; Veber, Benoît; Falcoz, Pierre-Emmanuel; Melki, Jean; Baste, Jean-Marc

    2015-01-01

    Extracorporeal membrane oxygenation (ECMO) for respiratory support is increasingly used in intensive care units (ICU), but rarely during thoracic surgical procedures outside the transplantation setting. ECMO can be an alternative to cardiopulmonary bypass for major trachea-bronchial surgery and single-lung procedures without in-field ventilation. Our aim was to evaluate the intraoperative use of ECMO as respiratory support in thoracic surgery: benefits, indications and complications. This was a multicentre retrospective study (questionnaire) of use of ECMO as respiratory support during the thoracic surgical procedure. Lung transplantation and lung resection for tumour invading the great vessels and/or the left atrium were excluded, because they concern respiratory and circulatory support. From March 2009 to September 2012, 17 of the 34 centres in France applied ECMO within veno-venous (VV) (n=20) or veno-arterial (VA) (n=16) indications in 36 patients. Ten VA ECMO were performed with peripheral cannulation and 6 with central cannulation; all VV ECMO were achieved through peripheral cannulation. Group 1 (total respiratory support) was composed of 28 patients without mechanical ventilation, involving 23 tracheo-bronchial and 5 single-lung procedures. Group 2 (partial respiratory support) was made up of 5 patients with respiratory insufficiency. Group 3 was made up of 3 patients who underwent thoracic surgery in a setting of acute respiratory distress syndrome (ARDS) with preoperative ECMO. Mortality at 30 days in Groups 1, 2 and 3 was 7, 40 and 67%, respectively (PECMO was weaned intraoperatively or within 24 h in 75% of patients. In Group 2, ECMO was weaned in ICU over several days. In Group 1, 2 patients with VA support were converted to VV support for chronic respiratory indications. Bleeding was the major complication with 17% of patients requiring return to theatre for haemostasis. There were two cannulation-related complications (6%). VV or VA ECMO is a

  14. NIKEI: a new inexpensive and non-invasive scoring system to exclude advanced fibrosis in patients with NAFLD.

    Directory of Open Access Journals (Sweden)

    Münevver Demir

    Full Text Available AIMS: To develop, validate and compare a non-invasive fibrosis scoring system for non-alcoholic fatty liver disease (NAFLD derived from routinely obtained clinical and biochemical parameters. METHODS: 267 consecutive patients with biopsy proven fatty liver or non-alcoholic steatohepatitis were randomly assigned to the estimation (2/3 or validation (1/3 group to develop a model for the prediction of advanced fibrosis. Univariate statistics were performed to compare patients with and without advanced fibrosis, and following a multivariate logistic regression analysis a new scoring system was constructed. This non-invasive Koeln-Essen-index (NIKEI was validated and compared to the FIB-4 index by calculating the area under the receiver operating characteristic curve (AUC. We evaluated a stepwise combination of both scoring systems for the precise prediction of advanced fibrosis. To set in contrast, we additionally tested the diagnostic accuracy of the AST/ALT ratio, BARD score and the NAFLD fibrosis score in our cohort. RESULTS: Age, AST, AST/ALT ratio, and total bilirubin were identified as significant predictors of advanced fibrosis and used to construct the NIKEI with an AUC of 0.968 [0.937; 0.998] compared to 0.929 [0.869; 0.989] for the FIB-4 index. The absence of advanced fibrosis could be confirmed with excellent accuracy (99-100%. The positive predictive value of the FIB-4 index was higher (100% vs. 60%, however, the false negative rate was also high (33%. With a stepwise combination of both indices 82%-84% of biopsies would have been avoidable without a single misclassification. The AUROC for AST/ALT ratio, the NAFLD fibrosis score, and the BARD score were 0.81 (95% CI, 0.72-0.90, 0.96 (95% CI 0.92-0.99, and 0.67 (95% CI 0.55-0.78, respectively. CONCLUSION: The NIKEI can reliably exclude advanced fibrosis in subjects with NAFLD. In combination with the FIB-4 index misclassification with inadequate clinical management can be avoided while

  15. Surgical management for the first 48 h following blunt chest trauma: state of the art (excluding vascular injuries).

    Science.gov (United States)

    de Lesquen, Henri; Avaro, Jean-Philippe; Gust, Lucile; Ford, Robert Michael; Beranger, Fabien; Natale, Claudia; Bonnet, Pierre-Mathieu; D'Journo, Xavier-Benoît

    2015-03-01

    This review aims to answer the most common questions in routine surgical practice during the first 48 h of blunt chest trauma (BCT) management. Two authors identified relevant manuscripts published since January 1994 to January 2014. Using preferred reporting items for systematic reviews and meta-analyses statement, they focused on the surgical management of BCT, excluded both child and vascular injuries and selected 80 studies. Tension pneumothorax should be promptly diagnosed and treated by needle decompression closely followed with chest tube insertion (Grade D). All traumatic pneumothoraces are considered for chest tube insertion. However, observation is possible for selected patients with small unilateral pneumothoraces without respiratory disease or need for positive pressure ventilation (Grade C). Symptomatic traumatic haemothoraces or haemothoraces >500 ml should be treated by chest tube insertion (Grade D). Occult pneumothoraces and occult haemothoraces are managed by observation with daily chest X-rays (Grades B and C). Periprocedural antibiotics are used to prevent chest-tube-related infectious complications (Grade B). No sign of life at the initial assessment and cardiopulmonary resuscitation duration >10 min are considered as contraindications of Emergency Department Thoracotomy (Grade C). Damage Control Thoracotomy is performed for either massive air leakage or refractive shock or ongoing bleeding enhanced by chest tube output >1500 ml initially or >200 ml/h for 3 h (Grade D). In the case of haemodynamically stable patients, early video-assisted thoracic surgery is performed for retained haemothoraces (Grade B). Fixation of flail chest can be considered if mechanical ventilation for 48 h is probably required (Grade B). Fixation of sternal fractures is performed for displaced fractures with overlap or comminution, intractable pain or respiratory insufficiency (Grade D). Lung herniation, traumatic diaphragmatic rupture and pericardial rupture are life

  16. Successful off-label use of the GORE EXCLUDER Iliac Branch Endoprosthesis to preserve gluteal perfusion during staged endovascular repair of bilateral isolated hypogastric aneurysms

    Directory of Open Access Journals (Sweden)

    James W. Cornwall, MD

    2017-03-01

    Full Text Available Endovascular repair of iliac artery aneurysms has emerged as an alternative to traditional open surgical repair. Although there is little consensus on indications to preserve hypogastric blood flow during aneurysm repair, it is well understood that complications from bilateral hypogastric occlusion may be significant. The GORE EXCLUDER Iliac Branch Endoprosthesis (W. L. Gore and Associates, Flagstaff, Ariz received United States Food and Drug Administration approval in March 2016 for treatment of common iliac artery and aortoiliac aneurysms. This case report discusses an off-label use of GORE EXCLUDER Iliac Branch Endoprosthesis to maintain pelvic perfusion during treatment of bilateral internal iliac artery aneurysms without surrounding aortoiliac pathology.

