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Sample records for methyl-dna immunoprecipitation combined

  1. Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.

    PubMed

    Rebollo, Rita; Mager, Dixie L

    2016-01-01

    Endogenous retroviruses are repetitive sequences found abundantly in mammalian genomes which are capable of modulating host gene expression. Nevertheless, most endogenous retrovirus copies are under tight epigenetic control via histone-repressive modifications and DNA methylation. Here we describe a common method used in our laboratory to detect, quantify, and compare mammalian endogenous retrovirus DNA methylation. More specifically we describe methylated DNA immunoprecipitation (MeDIP) followed by quantitative PCR. PMID:26895065

  2. Optimized method for methylated DNA immuno-precipitation

    PubMed Central

    Guerrero-Bosagna, Carlos; Jensen, Per

    2015-01-01

    Methylated DNA immunoprecipitation (MeDIP) is one of the most widely used methods to evaluate DNA methylation on a whole genome scale, and involves the capture of the methylated fraction of the DNA by an antibody specific to methyl-cytosine. MeDIP was initially coupled with microarray hybridization to detect local DNA methylation enrichments along the genome. More recently, MeDIP has been coupled with next generation sequencing, which highlights its current and future applicability. In previous studies in which MeDIP was applied, the protocol took around 3 days to be performed. Given the importance of MeDIP for studies involving DNA methylation, it was important to optimize the method in order to deliver faster turnouts. The present article describes optimization steps of the MeDIP method. The length of the procedure was reduced in half without compromising the quality of the results. This was achieved by:•Reduction of the number of washes in different stages of the protocol, after a careful evaluation of the number of indispensable washes.•Reduction of reaction times for detaching methylated DNA fragments from the complex agarose beads:antibody.•Modification of the methods to purify methylated DNA, which incorporates new devices and procedures, and eliminates a lengthy phenol and chloroform:isoamyl alcohol extraction. PMID:26740923

  3. Analysis of the methylome of human embryonic stem cells employing methylated DNA immunoprecipitation coupled to next-generation sequencing.

    PubMed

    Grimm, Christina; Adjaye, James

    2012-01-01

    The analysis of DNA-methylation on a genome-wide scale by next-generation sequencing techniques is an invaluable tool towards the understanding of the epigenetic basis of cellular differentiation. Methylated DNA immunoprecipitation (MeDIP) is an immunocapturing method using an antibody targeting 5-methylcytidine (5 mC) and thereby enriching methylated DNA. MeDIP combined with next-generation sequencing (MeDIP-seq) provides a powerful tool for the analysis of genome-wide DNA-methylation profiles. Here, we describe a protocol for the preparation of MeDIP samples suitable for next-generation sequencing on a Genome Analyser (Illumina). PMID:22528363

  4. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) using low amounts of genomic DNA.

    PubMed

    Zhao, Ming-Tao; Whyte, Jeffrey J; Hopkins, Garrett M; Kirk, Mark D; Prather, Randall S

    2014-06-01

    DNA modifications, such as methylation and hydroxymethylation, are pivotal players in modulating gene expression, genomic imprinting, X-chromosome inactivation, and silencing repetitive sequences during embryonic development. Aberrant DNA modifications lead to embryonic and postnatal abnormalities and serious human diseases, such as cancer. Comprehensive genome-wide DNA methylation and hydroxymethylation studies provide a way to thoroughly understand normal development and to identify potential epigenetic mutations in human diseases. Here we established a working protocol for methylated DNA immunoprecipitation combined with next-generation sequencing [methylated DNA immunoprecipitation (MeDIP)-seq] for low starting amounts of genomic DNA. By using spike-in control DNA sets with standard cytosine, 5-methylcytosine (5mC), and 5-hydroxymethylcytosine (5hmC), we demonstrate the preferential binding of antibodies to 5mC and 5hmC, respectively. MeDIP-PCRs successfully targeted highly methylated genomic loci with starting genomic DNA as low as 1 ng. The enrichment efficiency declined for constant spiked-in controls but increased for endogenous methylated regions. A MeDIP-seq library was constructed starting with 1 ng of DNA, with the majority of fragments between 250 bp and 600 bp. The MeDIP-seq reads showed higher quality than the Input control. However, after being preprocessed by Cutadapt, MeDIP (97.53%) and Input (94.98%) reads showed comparable alignment rates. SeqMonk visualization tools indicated MeDIP-seq reads were less uniformly distributed across the genome than Input reads. Several commonly known unmethylated and methylated genomic loci showed consistent methylation patterns in the MeDIP-seq data. Thus, we provide proof-of-principle that MeDIP-seq technology is feasible to profile genome-wide DNA methylation in minute DNA samples, such as oocytes, early embryos, and human biopsies. PMID:24773292

  5. A comparison of digital gene expression profiling and methyl DNA immunoprecipitation as methods for gene discovery in honeybee (Apis mellifera) behavioural genomic analyses.

    PubMed

    Guan, Cui; Barron, Andrew B; He, Xu Jiang; Wang, Zi Long; Yan, Wei Yu; Zeng, Zhi Jiang

    2013-01-01

    The honey bee has a well-organized system of division of labour among workers. Workers typically progress through a series of discrete behavioural castes as they age, and this has become an important case study for exploring how dynamic changes in gene expression can influence behaviour. Here we applied both digital gene expression analysis and methyl DNA immunoprecipitation analysis to nurse, forager and reverted nurse bees (nurses that have returned to the nursing state after a period spent foraging) from the same colony in order to compare the outcomes of these different forms of genomic analysis. A total of 874 and 710 significantly differentially expressed genes were identified in forager/nurse and reverted nurse/forager comparisons respectively. Of these, 229 genes exhibited reversed directions of gene expression differences between the forager/nurse and reverted nurse/forager comparisons. Using methyl-DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) we identified 366 and 442 significantly differentially methylated genes in forager/nurse and reverted nurse/forager comparisons respectively. Of these, 165 genes were identified as differentially methylated in both comparisons. However, very few genes were identified as both differentially expressed and differentially methylated in our comparisons of nurses and foragers. These findings confirm that changes in both gene expression and DNA methylation are involved in the nurse and forager behavioural castes, but the different analytical methods reveal quite distinct sets of candidate genes. PMID:24040006

  6. Identification and validation of protein-protein interactions by combining co-immunoprecipitation, antigen competition, and stable isotope labeling.

    PubMed

    Sommer, Frederik; Mühlhaus, Timo; Hemme, Dorothea; Veyel, Daniel; Schroda, Michael

    2014-01-01

    Co-immunoprecipitation (coIP) in combination with mass spectrometry (MS) is a powerful tool to identify potential protein-protein interactions. However, unspecifically precipitated proteins usually result in large numbers of false-positive identifications. Here we describe a detailed protocol particularly useful in plant sciences that is based on (15)N stable isotope labeling of cells, (14)N antigen titration, and coIP/MS to distinguish true from false protein-protein interactions. PMID:25059616

  7. Combining Ultracentrifugation and Peptide Termini Group-specific Immunoprecipitation for Multiplex Plasma Protein Analysis

    PubMed Central

    Volk, Sonja; Schreiber, Thomas D.; Eisen, David; Wiese, Calvin; Planatscher, Hannes; Pynn, Christopher J.; Stoll, Dieter; Templin, Markus F.; Joos, Thomas O.; Pötz, Oliver

    2012-01-01

    Blood plasma is a valuable source of potential biomarkers. However, its complexity and the huge dynamic concentration range of its constituents complicate its analysis. To tackle this problem, an immunoprecipitation strategy was employed using antibodies directed against short terminal epitope tags (triple X proteomics antibodies), which allow the enrichment of groups of signature peptides derived from trypsin-digested plasma. Isolated signature peptides are subsequently detected using MALDI-TOF/TOF mass spectrometry. Sensitivity of the immunoaffinity approach was, however, compromised by the presence of contaminant peaks derived from the peptides of nontargeted high abundant proteins. A closer analysis of the enrichment strategy revealed nonspecific peptide binding to the solid phase affinity matrix as the major source of the contaminating peptides. We therefore implemented a sucrose density gradient ultracentrifugation separation step into the procedure. This yielded a 99% depletion of contaminating peptides from a sucrose fraction containing 70% of the peptide-antibody complexes and enabled the detection of the previously undetected low abundance protein filamin-A. Assessment of this novel approach using 15 different triple X proteomics antibodies demonstrated a more consistent detection of a greater number of targeted peptides and a significant reduction in the intensity of nonspecific peptides. Ultracentrifugation coupled with immunoaffinity MS approaches presents a powerful tool for multiplexed plasma protein analysis without the requirement for demanding liquid chromatography separation techniques. PMID:22527512

  8. Keratin proteins in human lung carcinomas. Combined use of morphology, keratin immunocytochemistry, and keratin immunoprecipitation.

    PubMed Central

    Banks-Schlegel, S. P.; McDowell, E. M.; Wilson, T. S.; Trump, B. F.; Harris, C. C.

    1984-01-01

    Light-microscopic immunocytochemistry and electron microscopy demonstrated that adenocarcinomas (AC) and squamous cell (epidermoid) carcinomas (SCCs) of human lung contained keratin proteins in the form of tonofilament bundles. However, moderately differentiated (md) SCCs contained abundant keratin, whereas poorly differentiated (pd) SCCs and all ACs contained lesser amounts. Lung tumors with the diagnosis of AC or SCC, as defined by WHO criteria, were also analyzed by immunoprecipitation techniques for the presence of keratin proteins. Regardless of the degree of tumor differentiation, SCCs contained a 44 kd keratin which was lacking in ACs. Interestingly, normal bronchial epithelium also contained the same 44 kd keratin. In addition, as SCCs became more differentiated, they exhibited even greater differences in the profile of synthesized keratins. Specifically, the relative abundance of the intermediate-sized keratins (57 and 59 kd) was increased in the md SCCs. Although keratin protein patterns appear to be a valuable adjunct in distinguishing AC from SCC, their usefulness as a diagnostic tool will require survey of a larger number of poorly differentiated tumors. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 PMID:6198920

  9. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

    PubMed

    Down, Thomas A; Rakyan, Vardhman K; Turner, Daniel J; Flicek, Paul; Li, Heng; Kulesha, Eugene; Gräf, Stefan; Johnson, Nathan; Herrero, Javier; Tomazou, Eleni M; Thorne, Natalie P; Bäckdahl, Liselotte; Herberth, Marlis; Howe, Kevin L; Jackson, David K; Miretti, Marcos M; Marioni, John C; Birney, Ewan; Hubbard, Tim J P; Durbin, Richard; Tavaré, Simon; Beck, Stephan

    2008-07-01

    DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm-Bayesian tool for methylation analysis (Batman)-for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation. PMID:18612301

  10. Immunoprecipitation of ROR1

    PubMed Central

    Bicocca, Vincent T.; Tyner, Jeffrey W.

    2016-01-01

    ROR1 is a receptor tyrosine kinase family member studied for its roles in development and cancer. Here we describe a protocol for immunoprecipitation of endogenous ROR1 from t(1;19) (a disease subtype categorized by its chromosome translocation) acute lymphoblastic leukemia immortalized cell lines.

  11. Combination of immunoprecipitation (IP)-ATP_Glo kinase assay and melanogenesis for the assessment of potent and safe PAK1-blockers in cell culture.

    PubMed

    Nguyen, Binh Cao Quan; Be Tu, Pham Thi; Tawata, Shinkichi; Maruta, Hiroshi

    2015-08-01

    Cucurbitacin I (CBI) is a triterpene from a bitter melon called Goya grown in Okinawa, Japan, and directly inhibits both the Tyr-kinase JAK2 and the G protein RAC, leading to the inactivation of PAK1 (RAC/CDC42-activated kinase 1). Bio 30, a propolis produced in New Zealand, contains CAPE (caffeic acid phenethyl ester) as the major anti-cancer ingredient which directly down-regulates RAC, leading to the inactivation of PAK1. Since PAK1 is essential for the growth of RAS cancer cells such as A549 cell line which carry an oncogenic K-RAS mutant, and the melanogenesis in skin cells, here using these PAK1-blockers as model compounds, we introduce a new approach to the quick assessment of PAK1-blockers in cell culture. First, combining the immuno-precipitation (IP) of PAK1 from cell lysate and the in vitro ATP_Glo kinase assay kit (called "Macaroni-Western" assay), we confirmed that both CBI and Bio 30 inactivate PAK1 in A549 lung cancer cells in 24 h, and inhibit their PAK1-dependent growth in 72 h. Furthermore, we verified that CBI inhibits the PAK1/PAK4-dependent melanogenesis in melanoma cells by far more than 50%, while Bio 30 inhibits the melanogenesis only by 50%, with only a merginal effect on their growth per se. Since the "Macaroni-Western" kinase assay and melanogenesis are both rather simple and quick, the combination of these two cell culture assays would be highly useful for selecting both "potent" (highly cell-permeable) and "safe" (non-toxic) natural or synthetic PAK1-blockers. PMID:26370527

  12. Structural basis for Klf4 recognition of methylated DNA.

    PubMed

    Liu, Yiwei; Olanrewaju, Yusuf Olatunde; Zheng, Yu; Hashimoto, Hideharu; Blumenthal, Robert M; Zhang, Xing; Cheng, Xiaodong

    2014-04-01

    Transcription factor Krüppel-like factor 4 (Klf4), one of the factors directing cellular reprogramming, recognizes the CpG dinucleotide (whether methylated or unmodified) within a specific G/C-rich sequence. The binding affinity of the mouse Klf4 DNA-binding domain for methylated DNA is only slightly stronger than that for an unmodified oligonucleotide. The structure of the C-terminal three Krüppel-like zinc fingers (ZnFs) of mouse Klf4, in complex with fully methylated DNA, was determined at 1.85 Å resolution. An arginine and a glutamate interact with the methyl group. By comparison with two other recently characterized structures of ZnF protein complexes with methylated DNA, we propose a common principle of recognition of methylated CpG by C2H2 ZnF proteins, which involves a spatially conserved Arg-Glu pair. PMID:24520114

  13. Promoter-restricted histone code, not the differentially methylated DNA regions or antisense transcripts, marks the imprinting status of IGF2R in human and mouse.

    PubMed

    Vu, Thanh H; Li, Tao; Hoffman, Andrew R

    2004-10-01

    Imprinting of the mouse Igf2r depends upon an intronic differentially methylated DNA region (DMR) and the presence of the Air antisense transcript. However, biallelic expression of mouse Igf2r in brain occurs despite the presence of Air, and biallelic expression of human IGF2R in peripheral tissues occurs despite the presence of an intronic DMR. We examined histone modifications throughout the mouse and human Igf2r/IGF2R using chromatin immuno-precipitation (ChIP) assays in combination with quantitative real time PCR. Methylation of Lys4 and Lys9 of histone H3 in the promoter regions marks the active and silenced alleles, respectively. We measured di- and tri-methyl Lys4 and Lys9 across the Igf2r and Air promoters. While both di- and tri-methyl Lys4 marked the active Igf2r and the active Air allele, tri-methyl Lys9, but not di-methyl Lys9, marked the suppressed Air allele. We show here that enrichment of parental allele-specific histone modifications in the promoter region, rather than the presence of DNA methylation or antisense transcription, correctly identifies the tissue- and species- specific imprinting status of Igf2r/IGF2R. We discuss these findings in light of recent progress in identifying specific components of the epigenetic marks in imprinted genes. PMID:15294879

  14. A Two-Gene Blood Test for Methylated DNA Sensitive for Colorectal Cancer

    PubMed Central

    Pedersen, Susanne K.; Baker, Rohan T.; McEvoy, Aidan; Murray, David H.; Thomas, Melissa; Molloy, Peter L.; Mitchell, Sue; Lockett, Trevor; Young, Graeme P.; LaPointe, Lawrence C.

    2015-01-01

    Background Specific genes are methylated with high frequency in colorectal neoplasia, and may leak into blood. Detection of multiple methylated DNA biomarkers in blood may improve assay sensitivity for colorectal cancer (CRC) relative to a single marker. We undertook a case-control study evaluating the presence of two methylation DNA markers, BCAT1 and IKZF1, in circulation to determine if they were complementary for detection of CRC. Methods Methylation-specific PCR assays were developed to measure the level of methylated BCAT1 and IKZF1 in DNA extracted from plasma obtained from colonoscopy-confirmed 144 healthy controls and 74 CRC cases. Results DNA yields ranged from 2 to 730 ng/mL plasma (mean 18.6ng/mL; 95% CI 11-26 ng/mL) and did not correlate with gender, age or CRC status. Methylated BCAT1 and IKZF1 DNA were detected in respectively 48 (65%) and 50 (68%) of the 74 cancers. In contrast, only 5 (4%) and 7 (5%) controls were positive for BCAT1 and IKZF1 DNA methylation, respectively. A two-gene classifier model (“either or” rule) improved segregation of CRC from controls, with 57 of 74 cancers (77%) compared to only 11 of 144 (7.6%) controls being positive for BCAT1 and/or IKZF1 DNA methylation. Increasing levels of methylated DNA were observed as CRC stage progressed. Conclusions Detection of methylated BCAT1 and/or IKZF1 DNA in plasma may have clinical application as a novel blood test for CRC. Combining the results from the two methylation-specific PCR assays improved CRC detection with minimal change in specificity. Further validation of this two-gene blood test with a view to application in screening is now indicated. PMID:25928810