  17. Diagnostic performance of computed tomography coronary angiography to detect and exclude left main and/or three-vessel coronary artery disease

    DEFF Research Database (Denmark)

    Dharampal, Anoeshka S; Papadopoulou, Stella L; Rossi, Alexia

    2013-01-01

    To determine the diagnostic performance of CT coronary angiography (CTCA) in detecting and excluding left main (LM) and/or three-vessel CAD ("high-risk" CAD) in symptomatic patients and to compare its discriminatory value with the Duke risk score and calcium score.......To determine the diagnostic performance of CT coronary angiography (CTCA) in detecting and excluding left main (LM) and/or three-vessel CAD ("high-risk" CAD) in symptomatic patients and to compare its discriminatory value with the Duke risk score and calcium score....

  18. Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides

    Directory of Open Access Journals (Sweden)

    Cooper David N

    2010-08-01

    Full Text Available Abstract The cytosine-guanine (CpG dinucleotide has long been known to be a hotspot for pathological mutation in the human genome. This hypermutability is related to its role as the major site of cytosine methylation with the attendant risk of spontaneous deamination of 5-methylcytosine (5mC to yield thymine. Cytosine methylation, however, also occurs in the context of CpNpG sites in the human genome, an unsurprising finding since the intrinsic symmetry of CpNpG renders it capable of supporting a semi-conservative model of replication of the methylation pattern. Recently, it has become clear that significant DNA methylation occurs in a CpHpG context (where H = A, C or T in a variety of human somatic tissues. If we assume that CpHpG methylation also occurs in the germline, and that 5mC deamination can occur within a CpHpG context, then we might surmise that methylated CpHpG sites could also constitute mutation hotspots causing human genetic disease. To test this postulate, 54,625 missense and nonsense mutations from 2,113 genes causing inherited disease were retrieved from the Human Gene Mutation Database http://www.hgmd.org. Some 18.2 per cent of these pathological lesions were found to be C → T and G → A transitions located in CpG dinucleotides (compatible with a model of methylation-mediated deamination of 5mC, an approximately ten-fold higher proportion than would have been expected by chance alone. The corresponding proportion for the CpHpG trinucleotide was 9.9 per cent, an approximately two-fold higher proportion than would have been expected by chance. We therefore estimate that ~5 per cent of missense/nonsense mutations causing human inherited disease may be attributable to methylation-mediated deamination of 5mC within a CpHpG context.

  19. 2 CFR 3700.137 - Who in the Peace Corps may grant an exception to let an excluded person participate in a covered...

    Science.gov (United States)

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false Who in the Peace Corps may grant an... and Agreements Federal Agency Regulations for Grants and Agreements PEACE CORPS NONPROCUREMENT DEBARMENT AND SUSPENSION § 3700.137 Who in the Peace Corps may grant an exception to let an excluded person...

  20. 26 CFR 1.955A-1 - Shareholder's pro rata share of amount of previously excluded subpart F income withdrawn from...

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 10 2010-04-01 2010-04-01 false Shareholder's pro rata share of amount of... rata share of amount of previously excluded subpart F income withdrawn from investment in foreign base... foreign corporation must include in his gross income his pro rata share of such amount as determined in...

  1. Qualitative point-of-care D-dimer testing compared with quantitative D-dimer testing in excluding pulmonary embolism in primary care

    NARCIS (Netherlands)

    Lucassen, W. A M; Erkens, P. M G; Geersing, G. J.; Büller, H. R.; Moons, K. G M; Stoffers, H. E J H; van Weert, H. C P M

    2015-01-01

    Background: General practitioners can safely exclude pulmonary embolism (PE) by using the Wells PE rule combined with D-dimer testing. Objective: To compare the accuracy of a strategy using the Wells rule combined with either a qualitative point-of-care (POC) D-dimer test performed in primary care

  2. 24 CFR 203.18c - One-time or up-front mortgage insurance premium excluded from limitations on maximum mortgage...

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false One-time or up-front mortgage...-front mortgage insurance premium excluded from limitations on maximum mortgage amounts. After... amount of any mortgage may be increased by the amount of any one-time or up-front mortgage insurance...

  3. Revision of the Platystictidae of the Philippines (Odonata), excluding the Drepanosticta halterata group, with descriptions of twenty-one new species

    NARCIS (Netherlands)

    Tol, van J.

    2005-01-01

    Thirty-one species of the family Platystictidae of the Philippines are revised, i.e. all species recognised, excluding the species of the Drepanosticta halterata-group. The following new taxa are described: 16 species in Drepanosticta Laidlaw: D. acuta spec. nov., D. aurita spec. nov., D.

  4. 41 CFR 105-68.415 - What must I do if a Federal agency excludes the participant or a principal after I enter into a...

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What must I do if a Federal agency excludes the participant or a principal after I enter into a covered transaction? 105-68.415 Section 105-68.415 Public Contracts and Property Management Federal Property Management Regulations System (Continued) GENERAL SERVICES...

  5. 29 CFR 98.415 - What must I do if a Federal agency excludes the participant or a principal after I enter into a...

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true What must I do if a Federal agency excludes the participant or a principal after I enter into a covered transaction? 98.415 Section 98.415 Labor Office of the Secretary of Labor GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) Responsibilities of Department of Labor Officials Regarding Transactions §...

  6. 41 CFR 105-68.310 - What must I do if a Federal agency excludes a person with whom I am already doing business in a...

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What must I do if a Federal agency excludes a person with whom I am already doing business in a covered transaction? 105-68.310 Section 105-68.310 Public Contracts and Property Management Federal Property Management Regulations System (Continued) GENERAL SERVICES...

  7. 29 CFR 98.310 - What must I do if a Federal agency excludes a person with whom I am already doing business in a...

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true What must I do if a Federal agency excludes a person with whom I am already doing business in a covered transaction? 98.310 Section 98.310 Labor Office of the Secretary of Labor GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) Responsibilities of Participants Regarding Transactions Doing Business wit...

  8. Performance of a checklist to exclude pregnancy at the time of contraceptive initiation among women with a negative urine pregnancy test.

    Science.gov (United States)

    Min, Jaspur; Buckel, Christina; Secura, Gina M; Peipert, Jeffrey F; Madden, Tessa

    2015-01-01

    Our objective was to measure the sensitivity and specificity of a six-item "pregnancy checklist" at excluding early- or luteal-phase pregnancy among women with a negative urine pregnancy test who were initiating contraception. This was a secondary analysis of the Contraceptive CHOICE Project, a prospective cohort study of 9256 women in the St. Louis region. Women who had a negative urine pregnancy test on the day of enrollment were included in this analysis. Women with a positive urine pregnancy test or without urine pregnancy testing were excluded. We identified all luteal-phase pregnancies that occurred among women with a negative urine pregnancy test. We calculated the sensitivity, specificity, positive predictive value and negative predictive value (NPV) and likelihood ratios of the pregnancy checklist for excluding luteal-phase pregnancies. There were 6929 women included in this analysis; 69% of these women met at least one checklist criterion to exclude pregnancy ("negative screen"). There were 36 luteal-phase pregnancies (0.5%) subsequently diagnosed among women with a negative urine pregnancy test. The sensitivity and specificity of the checklist were 77.7% and 69.1%, respectively. The NPV of the checklist was 99.8% and the positive predictive value was 1.3%. Among women with a negative urine pregnancy test, the pregnancy checklist can be used to safely exclude more than 99% of early pregnancies at the time of contraceptive initiation. In patients with a negative urine pregnancy test, a pregnancy checklist using six criteria based on patient history has high NPV in excluding early pregnancy. This checklist can be used to facilitate same-day initiation of contraceptive methods, including long-acting reversible contraception. Although the checklist had a high false positive rate, initiation of contraception should not be delayed in women with a "positive screen." Rather women who desire an intrauterine device or implant can be "bridged" with a shorter

  9. Co-culture of primary CLL cells with bone marrow mesenchymal cells, CD40 ligand and CpG ODN promotes proliferation of chemoresistant CLL cells phenotypically comparable to those proliferating in vivo.