  15. DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments.

    PubMed

    Wu, Feinan; Olson, Brennan G; Yao, Jie

    2016-01-01

    The DNA adenine methyltransferase identification (DamID) assay is a powerful method to detect protein-DNA interactions both locally and genome-wide. It is an alternative approach to chromatin immunoprecipitation (ChIP). An expressed fusion protein consisting of the protein of interest and the E. coli DNA adenine methyltransferase can methylate the adenine base in GATC motifs near the sites of protein-DNA interactions. Adenine-methylated DNA fragments can then be specifically amplified and detected. The original DamID assay detects the genomic locations of methylated DNA fragments by hybridization to DNA microarrays, which is limited by the availability of microarrays and the density of predetermined probes. In this paper, we report the detailed protocol of integrating high throughput DNA sequencing into DamID (DamID-seq). The large number of short reads generated from DamID-seq enables detecting and localizing protein-DNA interactions genome-wide with high precision and sensitivity. We have used the DamID-seq assay to study genome-nuclear lamina (NL) interactions in mammalian cells, and have noticed that DamID-seq provides a high resolution and a wide dynamic range in detecting genome-NL interactions. The DamID-seq approach enables probing NL associations within gene structures and allows comparing genome-NL interaction maps with other functional genomic data, such as ChIP-seq and RNA-seq. PMID:26862720

  16. Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells

    PubMed Central

    Devailly, Guillaume; Grandin, Mélodie; Perriaud, Laury; Mathot, Pauline; Delcros, Jean-Guy; Bidet, Yannick; Morel, Anne-Pierre; Bignon, Jean-Yves; Puisieux, Alain; Mehlen, Patrick; Dante, Robert

    2015-01-01

    DNA methylation is thought to induce transcriptional silencing through the combination of two mechanisms: the repulsion of transcriptional activators unable to bind their target sites when methylated, and the recruitment of transcriptional repressors with specific affinity for methylated DNA. The Methyl CpG Binding Domain proteins MeCP2, MBD1 and MBD2 belong to the latter category. Here, we present MBD2 ChIPseq data obtained from the endogenous MBD2 in an isogenic cellular model of oncogenic transformation of human mammary cells. In immortalized (HMEC-hTERT) or transformed (HMLER) cells, MBD2 was found in a large proportion of methylated regions and associated with transcriptional silencing. A redistribution of MBD2 on methylated DNA occurred during oncogenic transformation, frequently independently of local DNA methylation changes. Genes downregulated during HMEC-hTERT transformation preferentially gained MBD2 on their promoter. Furthermore, depletion of MBD2 induced an upregulation of MBD2-bound genes methylated at their promoter regions, in HMLER cells. Among the 3,160 genes downregulated in transformed cells, 380 genes were methylated at their promoter regions in both cell lines, specifically associated by MBD2 in HMLER cells, and upregulated upon MBD2 depletion in HMLER. The transcriptional MBD2-dependent downregulation occurring during oncogenic transformation was also observed in two additional models of mammary cell transformation. Thus, the dynamics of MBD2 deposition across methylated DNA regions was associated with the oncogenic transformation of human mammary cells. PMID:26007656

  17. Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation.

    PubMed

    He, Yan; Wang, Minghui; Sun, Qi; Pawlowski, Wojciech P

    2016-01-01

    Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi. PMID:27511175

  18. Expression, purification and characterization of methyl DNA binding protein from Bombyx mori.

    PubMed

    Uno, Tomohide; Nomura, Yuka; Nakamura, Masahiko; Nakao, Atsushi; Tajima, Shoji; Kanamaru, Kengo; Yamagata, Hiroshi; Iwanaga, Yousuke

    2005-01-01

    A cDNA clone encoding methyl DNA binding domain-containing protein (bMBD2/3) was obtained by homology searches using a Bombyx mori fat body cDNA library. The cDNA encoded a polypeptide with 249 amino acids sharing 54% similarity with the methyl DNA binding protein from Drosophila melanogaster. To characterize the biochemical properties of bMBD2/3, the clone was expressed in Escherichia coli as His-tagged protein. The recombinant protein was purified to homogeneity using Ni-NTA superflow resin and heparin agarose. The protein showed specific methyl DNA binding activity and was phosphorylated by protein kinase in vitro. Immunoblotting using the purified antibody indicated that bMBD2/3 was expressed in almost all tissues. Using west-western blotting analysis, some proteins that interact with bMBD2/3 were identified in the brain. This is the first report that insect MBD is phosphorylated and is present in adult tissues. These results suggest that bMBD2/3 plays important roles in the DNA methylation-specific transcription of Bombyx mori. PMID:16299598

  19. Immunoprecipitation of the parathyroid hormone receptor

    SciTech Connect

    Wright, B.S.; Tyler, G.A.; O'Brien, R.; Caporale, L.H.; Rosenblatt, M.

    1987-01-01

    An /sup 125/I-labeled synthetic analog of bovine parathyroid hormone, (8-norleucine,18-norleucine,34-tyrosine)PTH-(1-34) amide ((Nle)PTH-(1-34)-NH/sub 2/), purified by high-pressure liquid chromatography (HPLC), was employed to label the parathyroid hormone (PTH) receptor in cell lines derived from PTH target tissues: the ROS 17/2.8 rat osteosarcoma of bone and the CV1 and COS monkey kidney lines. After incubation of the radioligand with intact cultured cells, the hormone was covalently attached to receptors by using either a photoaffinity technique or chemical (affinity) crosslinking. In each case, covalent labeling was specific, as evidenced by a reduction of labeling when excess competing nonradioactive ligand was present. After covalent attachment of radioligand, membranes were prepared form the cells and solubilized in the nonionic detergent Nonidet P-40 or octyl glucoside. Analysis of the immunoprecipitate on NaDod-SO/sub 4//polyacrylamide gel electrophoresis followed by autoradiography revealed the presence of a doublet of apparent molecular mass 69-70 kDa. Specifically labeled bands of approximate molecular mass 95 and 28 kDa were also observed. The anti-PTH IgG was affinity purified by passage over a PTH-Sepharose column and used to made an immunoaffinity column. These studies suggest that the use of an anti-PTH antiserum that binds receptor-bound hormone is likely to be a useful step in the further physicochemical characterization and purification of the PTH receptor.

  20. Immunoprecipitation and Characterization of Membrane Protein Complexes from Yeast

    ERIC Educational Resources Information Center

    Parra-Belky, Karlett; McCulloch, Kathryn; Wick, Nicole; Shircliff, Rebecca; Croft, Nicolas; Margalef, Katrina; Brown, Jamie; Crabill, Todd; Jankord, Ryan; Waldo, Eric

    2005-01-01

    In this undergraduate biochemistry laboratory experiment, the vacuolar ATPase protein complex is purified from yeast cell extracts by doing immunoprecipitations under nondenaturing conditions. Immunoprecipitations are performed using monoclonal antibodies to facilitate data interpretation, and subunits are separated on the basis of their molecular…

  1. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates.

    PubMed

    Long, Hannah K; Sims, David; Heger, Andreas; Blackledge, Neil P; Kutter, Claudia; Wright, Megan L; Grützner, Frank; Odom, Duncan T; Patient, Roger; Ponting, Chris P; Klose, Robert J

    2013-01-01

    Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation on chromatin. In cold-blooded vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution. DOI:http://dx.doi.org/10.7554/eLife.00348.001. PMID:23467541

  2. Methylated DNA-binding protein is present in various mammalian cell types

    SciTech Connect

    Supakar, P.C.; Weist, D.; Zhang, D.; Inamdar, N.; Zhang, Xianyang; Khan, R.; Ehrlich, M. ); Ehrlich, K.C. )

    1988-08-25

    A DNA-binding protein from human placenta, methylated DNA-binding protein (MDBP), binds to certain DNA sequences only when they contain 5-methylcytosine (m{sup 5}C) residues at specific positions. The authors found a very similar DNA-binding activity in nuclear extracts of rat tissues, calf thymus, human embryonal carcinoma cells, HeLa cells, and mouse LTK cells. Like human placental MDBP, the analogous DNA-binding proteins from the above mammalian cell lines formed a number of different low-electrophoretic-mobility complexes with a 14-bp MDBP-specific oligonucleotide duplex. All of these complexes exhibited the same DNA methylation specificity and DNA sequence specificity. Although MDBP activity was found in various mammalian cell types, it was not detected in extracts of cultured mosquito cells and so may be associated only with cells with vertebrate-type DNA methylation.

  3. Label free colorimetric and fluorimetric direct detection of methylated DNA based on silver nanoclusters for cancer early diagnosis.