    Science.gov (United States)

    Purroy, Noelia; Abrisqueta, Pau; Carabia, Júlia; Carpio, Cecilia; Palacio, Carles; Bosch, Francesc; Crespo, Marta

    2015-04-10

    Chronic lymphocytic leukemia (CLL) cells residing in the bone marrow (BM) and in secondary lymphoid tissues receive survival and proliferative signals from the microenvironment, resulting in persistence of residual disease after treatment. In this study, we characterized primary CLL cells cultured with BM stromal cells, CD40 ligand and CpG ODN to partially mimic the microenvironment in the proliferative centers. This co-culture system induced proliferation and chemoresistance in primary CLL cells. Importantly, co-cultured primary CLL cells shared many phenotypical features with circulating proliferative CLL cells, such as upregulation of ZAP-70 and CD38 and higher CD49d and CD62L expression. This indicates aggressiveness and capability to interact with surrounding cells, respectively. In addition, levels of CXCR4 were decreased due to CXCR4 internalization after CXCL12 stimulation by BM stromal cells. We suggest that this co-culture system can be used to test drugs and their combinations that target the proliferative and drug resistant CLL cells.

  10. Toxicity of food additives (excluding antioxidants). January 1978-November 1987 (citations from the Life Sciences Collection data base). Report for January 1978-November 1987

    Energy Technology Data Exchange (ETDEWEB)

    1987-12-01

    This bibliography contains citations concerning the toxicity of food additives (excluding antioxidants) and their effects on the liver, kidneys, bladder, and other organs. The carcinogenic and teratogenic properties of these substances are also considered. The synthetic sweeteners, particularly the saccharins and cyclamates, and other additives, including nitrates and nitrites are discussed. Methods to detect and quantitate these additives are also included. (This updated bibliography contains 340 citations, 132 of which are new entries to the previous edition.)

  11. A systematic search for linkage with nonsyndromic recessive deafness in two large Middle Eastern inbred kindreds excludes more than 30% of the genome

    Energy Technology Data Exchange (ETDEWEB)

    Weiss, S.; Korostishevsky, M. [Sackler Faculty of Medicine, Ramat-Aviv (Israel); Frydman, M. [Haim Sheba Medical Center, Tel-Hashomer (Israel)] [and others

    1994-09-01

    It has been estimated that as many as 35 loci may individually cause autosomal recessive non-syndromic deafness. The extreme genetic heterogeneity, limited clinical differentiation and phenotypic assortative mating in many western countries make many families unsuitable for genetic linkage studies. Recently the first of those loci was mapped (to 13q) in two consanguineous families from northern Tunisia. We are studying two large highly consanguineous Middle Eastern kindreds (a total of 26 deaf in 98 sampled individuals). Examination in each family showed no evidence of clinical heterogeneity and indicated an uncomplicated profound bilateral sensorineural deafness. We have been able to exclude the 13q locus as the cause of deafness in each kindred and have also excluded such `candidate` loci as regions as those causing Usher`s syndrome type 1 (11q13)(11p), Usher`s syndrome type II (1q32-q41), Waardenburg syndrome type I (2q37), branchio-oto-renal syndrome (8q12-q13), Monge`s deafness (5q31), and Treacher Collins syndrome (5q31.3-q33.3). To date, no lod scores greater than 1 have been obtained in either kindred using 150 RFLT`s, VNTR`s and highly polymorphic microsatellite markers (CA repeats and tetranucleotides). By Morton`s criterion a minimum of 30% of the autosomal genome can be excluded for each kindred separately.

  12. CpG oligodeoxynucleotide-enhanced humoral immune response and production of antibodies to prion protein PrPSc in mice immunized with 139A scrapie-associated fibrils.

    Science.gov (United States)

    Spinner, Daryl S; Kascsak, Regina B; Lafauci, Giuseppe; Meeker, Harry C; Ye, Xuemin; Flory, Michael J; Kim, Jae Il; Schuller-Levis, Georgia B; Levis, William R; Wisniewski, Thomas; Carp, Richard I; Kascsak, Richard J

    2007-06-01

    Prion diseases are characterized by conversion of the cellular prion protein (PrP(C)) to a protease-resistant conformer, the srapie form of PrP (PrP(Sc)). Humoral immune responses to nondenatured forms of PrP(Sc) have never been fully characterized. We investigated whether production of antibodies to PrP(Sc) could occur in PrP null (Prnp(-/-)) mice and further, whether innate immune stimulation with the TLR9 agonist CpG oligodeoxynucleotide (ODN) 1826 could enhance this process. Whether such stimulation could raise anti-PrP(Sc) antibody levels in wild-type (Prnp(+/+)) mice was also investigated. Prnp(-/-) and Prnp(+/+) mice were immunized with nondenatured 139A scrapie-associated fibrils (SAF), with or without ODN 1826, and were tested for titers of PrP-specific antibodies. In Prnp(-/-) mice, inclusion of ODN 1826 in the immunization regime increased anti-PrP titers more than 13-fold after two immunizations and induced, among others, antibodies to an N-terminal epitope, which were only present in the immune repertoire of mice receiving ODN 1826. mAb 6D11, derived from such a mouse, reacts with the N-terminal epitope QWNK in native and denatured forms of PrP(Sc) and recombinant PrP and exhibits a K(d) in the 10(-)(11) M range. In Prnp(+/+) mice, ODN 1826 increased anti-PrP levels as much as 84% after a single immunization. Thus, ODN 1826 potentiates adaptive immune responses to PrP(Sc) in 139A SAF-immunized mice. These results represent the first characterization of humoral immune responses to nondenatured, infectious PrP(Sc) and suggest methods for optimizing the generation of mAbs to PrP(Sc), many of which could be used for diagnosis and treatment of prion diseases.

  13. Novel computational approach for studying ph effects, excluded volume and ion-ion correlations in electrical double layers around polyelectrolytes and nanoparticles

    Science.gov (United States)

    Ovanesyan, Zaven

    Highly charged cylindrical and spherical objects (macroions) are probably the simplest structures for modeling nucleic acids, proteins and nanoparticles. Their ubiquitous presence within biophysical systems ensures that Coulomb forces are among the most important interactions that regulate the behavior of these systems. In these systems, ions position themselves in a strongly correlated manner near the surface of a macroion and form electrical double layers (EDLs). These EDLs play an important role in many biophysical and biochemical processes. For instance, the macroion's net charge can change due to the binding of many multivalent ions to its surface. Thus, proper description of EDLs near the surface of a macroion may reveal a counter-intuitive charge inversion behavior, which can generate attraction between like-charged objects. This is relevant for the variety of fields such as self-assembly of DNA and RNA folding, as well as for protein aggregation and neurodegenerative diseases. Certainly, the key factors that contribute to these phenomena cannot be properly understood without an accurate solvation model. With recent advancements in computer technologies, the possibility to use computational tools for fundamental understanding of the role of EDLs around biomolecules and nanoparticles on their physical and chemical properties is becoming more feasible. Establishing the impact of the excluded volume and ion-ion correlations, ionic strength and pH of the electrolyte on the EDL around biomolecules and nanoparticles, and how changes in these properties consequently affect the Zeta potential and surface charge density are still not well understood. Thus, modeling and understanding the role of these properties on EDLs will provide more insights on the stability, adsorption, binding and function of biomolecules and nanoparticles. Existing mean-field theories such as Poisson Boltzmann (PB) often neglect the ion-ion correlations, solvent and ion excluded volume effects