    PubMed

    Dadmehr, Mehdi; Hosseini, Morteza; Hosseinkhani, Saman; Ganjali, Mohammad Reza; Sheikhnejad, Reza

    2015-11-15

    Epigenetic changes such as DNA methylation of CpG islands located in the promoter region of some tumor suppressor genes are very common in human diseases such as cancer. Detection of aberrant methylation pattern could serve as an excellent diagnostic approach. Recently, the direct detection of methylated DNA sequences without using chemical and enzymatic treatments or antibodies has received great deal of attentions. In this study, we report a colorimetric and fluorimetric technique for direct detection of DNA methylation. Here, the DNA is being used as an effective template for fluorescent silver nanoclusters formation without any chemical modification or DNA labeling. The sensitivity test showed that upon the addition of target methylated DNA, the fluorescence intensity is decreased in a linear range when the concentration of methylated DNA has increased from 2.0×10(-9) to 6.3 ×10(-7) M with the detection limit of 9.4×10(-10) M. The optical and fluorescence spectral behaviors were highly reproducible and clearly discriminated between unmethylated, methylated and even partially methylated DNA in CpG rich sequences. The results were also reproducible when the human plasma was present in our assay system. PMID:26056954

  4. Mapping regulatory factors by immunoprecipitation from native chromatin

    PubMed Central

    Orsi, Guillermo A.; Kasinathan, Sivakanthan; Zentner, Gabriel E.; Henikoff, Steven; Ahmad, Kami

    2015-01-01

    Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin (ORGANIC) is a high-resolution method that can be used to quantitatively map protein-DNA interactions with high specificity and sensitivity. This method uses micrococcal nuclease (MNase) digestion of chromatin and low-salt solubilization to preserve protein-DNA complexes followed by immunoprecipitation and paired-end sequencing for genome-wide mapping of binding sites. In this Unit, we describe methods for isolation of nuclei and MNase digestion of unfixed chromatin, immunoprecipitation of protein-DNA complexes, and high-throughput sequencing to map sites of bound factors. PMID:25827087

  5. Rhein Inhibits AlkB Repair Enzymes and Sensitizes Cells to Methylated DNA Damage.

    PubMed

    Li, Qi; Huang, Yue; Liu, Xichun; Gan, Jianhua; Chen, Hao; Yang, Cai-Guang

    2016-05-20

    The AlkB repair enzymes, including Escherichia coli AlkB and two human homologues, ALKBH2 and ALKBH3, are iron(II)- and 2-oxoglutarate-dependent dioxygenases that efficiently repair N(1)-methyladenine and N(3)-methylcytosine methylated DNA damages. The development of small molecule inhibitors of these enzymes has seen less success. Here we have characterized a previously discovered natural product rhein and tested its ability to inhibit AlkB repair enzymes in vitro and to sensitize cells to methyl methane sulfonate that mainly produces N(1)-methyladenine and N(3)-methylcytosine lesions. Our investigation of the mechanism of rhein inhibition reveals that rhein binds to AlkB repair enzymes in vitro and promotes thermal stability in vivo In addition, we have determined a new structural complex of rhein bound to AlkB, which shows that rhein binds to a different part of the active site in AlkB than it binds to in fat mass and obesity-associated protein (FTO). With the support of these observations, we put forth the hypothesis that AlkB repair enzymes would be effective pharmacological targets for cancer treatment. PMID:27015802

  6. Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition.

    PubMed

    Fang, Jian; Cheng, Jingdong; Wang, Jiaolong; Zhang, Qiao; Liu, Mengjie; Gong, Rui; Wang, Ping; Zhang, Xiaodan; Feng, Yangyang; Lan, Wenxian; Gong, Zhou; Tang, Chun; Wong, Jiemin; Yang, Huirong; Cao, Chunyang; Xu, Yanhui

    2016-01-01

    UHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD-PHD. The Spacer also facilitates UHRF1-DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD-PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1. PMID:27045799

  7. Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

    PubMed Central

    Fang, Jian; Cheng, Jingdong; Wang, Jiaolong; Zhang, Qiao; Liu, Mengjie; Gong, Rui; Wang, Ping; Zhang, Xiaodan; Feng, Yangyang; Lan, Wenxian; Gong, Zhou; Tang, Chun; Wong, Jiemin; Yang, Huirong; Cao, Chunyang; Xu, Yanhui

    2016-01-01

    UHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD–PHD. The Spacer also facilitates UHRF1–DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD–PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1. PMID:27045799

  8. ASCIZ regulates lesion-specific Rad51 focus formation and apoptosis after methylating DNA damage.

    PubMed

    McNees, Carolyn J; Conlan, Lindus A; Tenis, Nora; Heierhorst, Jörg

    2005-07-01

    Nuclear Rad51 focus formation is required for homology-directed repair of DNA double-strand breaks (DSBs), but its regulation in response to non-DSB lesions is poorly understood. Here we report a novel human SQ/TQ cluster domain-containing protein termed ASCIZ that forms Rad51-containing foci in response to base-modifying DNA methylating agents but not in response to DSB-inducing agents. ASCIZ foci seem to form prior to Rad51 recruitment, and an ASCIZ core domain can concentrate Rad51 in focus-like structures independently of DNA damage. ASCIZ depletion dramatically increases apoptosis after methylating DNA damage and impairs Rad51 focus formation in response to methylating agents but not after ionizing radiation. ASCIZ focus formation and increased apoptosis in ASCIZ-depleted cells depend on the mismatch repair protein MLH1. Interestingly, ASCIZ foci form efficiently during G1 phase, when sister chromatids are unavailable as recombination templates. We propose that ASCIZ acts as a lesion-specific focus scaffold in a Rad51-dependent pathway that resolves cytotoxic repair intermediates, most likely single-stranded DNA gaps, resulting from MLH1-dependent processing of base lesions. PMID:15933716

  9. ASCIZ regulates lesion-specific Rad51 focus formation and apoptosis after methylating DNA damage

    PubMed Central

    McNees, Carolyn J; Conlan, Lindus A; Tenis, Nora; Heierhorst, Jörg

    2005-01-01

    Nuclear Rad51 focus formation is required for homology-directed repair of DNA double-strand breaks (DSBs), but its regulation in response to non-DSB lesions is poorly understood. Here we report a novel human SQ/TQ cluster domain-containing protein termed ASCIZ that forms Rad51-containing foci in response to base-modifying DNA methylating agents but not in response to DSB-inducing agents. ASCIZ foci seem to form prior to Rad51 recruitment, and an ASCIZ core domain can concentrate Rad51 in focus-like structures independently of DNA damage. ASCIZ depletion dramatically increases apoptosis after methylating DNA damage and impairs Rad51 focus formation in response to methylating agents but not after ionizing radiation. ASCIZ focus formation and increased apoptosis in ASCIZ-depleted cells depend on the mismatch repair protein MLH1. Interestingly, ASCIZ foci form efficiently during G1 phase, when sister chromatids are unavailable as recombination templates. We propose that ASCIZ acts as a lesion-specific focus scaffold in a Rad51-dependent pathway that resolves cytotoxic repair intermediates, most likely single-stranded DNA gaps, resulting from MLH1-dependent processing of base lesions. PMID:15933716

  10. Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

    NASA Astrophysics Data System (ADS)

    Fang, Jian; Cheng, Jingdong; Wang, Jiaolong; Zhang, Qiao; Liu, Mengjie; Gong, Rui; Wang, Ping; Zhang, Xiaodan; Feng, Yangyang; Lan, Wenxian; Gong, Zhou; Tang, Chun; Wong, Jiemin; Yang, Huirong; Cao, Chunyang; Xu, Yanhui

    2016-04-01

    UHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD-PHD. The Spacer also facilitates UHRF1-DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD-PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1.

  11. Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

    PubMed Central

    Emmott, Edward; Goodfellow, Ian

    2014-01-01

    Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants. Low affinity interactions can be preserved through the use of less-stringent buffer conditions and remain readily identifiable. This protocol discusses the labeling of tissue culture cells with stable isotope labeled amino acids, transfection and immunoprecipitation of an affinity tagged protein of interest, followed by the preparation for submission to a mass spectrometry facility. This protocol then discusses how to analyze and interpret the data returned from the mass spectrometer in order to identify cellular partners interacting with a protein of interest. As an example this technique is applied to identify proteins binding to the eukaryotic translation initiation factors: eIF4AI and eIF4AII. PMID:25046639

  12. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.

    SciTech Connect

    Avvakumov, George V.; Walker, John R.; Xue, Sheng; Li, Yanjun; Duan, Shili; Bronner, Christian; Arrowsmith, Cheryl H.; Dhe-Paganon, Sirano

    2008-11-17

    Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development. UHRF1 (also known as ICBP90 in humans and Np95 in mouse) is an E3 ligase important for the maintenance of global and local DNA methylation in vivo. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code. Here we report the 1.7 {angstrom} crystal structure of the apo SRA domain of human UHRF1 and a 2.2 {angstrom} structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA-DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.

  13. Chromatin Immunoprecipitation to Detect DNA Replication and Repair Factors

    PubMed Central

    Gadaleta, Mariana C.; Iwasaki, Osamu; Noguchi, Chiaki; Noma, Ken-Ichi; Noguchi, Eishi

    2015-01-01

    DNA replication is tightly coupled with DNA repair processes in order to preserve genomic integrity. During DNA replication, the replication fork encounters a variety of obstacles including DNA damage/adducts, secondary structures, and programmed fork-blocking sites, which are all difficult to replicate. The replication fork also collides with the transcription machinery, which shares the template DNA with the replisome complex. Under these conditions, replication forks stall, causing replication stress and/or fork collapse, ultimately leading to genomic instability. The mechanisms to overcome these replication problems remain elusive. Therefore, it is important to investigate how DNA repair and replication factors are recruited and coordinated at chromosomal regions that are difficult to replicate. In this chapter, we describe a chromatin immunoprecipitation method to locate proteins required for DNA repair during DNA replication in the fission yeast Schizosaccharomyces pombe. This method can also easily be adapted to study replisome components or chromatin-associated factors. PMID:25916713

  14. Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation.

    PubMed

    Wu, Angela R; Quake, Stephen R

    2016-01-01

    Protein-DNA interactions are responsible for numerous critical cellular events: For example, gene expression and silencing are mediated by transcription factor protein binding and histone protein modifications, and DNA replication and repair rely on site-specific protein binding. Chromatin immunoprecipitation (ChIP) is the only molecular assay that directly determines, in a living cell, the binding association between a protein of interest and specific genomic loci. It is an indispensible tool in the biologist's toolbox, but the many limitations of this technique prevent broad adoption of ChIP in biological studies. The typical ChIP assay can take up to 1 wk to complete, and the process is technically tricky, yet tedious. The ChIP assay yields are also low, thus requiring on the order of millions to billions of cells as starting material, which makes the assay unfeasible for studies using rare or precious samples. For example, fluorescence-activated cell sorting (FACS) of cancer stem cells (CSCs) obtained from primary tumors, rarely yields more than ~100,000 CSCs per tumor. This protocol describes a microfluidics-based strategy for performing ChIP, which uses automation and scalability to reduce both total and hands-on assay time, and improve throughput. It allows whole fixed cells as input, and enables automated ChIP from as few as 2000 cells. PMID:26700100

  15. Co-Immunoprecipitation of Membrane-Bound Receptors

    PubMed Central

    Avila, Julian R.; Lee, Jin Suk; Torii, Keiko U.

    2015-01-01

    The study of cell-surface receptor dynamics is critical for understanding how cells sense and respond to changing environments. Therefore, elucidating the mechanisms by which signals are perceived and communicated into the cell is necessary to understand immunity, development, and stress. Challenges in testing interactions of membrane-bound proteins include their dynamic nature, their abundance, and the complex dual environment (lipid/soluble) in which they reside. Co-Immunoprecipitation (Co-IP) of tagged membrane proteins is a widely used approach to test protein-protein interaction in vivo. In this protocol we present a method to perform Co-IP using enriched membrane proteins in isolated microsomal fractions. The different variations of this protocol are highlighted, including recommendations and troubleshooting guides in order to optimize its application. This Co-IP protocol has been developed to test the interaction of receptor-like kinases, their interacting partners, and peptide ligands in stable Arabidopsis thaliana lines, but can be modified to test interactions in transiently expressed proteins in tobacco, and potentially in other plant models, or scaled for large-scale protein-protein interactions at the membrane. PMID:26097438

  16. Searching for biomarkers: humoral response profiling with luciferase immunoprecipitation systems.

    PubMed

    Burbelo, Peter D; Ching, Kathryn H; Bren, Kathleen E; Iadarola, Michael J

    2011-06-01

    B-cell-mediated humoral responses are triggered in many human diseases, including autoimmune diseases, cancer, and neurologic and infectious diseases. However, the full exploitation of the information contained within a patient's antibody repertoire for diagnosis, monitoring and even disease prediction has been limited due to the poor diagnostic performance of many immunoassay formats. We have developed luciferase immunoprecipitation systems (LIPS) that harnesses light-emitting proteins to generate high-definition antibody profiles that are optimal for both diagnostics and biomarker discovery. Here, we describe the results and implications from a range of LIPS-antibody profiling studies performed in our laboratory. These include highly sensitive diagnostics for domestic and global pathogens, insights into infection-related diseases, discovery of new biomarkers for human diseases, subcategorization of symptoms and identification of pathogenic autoantibodies against self-proteins. These investigations highlight the types of humoral response profiles associated with different diseases, provide new information related to disease pathogenesis and offer a framework for incorporating LIPS antibody profiling into global health initiatives and disease monitoring. PMID:21679112

  17. Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes.

    PubMed

    Yang, S; Ott, C J; Rossmann, M P; Superdock, M; Zon, L I; Zhou, Y

    2016-01-01

    Zebrafish is an excellent genetic and developmental model for the study of vertebrate development and disease. Its ability to produce an abundance of transparent, externally developed embryos has facilitated large-scale genetic and chemical screens for the identification of critical genes and chemical factors that modulate developmental pathways. These studies can have profound implications for the diagnosis and treatment of a variety of human diseases. Recent advancements in molecular and genomic studies have provided valuable tools and resources for comprehensive and high-resolution analysis of epigenomes during cell specification and lineage differentiation throughout development. In this chapter, we describe two simple methods to evaluate protein-DNA interaction and chromatin architecture in erythrocytes from adult zebrafish. These are chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) and an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). These techniques, together with gene expression profiling, are useful for analyzing epigenomic regulation of cell specification, differentiation, and function during zebrafish development in both normal and disease models. PMID:27443937

  18. Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies

    PubMed Central

    Fujita, Toshitsugu; Fujii, Hodaka

    2016-01-01

    To isolate specific genomic regions that retain their molecular interactions, allowing direct identification of chromatin-bound molecules, we developed two locus-specific chromatin immunoprecipitation (locus-specific ChIP) technologies, insertional ChIP (iChIP) and engineered DNA-binding molecule-mediated ChIP (enChIP) using the clustered regularly interspaced short palindromic repeats (CRISPR) system or transcription activator-like (TAL) proteins. Essentially, a locus-specific ChIP consists of locus-tagging and affinity purification and can be combined with downstream analyses to identify molecules associated with the target genomic regions. In this review, we discuss the applications of locus-specific ChIP to analyze the genome functions, including transcription and epigenetic regulation. PMID:26819551

  19. Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts.

    PubMed

    Lohse, Matthew B; Kongsomboonvech, Pisiwat; Madrigal, Maria; Hernday, Aaron D; Nobile, Clarissa J

    2016-01-01

    Chromatin immunoprecipitation experiments are critical to investigating the interactions between DNA and a wide range of nuclear proteins within a cell or biological sample. In this chapter we outline an optimized protocol for genome-wide chromatin immunoprecipitation that has been used successfully for several distinct morphological forms of numerous yeast species, and include an optimized method for amplification of chromatin immunoprecipitated DNA samples and hybridization to a high-density oligonucleotide tiling microarray. We also provide detailed suggestions on how to analyze the complex data obtained from these experiments. PMID:26483022

  20. Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts

    PubMed Central

    Lohse, Matthew B.; Kongsomboonvech, Pisiwat; Madrigal, Maria; Hernday, Aaron D.; Nobile, Clarissa J.

    2016-01-01

    Chromatin immunoprecipitation experiments are critical to investigating the interactions between DNA and a wide range of nuclear proteins within a cell or biological sample. In this chapter we outline an optimized protocol for genome-wide chromatin immunoprecipitation that has been used successfully for several distinct morphological forms of numerous yeast species, and include an optimized method for amplification of chromatin immunoprecipitated DNA samples and hybridization to a high-density oligonucleotide tiling microarray. We also provide detailed suggestions on how to analyze the complex data obtained from these experiments. PMID:26483022

  1. Human age estimation from blood using mRNA, DNA methylation, DNA rearrangement, and telomere length.

    PubMed

    Zubakov, Dmitry; Liu, Fan; Kokmeijer, Iris; Choi, Ying; van Meurs, Joyce B J; van IJcken, Wilfred F J; Uitterlinden, André G; Hofman, Albert; Broer, Linda; van Duijn, Cornelia M; Lewin, Jörn; Kayser, Manfred

    2016-09-01

    Establishing the age of unknown persons, or persons with unknown age, can provide important leads in police investigations, disaster victim identification, fraud cases, and in other legal affairs. Previous methods mostly relied on morphological features available from teeth or skeletal parts. The development of molecular methods for age estimation allowing to use human specimens that possess no morphological age information, such as bloodstains, is extremely valuable as this type of samples is commonly found at crime scenes. Recently, we introduced a DNA-based approach for human age estimation from blood based on the quantification of T-cell specific DNA rearrangements (sjTRECs), which achieves accurate assignment of blood DNA samples to one of four 20-year-interval age categories. Aiming at improving the accuracy of molecular age estimation from blood, we investigated different types of biomarkers. We started out by systematic genome-wide surveys for new age-informative mRNA and DNA methylation markers in blood from the same young and old individuals using microarray technologies. The obtained candidate markers were validated in independent samples covering a wide age range using alternative technologies together with previously proposed DNA methylation, sjTREC, and telomere length markers. Cross-validated multiple regression analysis was applied for estimating and validating the age predictive power of various sets of biomarkers within and across different marker types. We found that DNA methylation markers outperformed mRNA, sjTREC, and telomere length in age predictive power. The best performing model included 8 DNA methylation markers derived from 3 CpG islands reaching a high level of accuracy (cross-validated R(2)=0.88, SE±6.97 years, mean absolute deviation 5.07 years). However, our data also suggest that mRNA markers can provide independent age information: a model using a combined set of 5 DNA methylation markers and one mRNA marker could provide