  14. {sup 18}F-Fluoride PET/CT is highly effective for excluding bone metastases even in patients with equivocal bone scintigraphy

    Energy Technology Data Exchange (ETDEWEB)

    Bortot, Daniel C.; Amorim, Barbara J.; Oki, Glaucia C.; Santos, Allan O.; Lima, Mariana C.L.; Etchebehere, Elba C.S.C.; Ramos, Celso Dario [State University of Campinas (UNICAMP), Division of Nuclear Medicine, Department of Radiology, Avenue Zeferino Vaz, S/N., PO Box 6149, Campinas (Brazil); Gapski, Sergio B. [Medicina Nuclear Diagnostico e Terapia, Nuclear Medicine Clinic, Campinas (Brazil); Barboza, Marycel F.; Mengatti, Jair [Nuclear and Energy Research Institute (IPEN)-CNEN, Radiopharmacy Directory, Sao Paulo (Brazil)

    2012-11-15

    Bone scintigraphy (BS) has been used extensively for many years for the diagnosis of bone metastases despite its low specificity and significant rate of equivocal lesions. {sup 18}F-Fluoride PET/CT has been proven to have a high sensitivity and specificity in the detection of malignant bone lesions, but its effectiveness in patients with inconclusive lesions on BS is not well documented. This study evaluated the ability of {sup 18}F-fluoride PET/CT to exclude bone metastases in patients with various malignant primary tumours and nonspecific findings on BS. We prospectively studied 42 patients (34-88 years of age, 26 women) with different types of tumour. All patients had BS performed for staging or restaging purposes but with inconclusive findings. All patients underwent {sup 18}F-fluoride PET/CT. All abnormalities identified on BS images were visually compared with their appearance on the PET/CT images. All the 96 inconclusive lesions found on BS images of the 42 patients were identified on PET/CT images. {sup 18}F-Fluoride PET/CT correctly excluded bone metastases in 23 patients (68 lesions). Of 19 patients (28 lesions) classified by PET/CT as having metastases, 3 (5 lesions) were finally classified as free of bone metastases on follow-up. The sensitivity, specificity, and positive and negative predictive values of {sup 18}F-fluoride PET/CT were, respectively, 100 %, 88 %, 84 % and 100 % for the identification of patients with metastases (patient analysis) and 100 %, 82 % and 100 % for the identification of metastatic lesions (lesion analysis). The factors that make BS inconclusive do not affect {sup 18}F-fluoride PET/CT which shows a high sensitivity and negative predictive value for excluding bone metastases even in patients with inconclusive conventional BS. (orig.)

  15. Preoperative axillary lymph node evaluation in breast cancer patients by breast magnetic resonance imaging (MRI): Can breast MRI exclude advanced nodal disease?

    Energy Technology Data Exchange (ETDEWEB)

    Hyun, Su Jeong [Yonsei University College of Medicine, Department of Radiology, Breast Cancer Clinic, Severance Hospital, Research Institute of Radiological Science, Seoul (Korea, Republic of); Hallym University Medical Center, Department of Radiology, Kangnam Sacred Heart Hospital, Seoul (Korea, Republic of); Kim, Eun-Kyung; Moon, Hee Jung; Yoon, Jung Hyun; Kim, Min Jung [Yonsei University College of Medicine, Department of Radiology, Breast Cancer Clinic, Severance Hospital, Research Institute of Radiological Science, Seoul (Korea, Republic of)

    2016-11-15

    To evaluate the diagnostic performance of breast magnetic resonance imaging (MRI) in preoperative evaluation of axillary lymph node metastasis (ALNM) in breast cancer patients and to assess whether breast MRI can be used to exclude advanced nodal disease. A total of 425 patients were included in this study and breast MRI findings were retrospectively reviewed. The diagnostic performance of breast MRI for diagnosis of ALNM was evaluated in all patients, patients with neoadjuvant chemotherapy (NAC), and those without NAC (no-NAC). We evaluated whether negative MRI findings (cN0) can exclude advanced nodal disease (pN2-pN3) using the negative predictive value (NPV) in each group. The sensitivity and NPV of breast MRI in evaluation of ALNM was 51.3 % (60/117) and 83.3 % (284/341), respectively. For cN0 cases on MRI, pN2-pN3 manifested in 1.8 % (6/341) of the overall patients, 0.4 % (1/257) of the no-NAC group, and 6 % (5/84) of the NAC group. The NPV of negative MRI findings for exclusion of pN2-pN3 was higher for the no-NAC group than for the NAC group (99.6 % vs. 94.0 %, p = 0.039). Negative MRI findings (cN0) can exclude the presence of advanced nodal disease with an NPV of 99.6 % in the no-NAC group. (orig.)

  16. Establishing and Prioritising Research Questions for the Prevention, Diagnosis and Treatment of Hair Loss (excluding Alopecia Areata): The Hair Loss Priority Setting Partnership.

    Science.gov (United States)

    Macbeth, A; Tomlinson, J; Messenger, A; Moore-Millar, K; Michaelides, C; Shipman, A; Kassim, J; Brockley, J; Szczecinska, W; Farrant, P; Robinson, R; Rodgers, J; Chambers, J; Upadhyaya, S; Harries, M

    2017-07-17

    Hair and scalp problems are common. Unfortunately, many uncertainties exist around the most effective management and treatments strategies for these disorders. To identify uncertainties in hair loss management, prevention, diagnosis and treatment that are important to both people with hair loss and healthcare professionals. A hair loss priority setting partnership was established between patients, their carers and relatives, and healthcare professionals to identify the most important uncertainties in hair loss. The methodology of the James Lind Alliance was followed to ensure a balanced, inclusive and transparent process. In total 2747 treatment uncertainties were submitted by 912 participants; following exclusions 884 uncertainties relating to hair loss (excluding alopecia areata) were analyzed. Questions were combined into "indicative uncertainties" following a structured format. A series of ranking exercises further reduced this list to a top 25 that was taken to a final prioritization workshop where the top 10 priorities were agreed. We present the top 10 research priorities for hair loss (excluding alopecia areata) to guide researchers and funding bodies to support studies important to both patients and clinicians. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  17. Teacher efficacy and pupil behaviour: the structure of teachers' individual and collective beliefs and their relationship with numbers of pupils excluded from school.