  2. Low levels of cadmium chloride alter the immunoprecipitation of corneal cadherin-complex proteins.

    PubMed

    Weidner, W J; Waddell, D S; Sillman, A J

    2000-12-01

    The effect of cadmium chloride on the immunoprecipitation of cadherin and the associated adherens junctional proteins, alpha- and beta-catenin, was examined in isolated bullfrog (Rana catesbeiana) corneas utilizing Western blot and enhanced chemoluminescent techniques. Application of either 1.0 microM or 75.0 microM CdCl2 to the corneal endothelium for 2 h markedly decreased the immunoprecipitation of cadherins as compared to paired control corneas. Immunoprecipitation of alpha-catenin was increased in response to both doses of CdCl2, while the immunoprecipitation of beta-catenin was little changed by either cadmium dose. There is accumulating evidence that cadmium may increase epithelial paracellular permeability by interfering with cadherin complex activity at intercellular junctions. The present study suggests that inorganic cadmium in low micromolar concentrations may decrease the integrity of the corneal endothelium, at least in part through a similar mechanism involving disruption of junctional cadherin complex function. PMID:11201663

  3. Studying Protein-Protein Interactions in Budding Yeast Using Co-immunoprecipitation.

    PubMed

    Foltman, Magdalena; Sanchez-Diaz, Alberto

    2016-01-01

    Understanding protein-protein interactions and the architecture of protein complexes in which they work is essential to identify their biological role. Protein co-immunoprecipitation (co-IP) is an invaluable technique used in biochemistry allowing the identification of protein interactors. Here, we describe in detail an immunoaffinity purification protocol as a one-step or two-step immunoprecipitation from budding yeast Saccharomyces cerevisiae cells to subsequently detect interactions between proteins involved in the same biological process. PMID:26519317

  4. Isotope Coded Protein Labeling Coupled Immunoprecipitation (ICPL-IP): A Novel Approach for Quantitative Protein Complex Analysis From Native Tissue*

    PubMed Central

    Vogt, Andreas; Fuerholzner, Bettina; Kinkl, Norbert; Boldt, Karsten; Ueffing, Marius

    2013-01-01

    High confidence definition of protein interactions is an important objective toward the understanding of biological systems. Isotope labeling in combination with affinity-based isolation of protein complexes has increased in accuracy and reproducibility, yet, larger organisms—including humans—are hardly accessible to metabolic labeling and thus, a major limitation has been its restriction to small animals, cell lines, and yeast. As composition as well as the stoichiometry of protein complexes can significantly differ in primary tissues, there is a great demand for methods capable to combine the selectivity of affinity-based isolation as well as the accuracy and reproducibility of isotope-based labeling with its application toward analysis of protein interactions from intact tissue. Toward this goal, we combined isotope coded protein labeling (ICPL)1 with immunoprecipitation (IP) and quantitative mass spectrometry (MS). ICPL-IP allows sensitive and accurate analysis of protein interactions from primary tissue. We applied ICPL-IP to immuno-isolate protein complexes from bovine retinal tissue. Protein complexes of immunoprecipitated β-tubulin, a highly abundant protein with known interactors as well as the lowly expressed small GTPase RhoA were analyzed. The results of both analyses demonstrate sensitive and selective identification of known as well as new protein interactions by our method. PMID:23268931

  5. Isotope coded protein labeling coupled immunoprecipitation (ICPL-IP): a novel approach for quantitative protein complex analysis from native tissue.

    PubMed

    Vogt, Andreas; Fuerholzner, Bettina; Kinkl, Norbert; Boldt, Karsten; Ueffing, Marius

    2013-05-01

    High confidence definition of protein interactions is an important objective toward the understanding of biological systems. Isotope labeling in combination with affinity-based isolation of protein complexes has increased in accuracy and reproducibility, yet, larger organisms--including humans--are hardly accessible to metabolic labeling and thus, a major limitation has been its restriction to small animals, cell lines, and yeast. As composition as well as the stoichiometry of protein complexes can significantly differ in primary tissues, there is a great demand for methods capable to combine the selectivity of affinity-based isolation as well as the accuracy and reproducibility of isotope-based labeling with its application toward analysis of protein interactions from intact tissue. Toward this goal, we combined isotope coded protein labeling (ICPL)(1) with immunoprecipitation (IP) and quantitative mass spectrometry (MS). ICPL-IP allows sensitive and accurate analysis of protein interactions from primary tissue. We applied ICPL-IP to immuno-isolate protein complexes from bovine retinal tissue. Protein complexes of immunoprecipitated β-tubulin, a highly abundant protein with known interactors as well as the lowly expressed small GTPase RhoA were analyzed. The results of both analyses demonstrate sensitive and selective identification of known as well as new protein interactions by our method. PMID:23268931

  6. Combined analysis of DNA methylome and transcriptome reveal novel candidate genes with susceptibility to bovine Staphylococcus aureus subclinical mastitis

    PubMed Central

    Song, Minyan; He, Yanghua; Zhou, Huangkai; Zhang, Yi; Li, Xizhi; Yu, Ying

    2016-01-01

    Subclinical mastitis is a widely spread disease of lactating cows. Its major pathogen is Staphylococcus aureus (S. aureus). In this study, we performed genome-wide integrative analysis of DNA methylation and transcriptional expression to identify candidate genes and pathways relevant to bovine S. aureus subclinical mastitis. The genome-scale DNA methylation profiles of peripheral blood lymphocytes in cows with S. aureus subclinical mastitis (SA group) and healthy controls (CK) were generated by methylated DNA immunoprecipitation combined with microarrays. We identified 1078 differentially methylated genes in SA cows compared with the controls. By integrating DNA methylation and transcriptome data, 58 differentially methylated genes were shared with differently expressed genes, in which 20.7% distinctly hypermethylated genes showed down-regulated expression in SA versus CK, whereas 14.3% dramatically hypomethylated genes showed up-regulated expression. Integrated pathway analysis suggested that these genes were related to inflammation, ErbB signalling pathway and mismatch repair. Further functional analysis revealed that three genes, NRG1, MST1 and NAT9, were strongly correlated with the progression of S. aureus subclinical mastitis and could be used as powerful biomarkers for the improvement of bovine mastitis resistance. Our studies lay the groundwork for epigenetic modification and mechanistic studies on susceptibility of bovine mastitis. PMID:27411928

  7. Co-immunoprecipitation of the Mouse Mx1 Protein with the Influenza A Virus Nucleoprotein.

    PubMed

    Verhelst, Judith; De Vlieger, Dorien; Saelens, Xavier

    2015-01-01

    Studying the interaction between proteins is key in understanding their function(s). A very powerful method that is frequently used to study interactions of proteins with other macromolecules in a complex sample is called co-immunoprecipitation. The described co-immunoprecipitation protocol allows to demonstrate and further investigate the interaction between the antiviral myxovirus resistance protein 1 (Mx1) and one of its viral targets, the influenza A virus nucleoprotein (NP). The protocol starts with transfected mammalian cells, but it is also possible to use influenza A virus infected cells as starting material. After cell lysis, the viral NP protein is pulled-down with a specific antibody and the resulting immune-complexes are precipitated with protein G beads. The successful pull-down of NP and the co-immunoprecipitation of the antiviral Mx1 protein are subsequently revealed by western blotting. A prerequisite for successful co-immunoprecipitation of Mx1 with NP is the presence of N-ethylmaleimide (NEM) in the cell lysis buffer. NEM alkylates free thiol groups. Presumably this reaction stabilizes the weak and/or transient NP-Mx1 interaction by preserving a specific conformation of Mx1, its viral target or an unknown third component. An important limitation of co-immunoprecipitation experiments is the inadvertent pull-down of contaminating proteins, caused by nonspecific binding of proteins to the protein G beads or antibodies. Therefore, it is very important to include control settings to exclude false positive results. The described co-immunoprecipitation protocol can be used to study the interaction of Mx proteins from different vertebrate species with viral proteins, any pair of proteins, or of a protein with other macromolecules. The beneficial role of NEM to stabilize weak and/or transient interactions needs to be tested for each interaction pair individually. PMID:25938860

  8. Immunoprecipitation of Plasma Membrane Receptor-Like Kinases for Identification of Phosphorylation Sites and Associated Proteins.