    Science.gov (United States)

    Gibbs, Simon; Powell, Ben

    2012-12-01

    Previous work has yielded knowledge of teachers' attributions for children's behaviour. Other studies have helped to develop understanding of teachers' efficacy beliefs. Little work has been undertaken to examine teachers' efficacy beliefs with regard to classroom behaviour. This study aimed to investigate the relationship between teachers' individual and collective beliefs about their efficacy with children's behaviour and whether these beliefs were associated with the use of exclusion as a sanction. A total of 197 teachers from 31 primary and nursery schools in the North East of England participated. Participants responded to questionnaires to assess their individual and collective efficacy beliefs. Demographic and school level data were also collected. Factor analysis indicated that teachers' individual efficacy beliefs were best represented by three factors: 'Classroom Management', 'Children's Engagement', 'Instructional Strategies' that corresponded well to previous findings. Analysis of collective efficacy beliefs showed a similar structure that differed from previous findings. Individual efficacy was not associated with numbers of children excluded. One factor 'Addressing External Influences' in the collective beliefs was negatively correlated with numbers of children excluded and appeared to mitigate the deleterious effects associated with socio-economic deprivation. This study adds weight to the importance of understanding and supporting teachers' beliefs in their collective efficacy. In particular, this study underlines the need for strategies that will endorse and develop teachers' beliefs in their ability to manage children's behaviour successfully. ©2011 The British Psychological Society.

  18. Linkage analysis of bipolar illness with X-chromosome DNA markers: A susceptibility gene in Xq27-q28 cannot be excluded

    Energy Technology Data Exchange (ETDEWEB)

    De bruyn, A.; Raeymaekers, P.; Raes, G. [Univ. of Antwerp (Belgium)] [and others

    1994-12-15

    Transmission studies have supported the presence of a susceptibility gene for bipolar (BP) illness on the X-chromosome. Initial linkage studies with color blindness (CB), glucose-6-phosphate dehydrogenase (G6PD) deficiency, and the blood coagulation factor IX (F9) have suggested that a gene for BP illness is located in the Xq27-q28 region. We tested linkage with several DNA markers located in Xq27-q28 in 2 families, MAD3 and MAD4, that previously were linked to F9, and 7 newly ascertained families of BP probands. Linkage was also examined with the gene encoding the {alpha}3 subunit of the gamma-amino butyric acid receptor (GABRA3), a candidate gene for BP illness located in this region. The genetic data were analyzed with the LOD score method using age-dependent penetrance of an autosomal dominant disease gene and narrow and broad clinical models. In MAD3 and MAD4 the multipoint LOD score data suggested a localization of a BPI gene again near F9. In the 7 new families the overall linkage data excluded the Xq27-q28 region. However, if the families were grouped according to their proband`s phenotype BPI or BPII, a susceptibility gene for BPI disorder at the DXS52-F8 cluster could not be excluded. 48 refs., 2 figs., 3 tabs.

  19. Zinc sulfate contributes to promote telomere length extension via increasing telomerase gene expression, telomerase activity and change in the TERT gene promoter CpG island methylation status of human adipose-derived mesenchymal stem cells.

    Directory of Open Access Journals (Sweden)

    Raheleh Farahzadi

    Full Text Available The use of mesenchymal stem cells (MSCs for cell therapy and regenerative medicine has received widespread attention over the past few years, but their application can be complicated by factors such as reduction in proliferation potential, the senescent tendency of the MSCs upon expansion and their age-dependent decline in number and function. It was shown that all the mentioned features were accompanied by a reduction in telomerase activity and telomere shortening. Furthermore, the role of epigenetic changes in aging, especially changes in promoter methylation, was reported. In this study, MSCs were isolated from the adipose tissue with enzymatic digestion. In addition, immunocytochemistry staining and flow cytometric analysis were performed to investigate the cell-surface markers. In addition, alizarin red-S, sudan III, toluidine blue, and cresyl violet staining were performed to evaluate the multi-lineage differentiation of hADSCs. In order to improve the effective application of MSCs, these cells were treated with 1.5 × 10-8 and 2.99 × 10-10 M of ZnSO4 for 48 hours. The length of the absolute telomere, human telomerase reverse transcriptase (hTERT gene expression, telomerase activity, the investigation of methylation status of the hTERT gene promoter and the percentage of senescent cells were analyzed with quantitative real-time PCR, PCR-ELISA TRAP assay, methylation specific PCR (MSP, and beta-galactosidase (SA-β-gal staining, respectively. The results showed that the telomere length, the hTERT gene expression, and the telomerase activity had significantly increased. In addition, the percentage of senescent cells had significantly decreased and changes in the methylation status of the CpG islands in the hTERT promoter region under treatment with ZnSO4 were seen. In conclusion, it seems that ZnSO4 as a proper antioxidant could improve the aging-related features due to lengthening of the telomeres, increasing the telomerase gene expression

  20. Modulation of Single-Cell IgG Secretion Frequency and Rates in Human Memory B Cells by CpG DNA, CD40L, IL-21 and Cell Division∥

    Science.gov (United States)

    Henn, Alicia D.; Rebhahn, Jonathan; Brown, Miguel A.; Murphy, Alison J.; Coca, Mircea N.; Hyrien, Ollivier; Pellegrin, Tina; Mosmann, Tim; Zand, Martin S.

    2009-01-01

    During the recall response by CD27+ IgG class switched human memory B cells, total IgG secreted is a function of (1) the number of IgG secreting cells (IgG-SC) and (2) the secretion rate of each cell. Here we report the quantitative ELISPOT method (qELISPOT) for simultaneous estimation of single cell IgG secretion rates and secreting cell frequencies in human B cell populations. We found that CD27+ IgMneg memory B cells activated with CpG and cytokines had considerable heterogeneity in the IgG secretion rates, with two major secretion rate subpopulations. B cell receptor cross-linking reduced the frequency of cells with high per-cell IgG secretion rates, with a parallel decrease in CD27hi B cell blasts. Increased cell death may account for the BCR-stimulated reduction in high-rate IgG-SC CD27hi B cell blasts. In contrast, the addition of IL-21 to CD40L +IL-4 activated human memory B cells induced a high-rate IgG-SC population in B cells with otherwise low per-cell IgG secretion rates. The profiles of human B cell IgG secretion rates followed the same biphasic distribution and range irrespective of division class. This, along with the presence of non-IgG-producing, dividing B cells in CpG+ck-activated B memory B cell populations, is suggestive of an “On/Off switch” regulating IgG secretion. Finally, these data support a mixture model of IgG secretion in which IgG secreted over time is modulated by the frequency of IgG secreting cells and the distribution of their IgG secretion rates. This is an author-produced version of a manuscript accepted for publication in The Journal of Immunology (The JI). The American Association of Immunologists, Inc. (AAI), publisher of The JI, holds the copyright to this manuscript. This version of the manuscript has not yet been copyedited or subjected to editorial proofreading by The JI; hence, it may differ from the final version published in The JI (online and in print). AAI (The JI) is not liable for errors or omissions in this

  1. Secondhand smoke in combination with ambient air pollution exposure is associated with increasedx CpG methylation and decreased expression of IFN-γ in T effector cells and Foxp3 in T regulatory cells in children

    Directory of Open Access Journals (Sweden)

    Kohli Arunima

    2012-09-01

    Full Text Available Abstract Background Secondhand smoke (SHS and ambient air pollution (AAP exposures have been associated with increased prevalence and severity of asthma and DNA modifications of immune cells. In the current study, we examined the association between SHS and AAP with DNA methylation and expression of interferon-gamma (IFN-γ and forkhead box protein 3 (Foxp3 in T cell populations. Methods Subjects 7–18 years old were recruited from Fresno (high AAP; n = 62 and Stanford, CA (low AAP; n = 40 and divided into SHS-exposed (Fresno: n = 31, Stanford: n = 6 and non-SHS-exposed (nSHS; Fresno: n = 31, Stanford: n = 34 groups. T cells purified from peripheral blood were assessed for levels of DNA methylation and expression of IFN-γ (in effector T cells or Foxp3 (in regulatory T cells. Results Analysis showed a significant increase in mean % CpG methylation of IFN-γ and Foxp3 associated with SHS exposure (IFN-γ: FSHS 62.10%, FnSHS 41.29%, p p Foxp3: FSHS 74.60%, FnSHS 54.44%, p p IFN-γ: FSHS 0.75, FnSHS 1.52, p p Foxp3: FSHS 0.75, FnSHS 3.29, p p IFN-γ: FSHS vs. SSHS, p p Foxp3: FSHS vs. SSHS, p p IFN-γ: FSHS vs. SSHS, p p Foxp3: FSHS vs. SSHS, p p IFN-γ: p = 0.15; Foxp3: p = 0.27, nor was Foxp3 expression (p = 0.08; IFN-γ expression was significantly decreased in AAP-only subjects (p  Conclusions Exposures to SHS and AAP are associated with significant hypermethylation and decreased expression of IFN-γ in Teffs and Foxp3 in Tregs. Relative contributions of each exposure to DNA modification and asthma pathogenesis warrant further investigation.

  2. Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations

    Directory of Open Access Journals (Sweden)

    Gregory A. Poland

    2017-04-01

    Full Text Available The development of a humoral immune response to influenza vaccines occurs on a multisystems level. Due to the orchestration required for robust immune responses when multiple genes and their regulatory components across multiple cell types are involved, we examined an influenza vaccination cohort using multiple high-throughput technologies. In this study, we sought a more thorough understanding of how immune cell composition and gene expression relate to each other and contribute to interindividual variation in response to influenza vaccination. We first hypothesized that many of the differentially expressed (DE genes observed after influenza vaccination result from changes in the composition of participants’ peripheral blood mononuclear cells (PBMCs, which were assessed using flow cytometry. We demonstrated that DE genes in our study are correlated with changes in PBMC composition. We gathered DE genes from 128 other publically available PBMC-based vaccine studies and identified that an average of 57% correlated with specific cell subset levels in our study (permutation used to control false discovery, suggesting that the associations we have identified are likely general features of PBMC-based transcriptomics. Second, we hypothesized that more robust models of vaccine response could be generated by accounting for the interplay between PBMC composition, gene expression, and gene regulation. We employed machine learning to generate predictive models of B-cell ELISPOT response outcomes and hemagglutination inhibition (HAI antibody titers. The top HAI and B-cell ELISPOT model achieved an area under the receiver operating curve (AUC of 0.64 and 0.79, respectively, with linear model coefficients of determination of 0.08 and 0.28. For the B-cell ELISPOT outcomes, CpG methylation had the greatest predictive ability, highlighting potentially novel regulatory features important for immune response. B-cell ELISOT models using only PBMC composition had

  3. 18q loss of heterozygosity in microsatellite stable colorectal cancer is correlated with CpG island methylator phenotype-negative (CIMP-0 and inversely with CIMP-low and CIMP-high

    Directory of Open Access Journals (Sweden)

    Kirkner Gregory J

    2007-05-01

    Full Text Available Abstract Background: The CpG island methylator phenotype (CIMP with widespread promoter methylation is a distinct epigenetic phenotype in colorectal cancer, associated with microsatellite instability-high (MSI-high and BRAF mutations. 18q loss of heterozygosity (LOH commonly present in colorectal cancer with chromosomal instability (CIN is associated with global hypomethylation in tumor cell. A recent study has shown an inverse correlation between CIN and CIMP (determined by MINTs, p16, p14 and MLH1 methylation in colorectal cancer. However, no study has examined 18q LOH in relation to CIMP-high, CIMP-low (less extensive promoter methylation and CIMP-0 (CIMP-negative, determined by quantitative DNA methylation analysis. Methods: Utilizing MethyLight technology (real-time PCR, we quantified DNA methylation in 8 CIMP-specific promoters {CACNA1G, CDKN2A (p16, CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1} in 758 non-MSI-high colorectal cancers obtained from two large prospective cohorts. Using four 18q microsatellite markers (D18S55, D18S56, D18S67 and D18S487 and stringent criteria for 18q LOH, we selected 374 tumors (236 LOH-positive tumors with ≥ 2 markers showing LOH; and 138 LOH-negative tumors with ≥ 3 informative markers and no LOH. Results: CIMP-0 (0/8 methylated promoters was significantly more common in 18q LOH-positive tumors (59% = 139/236, p = 0.002 than 18q LOH-negative tumors (44% = 61/138, while CIMP-low/high (1/8–8/8 methylated promoters was significantly more common (56% in 18q LOH-negative tumors than 18q LOH-positive tumors (41%. These relations persisted after stratification by sex, location, or the status of MSI, p53 expression (by immunohistochemistry, or KRAS/BRAF mutation. Conclusion: 18q LOH is correlated positively with CIMP-0 and inversely with CIMP-low and CIMP-high. Our findings provide supporting evidence for relationship between CIMP-0 and 18q LOH as well as a molecular difference between CIMP-0 and CIMP-low in

  4. Theory including future not excluded

    DEFF Research Database (Denmark)

    Nagao, K.; Nielsen, H.B.

    2013-01-01

    We study a complex action theory (CAT) whose path runs over not only past but also future. We show that, if we regard a matrix element defined in terms of the future state at time T and the past state at time TA as an expectation value in the CAT, then we are allowed to have the Heisenberg equation......, Ehrenfest's theorem, and the conserved probability current density. In addition,we showthat the expectation value at the present time t of a future-included theory for large T - t and large t - T corresponds to that of a future-not-included theory with a proper inner product for large t - T. Hence, the CAT...

  5. When apparent schizophrenia is excluded

    African Journals Online (AJOL)

    In the beginning. Mr R was a 30-year-old male who was diagnosed with schizophrenia at the age of 19, after he presented with a typical combination of disorganised behaviour and persecutory delusions, against a background of daily comorbid polysubstance abuse. Owing to a pattern of frequent readmissions and poor ...

  6. Forensic identification science evidence since Daubert: Part II--judicial reasoning in decisions to exclude forensic identification evidence on grounds of reliability.

    Science.gov (United States)

    Page, Mark; Taylor, Jane; Blenkin, Matt

    2011-07-01

    Many studies regarding the legal status of forensic science have relied on the U.S. Supreme Court's mandate in Daubert v. Merrell Dow Pharmaceuticals Inc., and its progeny in order to make subsequent recommendations or rebuttals. This paper focuses on a more pragmatic approach to analyzing forensic science's immediate deficiencies by considering a qualitative analysis of actual judicial reasoning where forensic identification evidence has been excluded on reliability grounds since the Daubert precedent. Reliance on general acceptance is becoming insufficient as proof of the admissibility of forensic evidence. The citation of unfounded statistics, error rates and certainties, a failure to document the analytical process or follow standardized procedures, and the existence of observe bias represent some of the concerns that have lead to the exclusion or limitation of forensic identification evidence. Analysis of these reasons may serve to refocus forensic practitioners' testimony, resources, and research toward rectifying shortfalls in these areas. © 2011 American Academy of Forensic Sciences.

  7. Surfactant therapy of pulmonary conditions excluding those with primary surfactant deficiency and bronchoscopy as delivery method: an overview of Russian patents and publications.