    PubMed

    Kadota, Yasuhiro; Macho, Alberto P; Zipfel, Cyril

    2016-01-01

    Membrane proteins are difficult to study for numerous reasons. The surface of membrane proteins is relatively hydrophobic and sometimes very unstable, additionally requiring detergents for their extraction from the membrane. This leads to challenges at all levels, including expression, solubilization, purification, identification of associated proteins, and the identification of post-translational modifications. However, recent advances in immunoprecipitation technology allow to isolate membrane proteins efficiently, facilitating the study of protein-protein interactions, the identification of novel associated proteins, and to identify post-translational modifications, such as phosphorylation. Here, we describe an optimized immunoprecipitation protocol for plant plasma membrane receptor-like kinases. PMID:26577786

  9. Detection of xenoestrogens in serum after immunoprecipitation of endogenous steroidal estrogens.

    PubMed Central

    Natarajan, Kala; Overstreet, James W; Rogers, Jane M; Denison, Michael S; Chen, Jiangang; Lohstroh, Peter N; McConnell, Daniel S; Lasley, Bill L

    2002-01-01

    In this article we report a simple and efficient method for detecting nonsteroidal estrogens in a biologic sample. This method uses polyclonal antibodies to estradiol (E2) to immunoprecipitate these major biologically active steroidal estrogens, leaving behind the nonsteroidal estrogens, which are then detected in a cell-based transcriptional activation bioassay for estrogen receptor agonist. The immunoprecipitation method efficiently removed 99% of radiolabeled E2 and estrone (E1) from human serum. In experiments in which supraphysiologic concentrations of E2 and E1 to human serum, all of the immunoreactive estrogens were still removed by the immunoprecipitation protocol. We carried out an in vivo validation study of this method in which we treated female macaques with the xenoestrogen nonylphenol (NP), during the late follicular phase of the menstrual cycle. We used blood samples collected before and after treatment to evaluate and characterize endogenous and exogenous serum estrogens. An immunoassay for E2 did not detect the NP in treated monkeys. The cell-based bioassay also did not detect the estrogenic activity of NP because of its saturation by the endogenous serum steroidal estrogens. However, when steroidal estrogens were removed by immunoprecipitation, we detected the estrogenic activity of NP in the bioassay. Thus, this approach is appropriate for detecting exogenous, nonsteroidal estrogens in serum samples. PMID:12153760

  10. Tandem immunoprecipitation approach to identify HIV-1 Gag associated host factors.

    PubMed

    Gao, Wei; Li, Min; Zhang, Jingxin

    2014-07-01

    HIV-1 Gag by itself is able to assemble and release from host cells and thus serves as a simplified model to identify host factors involved in this stage of the HIV-1 life cycle. In this study, a tandem immunoprecipitation approach is taken to immunoprecipitate Gag-interacting host proteins from transfected 293T cells. It is demonstrated that with the tandem immunoprecipitation method Gag-interacting host factors can be precipitated more efficiently than by single-step immunoprecipitation. Gag proteins are found to interact with multiple RNA-binding proteins such as hnRNPs, nucleolin, EF1a and ribosomal proteins. Such interactions are mediated by cellular RNAs and the Gag Nuclear Capsid (NC) domain. Deletion of the NC domain results in removal of most of the RNA-binding proteins, as well as a reduction of the Gag releasing capability, which can be restored by replacing the deleted NC domain with another multimerization motif. Importantly, interactions between Gag and host factors are relevant functionally, as evidenced by significantly increased nucleolin protein in the cytoplasm where it is recruited into the Gag complex, and enhanced Gag release when nucleolin is over-expressed. PMID:24690621

  11. Chapter 15. Co-immunoprecipitation techniques for assessing RNA-protein interactions in vivo.

    PubMed

    Conrad, Nicholas K

    2008-01-01

    From the moment a nascent transcript emerges from an RNA polymerase until its ultimate destruction, an RNA is bound by proteins that govern its fate. Thus, in order to understand posttranscriptional regulation of gene expression, it is essential to ascertain which proteins bind a given RNA in vivo. This chapter describes three immunoprecipitation-based assays designed to query the in vivo makeup of RNA-protein complexes. Two of these, UV cross-linking and RNA immunoprecipitation (RIP), include cross-linking steps that trap complexes formed in vivo. A third, a cell mixing experiment, verifies that an interaction occurs in vivo by controlling for RNA-protein association subsequent to cell lysis. Using these protocols, this chapter presents evidence that the abundant nuclear RNA-binding protein hnRNP C interacts with the Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA in vivo. PMID:19215765

  12. Immunoprecipitation of Cullin-RING Ligases (CRLs) in Arabidopsis thaliana Seedlings.

    PubMed

    Franciosini, Anna; Serino, Giovanna

    2016-01-01

    CRL (Cullin-RING ubiquitin ligase) is the major class of plant E3 ubiquitin ligases. Immunoprecipitation-based methods are useful techniques for revealing interactions among Cullin-RING Ligase (CRL) subunits or between CRLs and other proteins, as well as for detecting poly-ubiquitin modifications of the CRLs themselves. Here, we describe two immunoprecipitation (IP) procedures suitable for CRLs in Arabidopsis: a procedure for IP analysis of CRL subunits and their interactors and a second procedure for in vivo ubiquitination analysis of the CRLs. Both protocols can be divided into two major steps: (1) preparation of cell extracts without disruption of protein interactions and (2) affinity purification of the protein complexes and subsequent detection. We provide a thorough description of all the steps, as well as advice on how to choose proper buffers for these analyses. We also suggest a series of negative controls that can be used to verify the specificity of the procedure. PMID:27424742

  13. Identification of the immunoproteome of the meningococcus by cell surface immunoprecipitation and MS.

    PubMed

    Newcombe, Jane; Mendum, Tom A; Ren, Chuan-peng; McFadden, Johnjoe

    2014-02-01

    Most healthy adults are protected from meningococcal disease by the presence of naturally acquired anti-meningococcal antibodies; however, the identity of the target antigens of this protective immunity remains unclear, particularly for protection against serogroup B disease. To identify the protein targets of natural protective immunity we developed an immunoprecipitation and proteomics approach to define the immunoproteome of the meningococcus. Sera from 10 healthy individuals showing serum bactericidal activity against both a meningococcal C strain (L91543) and the B strain MC58, together with commercially available pooled human sera, were used as probe antisera. Immunoprecipitation was performed with each serum sample and live cells from both meningococcal strains. Immunoprecipitated proteins were identified by MS. Analysis of the immunoproteome from each serum demonstrated both pan-reactive antigens that were recognized by most sera as well as subject-specific antigens. Most antigens were found in both meningococcal strains, but a few were strain-specific. Many of the immunoprecipitated proteins have been characterized previously as surface antigens, including adhesins and proteases, several of which have been recognized as vaccine candidate antigens, e.g. factor H-binding protein, NadA and neisserial heparin-binding antigen. The data demonstrate clearly the presence of meningococcal antibodies in healthy individuals with no history of meningococcal infection and a wide diversity of immune responses. The identification of the immunoreactive proteins of the meningococcus provides a basis for understanding the role of each antigen in the natural immunity associated with carriage and may help to design vaccination strategies. PMID:24275101

  14. Pr-specific phytochrome phosphorylation in vitro by a protein kinase present in anti-phytochrome maize immunoprecipitates

    NASA Technical Reports Server (NTRS)

    Biermann, B. J.; Pao, L. I.; Feldman, L. J.

    1994-01-01

    Protein kinase activity has repeatedly been found to co-purify with the plant photoreceptor phytochrome, suggesting that light signals received by phytochrome may be transduced or modulated through protein phosphorylation. In this study immunoprecipitation techniques were used to characterize protein kinase activity associated with phytochrome from maize (Zea mays L.). A protein kinase that specifically phosphorylated phytochrome was present in washed anti-phytochrome immunoprecipitates of etiolated coleoptile proteins. No other substrate tested was phosphorylated by this kinase. Adding salts or detergents to disrupt low-affinity protein interactions reduced background phosphorylation in immunoprecipitates without affecting phytochrome phosphorylation, indicating that the protein kinase catalytic activity is either intrinsic to the phytochrome molecule or associated with it by high-affinity interactions. Red irradiation (of coleoptiles or extracts) sufficient to approach photoconversion saturation reduced phosphorylation of immunoprecipitated phytochrome. Subsequent far-red irradiation reversed the red-light effect. Phytochrome phosphorylation was stimulated about 10-fold by a co-immunoprecipitated factor. The stimulatory factor was highest in immunoprecipitates when Mg2+ was present in immunoprecipitation reactions but remained in the supernatant in the absence of Mg2+. These observations provide strong support for the hypothesis that phytochrome-associated protein kinase modulates light responses in vivo. Since only phytochrome was found to be phosphorylated, the co-immunoprecipitated protein kinase may function to regulate receptor activity.

  15. Characterization of human platelet glycoprotein antigens giving rise to individual immunoprecipitates in crossed-immunoelectrophoresis

    SciTech Connect

    Kunicki, T.J.; Nurden, A.T.; Pidard, D.; Russell, N.R.; Caen, J.P.