    Science.gov (United States)

    Jargin, Sergei V

    2013-08-01

    Preparations of pulmonary surfactant are used for the treatment of respiratory distress syndrome in a newborn. Their applicability as a method of routine for lung diseases beyond the neonatal period is questionable. Some publications from the former Soviet Union (SU) have reported on successful surfactant therapy of ARDS in children and adults as well as for inhalation injuries, pneumonia, and tuberculosis. Bronchoscopy was used and recommended as a method of surfactant delivery for ARDS, some types of pneumonia and tuberculosis. Manufacturing processes of surfactant preparations from bovine lung and amniotic fluid, described by Russian patents, and bronchoscopy as a delivery mode are discussed here. A concluding point is that some reports from the former SU about administration of exogenous surfactant in pulmonary conditions, excluding those with primary surfactant deficiency, are only partly confirmed by the international literature.

  8. Prevalence of Eligibility Criteria for the Systolic Blood Pressure Intervention Trial in US Adults Among Excluded Groups: Age Diabetes Mellitus, or a History of Stroke.

    Science.gov (United States)

    Bress, Adam P; Tanner, Rikki M; Hess, Rachel; Gidding, Samuel S; Colantonio, Lisandro D; Shimbo, Daichi; Muntner, Paul

    2016-07-12

    Adults diabetes mellitus, or a history of stroke were not enrolled in the Systolic Blood Pressure Intervention Trial (SPRINT). Estimating the size and characteristics of these excluded groups who meet the other SPRINT eligibility criteria may provide information on the potential impact of providers extending the SPRINT findings to these populations. We analyzed the National Health and Nutrition Examination Survey 2003-2012 (n=25 076) to estimate the percentage and characteristics of US adults ≥20 years in 3 populations (age diabetes mellitus, or history of stroke) excluded from SPRINT who otherwise meet the trial eligibility criteria: age ≥50 years, systolic blood pressure (SBP) 130-180 mm Hg, high cardiovascular disease risk, and not having trial exclusion criteria. Overall, 1.0% (95% CI 0.8-1.3) of US adults age diabetes mellitus, and 19.0% (95% CI 16.0-22.4) with history of stroke met the other SPRINT eligibility criteria. Among US adults with SBP ≥130 mm Hg, other SPRINT eligibility criteria were met by 7.5% (95% CI 6.1-9.2) of those age diabetes mellitus, and 23.0% (95% CI 19.4-27.0) with history of stroke. Among US adults meeting the other SPRINT eligibility criteria, antihypertensive medication was being taken by 31.0% (95% CI 23.9-41.3) of those diabetes mellitus, and 68.9% (95% CI 59.4-77.1) with a history of stroke. A substantial percentage of US adults with diabetes mellitus or history of stroke and a small percentage <50 years old meet the other SPRINT eligibility criteria. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

  9. Scavenger receptor B1 (SR-B1) profoundly excludes high density lipoprotein (HDL) apolipoprotein AII as it nibbles HDL-cholesteryl ester.

    Science.gov (United States)

    Gillard, Baiba K; Bassett, G Randall; Gotto, Antonio M; Rosales, Corina; Pownall, Henry J

    2017-05-26

    Reverse cholesterol transport (transfer of macrophage-cholesterol in the subendothelial space of the arterial wall to the liver) is terminated by selective high density lipoprotein (HDL)-cholesteryl ester (CE) uptake, mediated by scavenger receptor class B, type 1 (SR-B1). We tested the validity of two models for this process: "gobbling," i.e. one-step transfer of all HDL-CE to the cell and "nibbling," multiple successive cycles of SR-B1-HDL association during which a few CEs transfer to the cell. Concurrently, we compared cellular uptake of apoAI with that of apoAII, which is more lipophilic than apoAI, using HDL-[(3)H]CE labeled with [(125)I]apoAI or [(125)I]apoAII. The studies were conducted in CHO-K1 and CHO-ldlA7 cells (LDLR(-/-)) with (CHO-SR-B1) and without SR-B1 overexpression and in human Huh7 hepatocytes. Relative to CE, both apoAI and apoAII were excluded from uptake by all cells. However, apoAII was more highly excluded from uptake (2-4×) than apoAI. To distinguish gobbling versus nibbling mechanisms, media from incubations of HDL with CHO-SR-B1 cells were analyzed by non-denaturing PAGE, size-exclusion chromatography, and the distribution of apoAI, apoAII, cholesterol, and phospholipid among HDL species as a function of incubation time. HDL size gradually decreased, i.e. nibbling, with the concurrent release of lipid-free apoAI; apoAII was retained in an HDL remnant. Our data support an SR-B1 nibbling mechanism that is similar to that of streptococcal serum opacity factor, which also selectively removes CE and releases apoAI, leaving an apoAII-rich remnant. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. I. Excluded Volume Effects in Ising Cluster Distributions and Nuclear Multifragmentation II. Multiple-Chance Effects in α-Particle Evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Breus, Dimitry Eugene [Univ. of California, Berkeley, CA (United States)

    2005-05-16

    In Part 1, geometric clusters of the Ising model are studied as possible model clusters for nuclear multifragmentation. These clusters may not be considered as non-interacting (ideal gas) due to excluded volume effect which predominantly is the artifact of the cluster's finite size. Interaction significantly complicates the use of clusters in the analysis of thermodynamic systems. Stillinger's theory is used as a basis for the analysis, which within the RFL (Reiss, Frisch, Lebowitz) fluid-of-spheres approximation produces a prediction for cluster concentrations well obeyed by geometric clusters of the Ising model. If thermodynamic condition of phase coexistence is met, these concentrations can be incorporated into a differential equation procedure of moderate complexity to elucidate the liquid-vapor phase diagram of the system with cluster interaction included. The drawback of increased complexity is outweighted by the reward of greater accuracy of the phase diagram, as it is demonstrated by the Ising model. A novel nuclear-cluster analysis procedure is developed by modifying Fisher's model to contain cluster interaction and employing the differential equation procedure to obtain thermodynamic variables. With this procedure applied to geometric clusters, the guidelines are developed to look for excluded volume effect in nuclear multifragmentation. In part 2, an explanation is offered for the recently observed oscillations in the energy spectra of α-particles emitted from hot compound nuclei. Contrary to what was previously expected, the oscillations are assumed to be caused by the multiple-chance nature of α-evaporation. In a semi-empirical fashion this assumption is successfully confirmed by a technique of two-spectra decomposition which treats experimental α-spectra has having contributions from at least two independent emitters. Building upon the success of the multiple-chance explanation of the oscillations, Moretto's single

  11. Enhanced magnetic field probe array for improved excluded flux calculations on the C-2U advanced beam-driven field-reversed configuration plasma experiment

    Energy Technology Data Exchange (ETDEWEB)

    Roche, T., E-mail: troche@trialphaenergy.com; Thompson, M. C.; Mendoza, R.; Allfrey, I.; Garate, E.; Romero, J.; Douglass, J. [Tri Alpha Energy, P.O. Box 7010, Rancho Santa Margarita, California 92688 (United States)

    2016-11-15

    External flux conserving coils were installed onto the exterior of the C-2U [M. W. Binderbauer et al., Phys. Plasmas 22, 056110 (2015)] confinement vessel to increase the flux confinement time of the system. The 0.5 in. stainless steel vessel wall has a skin time of ∼5 ms. The addition of the external copper coils effectively increases this time to ∼7 ms. This led to better-confined/longer-lived field-reversed configuration (FRC) plasmas. The fringing fields generated by the external coils have the side effect of rendering external field measurements invalid. Such measurements were key to the previous method of excluded flux calculation [M. C. Thompson et al., Rev. Sci. Instrum. 83, 10D709 (2012)]. A new array of B-dot probes and Rogowski coils were installed to better determine the amount of flux leaked out of the system and ultimately provide a more robust measurement of plasma parameters related to pressure balance including the excluded flux radius. The B-dot probes are surface mountable chip inductors with inductance of 33 μH capable of measuring the DC magnetic field and transient field, due to resistive current decay in the wall/coils, when coupled with active integrators. The Rogowski coils measure the total change in current in each external coil (150 A/2 ms). Currents were also actively driven in the external coils. This renders the assumption of total flux conservation invalid which further complicates the analysis process. The ultimate solution to these issues and the record breaking resultant FRC lifetimes will be presented.

  12. Predictive Value of the Model for End-Stage Liver Disease Score Excluding International Normalized Ratio One Year After Orthotopic Heart Transplantation.

    Science.gov (United States)

    Szyguła-Jurkiewicz, B; Zakliczyński, M; Szczurek, W; Nadziakiewicz, P; Gąsior, M; Zembala, M

    2016-06-01

    The Model for End-Stage Liver Disease (MELD) scoring system incorporating a combination of hepatic and renal laboratory parameters does not adequately reflect the degree of multi-organ dysfunction in patients with heart failure, who need oral anticoagulation. In order to exclude the impact of oral anticoagulation on the international normalized ratio (INR), we used the MELD excluding INR (MELD-XI) score. The aims of the study were to calculate the individual preoperative MELD-XI score and its ability to predict 1-year mortality after heart transplantation and to identify other preoperative laboratory prognostic parameters. We retrospectively analysed data of 87 consecutive adults undergoing heart transplantation between 2011 and 2014. Clinical data and laboratory parameters for the calculation of the MELD-XI score were obtained at the time of admission for the heart transplantation. The average age of the patients was 48.8 ± 13.3 years and 68.9% of them were male. During the observation period, the mortality rate was 18.4%. Multivariate analysis of Cox proportional hazard confirmed that the pretransplantation MELD-XI score (hazard ratio [HR] = 1.625 [1.286-2.053]; P < .001), sodium serum concentration (HR = 0.824 [0.677-1.001]; P < .05) and highly sensitive C-reactive protein (hs-CRP) serum concentration (HR = 1.045 [1.008-1.083]; P < .02) were independent predictors of death during the first year after heart transplantation. Area under the receiver operating characteristic (ROC) curve (AUC) indicated a good discriminatory power of MELD-XI (AUC 0.997; P < .04) and plasma sodium concentration (AUC 0.901; P < .01) in death prediction. Our study confirms that the pretransplantation MELD-XI score, as well as serum sodium and hsCRP concentrations, may be used to estimate postoperative risk in heart transplant recipients during a 1-year follow-up. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. The pathophysiology of the aqueduct stroke volume in normal pressure hydrocephalus: can co-morbidity with other forms of dementia be excluded?

    Energy Technology Data Exchange (ETDEWEB)

    Bateman, Grant A. [John Hunter Hospital, Department of Medical Imaging, Newcastle (Australia); Levi, Christopher R.; Wang, Yang; Lovett, Elizabeth C. [Hunter Medical Research Institute, Clinical Neurosciences Program, Newcastle (Australia); Schofield, Peter [James Fletcher Hospital, Neuropsychiatry Unit, Newcastle (Australia)

    2005-10-01

    Variable results are obtained from the treatment of normal pressure hydrocephalus (NPH) by shunt insertion. There is a high correlation between NPH and the pathology of Alzheimer's disease (AD) on brain biopsy. There is an overlap between AD and vascular dementia (VaD), suggesting that a correlation exists between NPH and other forms of dementia. This study seeks to (1) understand the physiological factors behind, and (2) define the ability of, the aqueduct stroke volume to exclude dementia co-morbidity. Twenty-four patients from a dementia clinic were classified as having either early AD or VaD on the basis of clinical features, Hachinski score and neuropsychological testing. They were compared with 16 subjects with classical clinical findings of NPH and 12 aged-matched non-cognitively impaired subjects. MRI flow quantification was used to measure aqueduct stroke volume and arterial pulse volume. An arterio-cerebral compliance ratio was calculated from the two volumes in each patient. The aqueduct stroke volume was elevated in all three forms of dementia, with no significant difference noted between the groups. The arterial pulse volume was elevated by 24% in VaD and reduced by 35% in NPH, compared to normal (P=0.05 and P=0.002, respectively), and was normal in AD. There was a spectrum of relative compliance with normal compliance in VaD and reduced compliance in AD and NPH. The aqueduct stroke volume depends on the arterial pulse volume and the relative compliance between the arterial tree and brain. The aqueduct stroke volume cannot exclude significant co-morbidity in NPH. (orig.)

  14. Trails, Other, Proposed and existing recreational trails (excluding snowmobile trails). Proposed trails are coded as high, medium, or low priority., Published in 2010, 1:2400 (1in=200ft) scale, Manitowoc County Government.

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — Trails, Other dataset current as of 2010. Proposed and existing recreational trails (excluding snowmobile trails). Proposed trails are coded as high, medium, or low...

  15. Detecting in situ copepod diet diversity using molecular technique: development of a copepod/symbiotic ciliate-excluding eukaryote-inclusive PCR protocol.

    Science.gov (United States)

    Hu, Simin; Guo, Zhiling; Li, Tao; Carpenter, Edward J; Liu, Sheng; Lin, Senjie

    2014-01-01

    Knowledge of in situ copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole copepod-derived DNAs, we developed a copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 copepod species, 37 representative organisms that are potential prey of copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of copepods. All the predetermined food offered to copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of copepods without interference of copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as copepod prey

  16. Detecting in situ copepod diet diversity using molecular technique: development of a copepod/symbiotic ciliate-excluding eukaryote-inclusive PCR protocol.

    Directory of Open Access Journals (Sweden)

    Simin Hu

    Full Text Available Knowledge of in situ copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole copepod-derived DNAs, we developed a copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (copepod/symbiotic ciliate-excluding eukaryote-common: CEEC to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 copepod species, 37 representative organisms that are potential prey of copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of copepods. All the predetermined food offered to copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of copepods without interference of copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected copepods uncovered diverse prey species, including those currently known, and those that are unsuspected

  17. Ubiquitous human 'master' origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers.

    Science.gov (United States)

    Drillon, Guénola; Audit, Benjamin; Argoul, Françoise; Arneodo, Alain

    2015-02-18

    As the elementary building block of eukaryotic chromatin, the nucleosome is at the heart of the compromise between the necessity of compacting DNA in the cell nucleus and the required accessibility to regulatory proteins. The recent availability of genome-wide experimental maps of nucleosome positions for many different organisms and cell types has provided an unprecedented opportunity to elucidate to what extent the DNA sequence conditions the primary structure of chromatin and in turn participates in the chromatin-mediated regulation of nuclear functions, such as gene expression and DNA replication. In this study, we use in vivo and in vitro genome-wide nucleosome occupancy data together with the set of nucleosome-free regions (NFRs) predicted by a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix, to investigate the role of intrinsic nucleosome occupancy in the regulation of the replication spatio-temporal programme in human. We focus our analysis on the so-called replication U/N-domains that were s