    1981-12-01

    Washed human platelets were labeled with 125I by the lactoperoxidase-catalyzed method and solubilized in 1% Triton X-100. The soluble proteins were analyzed by crossed-immunoelectrophoresis in 1% agarose, employing a rabbit antibody raised against whole human platelets. Analysis of autoradiograms developed from dried agarose gels led to the establishment of a normal reference pattern that was consistent for platelets obtained from more than 50 normal individuals. Six platelet membrane glycoprotein antigens contained in four distinguishable precipitates were identified. Each identification was based on direct sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of 125I-antigens contained in individually excised precipitates. These platelet antigens include major membrane glycoproteins previously designated la, lb, lla, llb, llla, and lllb. Glycoproteins llb and llla were shown to be contained in a single immunoprecipitate, while glycoproteins la and lla were routinely detected in a single different immunoprecipitate. Analysis of soluble proteins from platelets of five patients with Glanzmann's thrombasthenia demonstrated either a complete absence or a marked reduction of only one radiolabeled precipitate, that containing membrane glycoproteins llb and llla. Platelet samples from two patients with Bernard-Soulier syndrome were devoid of a different precipitate, that containing membrane glycoprotein lb.

  16. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.

    PubMed

    Cejas, Paloma; Li, Lewyn; O'Neill, Nicholas K; Duarte, Melissa; Rao, Prakash; Bowden, Michaela; Zhou, Chensheng W; Mendiola, Marta; Burgos, Emilio; Feliu, Jaime; Moreno-Rubio, Juan; Guadalajara, Héctor; Moreno, Víctor; García-Olmo, Damián; Bellmunt, Joaquim; Mullane, Stephanie; Hirsch, Michelle; Sweeney, Christopher J; Richardson, Andrea; Liu, X Shirley; Brown, Myles; Shivdasani, Ramesh A; Long, Henry W

    2016-06-01

    Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation. PMID:27111282

  17. Effective Identification of Akt Interacting Proteins by Two-Step Chemical Crosslinking, Co-Immunoprecipitation and Mass Spectrometry

    PubMed Central

    Huang, Bill X.; Kim, Hee-Yong

    2013-01-01

    Akt is a critical protein for cell survival and known to interact with various proteins. However, Akt binding partners that modulate or regulate Akt activation have not been fully elucidated. Identification of Akt-interacting proteins has been customarily achieved by co-immunoprecipitation combined with western blot and/or MS analysis. An intrinsic problem of the method is loss of interacting proteins during procedures to remove non-specific proteins. Moreover, antibody contamination often interferes with the detection of less abundant proteins. Here, we developed a novel two-step chemical crosslinking strategy to overcome these problems which resulted in a dramatic improvement in identifying Akt interacting partners. Akt antibody was first immobilized on protein A/G beads using disuccinimidyl suberate and allowed to bind to cellular Akt along with its interacting proteins. Subsequently, dithiobis[succinimidylpropionate], a cleavable crosslinker, was introduced to produce stable complexes between Akt and binding partners prior to the SDS-PAGE and nanoLC-MS/MS analysis. This approach enabled identification of ten Akt partners from cell lysates containing as low as 1.5 mg proteins, including two new potential Akt interacting partners. None of these but one protein was detectable without crosslinking procedures. The present method provides a sensitive and effective tool to probe Akt-interacting proteins. This strategy should also prove useful for other protein interactions, particularly those involving less abundant or weakly associating partners. PMID:23613850

  18. The DNA Methyltransferase Dnmt1 Directly Interacts with the SET and RING Finger-associated (SRA) Domain of the Multifunctional Protein Uhrf1 to Facilitate Accession of the Catalytic Center to Hemi-methylated DNA*

    PubMed Central

    Berkyurek, Ahmet Can; Suetake, Isao; Arita, Kyohei; Takeshita, Kohei; Nakagawa, Atsushi; Shirakawa, Masahiro; Tajima, Shoji

    2014-01-01

    Dnmt1 is responsible for the maintenance DNA methylation during replication to propagate methylation patterns to the next generation. The replication foci targeting sequence (RFTS), which plugs the catalytic pocket, is necessary for recruitment of Dnmt1 to the replication site. In the present study we found that the DNA methylation activity of Dnmt1 was DNA length-dependent and scarcely methylated 12-bp short hemi-methylated DNA. Contrarily, the RFTS-deleted Dnmt1 and Dnmt1 mutants that destroyed the hydrogen bonds between the RFTS and catalytic domain showed significant DNA methylation activity even toward 12-bp hemi-methylated DNA. The DNA methylation activity of the RFTS-deleted Dnmt1 toward 12-bp hemi-methylated DNA was strongly inhibited on the addition of RFTS, but to a lesser extent by Dnmt1 harboring the mutations that impair the hydrogen bond formation. The SRA domain of Uhrf1, which is a prerequisite factor for maintenance methylation and selectively binds to hemi-methylated DNA, stimulated the DNA methylation activity of Dnmt1. The SRA to Dnmt1 concentration ratio was the determinant for the maximum stimulation. In addition, a mutant SRA, which had lost the DNA binding activity but was able to bind to Dnmt1, stimulated the DNA methylation activity of Dnmt1. The results indicate that the DNA methylation activity of Dnmt1 was stimulated on the direct interaction of the SRA and Dnmt1. The SRA facilitated acceptance of the 12-bp fluorocytosine-containing DNA by the catalytic center. We propose that the SRA removes the RFTS plug from the catalytic pocket to facilitate DNA acceptance by the catalytic center. PMID:24253042

  19. Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging.

    PubMed

    Tatavosian, Roubina; Zhen, Chao Yu; Duc, Huy Nguyen; Balas, Maggie M; Johnson, Aaron M; Ren, Xiaojun

    2015-11-20

    Epigenetic complexes play an essential role in regulating chromatin structure, but information about their assembly stoichiometry on chromatin within cells is poorly understood. The cellular assembly stoichiometry is critical for appreciating the initiation, propagation, and maintenance of epigenetic inheritance during normal development and in cancer. By combining genetic engineering, chromatin biochemistry, and single-molecule fluorescence imaging, we developed a novel and sensitive approach termed single-molecule chromatin immunoprecipitation imaging (Sm-ChIPi) to enable investigation of the cellular assembly stoichiometry of epigenetic complexes on chromatin. Sm-ChIPi was validated by using chromatin complexes with known stoichiometry. The stoichiometry of subunits within a polycomb complex and the assembly stoichiometry of polycomb complexes on chromatin have been extensively studied but reached divergent views. Moreover, the cellular assembly stoichiometry of polycomb complexes on chromatin remains unexplored. Using Sm-ChIPi, we demonstrated that within mouse embryonic stem cells, one polycomb repressive complex (PRC) 1 associates with multiple nucleosomes, whereas two PRC2s can bind to a single nucleosome. Furthermore, we obtained direct physical evidence that the nucleoplasmic PRC1 is monomeric, whereas PRC2 can dimerize in the nucleoplasm. We showed that ES cell differentiation induces selective alteration of the assembly stoichiometry of Cbx2 on chromatin but not other PRC1 components. We additionally showed that the PRC2-mediated trimethylation of H3K27 is not required for the assembly stoichiometry of PRC1 on chromatin. Thus, these findings uncover that PRC1 and PRC2 employ distinct mechanisms to assemble on chromatin, and the novel Sm-ChIPi technique could provide single-molecule insight into other epigenetic complexes. PMID:26381410

  20. Studying G protein-coupled receptors: immunoblotting, immunoprecipitation, phosphorylation, surface labeling, and cross-linking protocols.

    PubMed

    Pal, Kasturi; Badgandi, Hemant; Mukhopadhyay, Saikat

    2015-01-01

    Primary cilia are signaling organelles that have been shown to coordinate cellular responses to extracellular cues during physiological processes ranging from organ patterning to cell cycle regulation. A variety of receptors, including G protein-coupled receptors (GPCRs), downstream effectors (adenylyl cyclases), and second messengers, such as calcium, accumulate in the ciliary compartment. Isolation of GPCRs is essential for studying posttranslational modifications, intracellular trafficking, and protein-protein interactions that are important in downstream signaling. However, the presence of multiple hydrophobic transmembrane domains, and the inherent conformational flexibility of GPCRs make their extraction from membranes and solubilization particularly challenging. Here, we describe detailed methods for immunoblotting and immunoprecipitation of GPCRs from whole cell extracts. These methods are applicable for studying other multipass transmembrane proteins (such as adenylyl cyclases). We also describe methods for determining GPCR phosphorylation, surface labeling by biotinylation, and cross-linking to detect transient interactions with other proteins. These methods are amenable for studying both ciliary and nonciliary GPCRs in the context of cellular signaling pathways. PMID:25837398

  1. Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).

    PubMed

    Ouma, Wilberforce Zachary; Mejia-Guerra, Maria Katherine; Yilmaz, Alper; Pareja-Tobes, Pablo; Li, Wei; Doseff, Andrea I; Grotewold, Erich

    2015-01-01

    Establishing the architecture of gene regulatory networks (GRNs) relies on chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) methods that provide genome-wide transcription factor binding sites (TFBSs). ChIP-Seq furnishes millions of short reads that, after alignment, describe the genome-wide binding sites of a particular TF. However, in all organisms investigated an average of 40% of reads fail to align to the corresponding genome, with some datasets having as much as 80% of reads failing to align. We describe here the provenance of previously unaligned reads in ChIP-Seq experiments from animals and plants. We show that a substantial portion corresponds to sequences of bacterial and metazoan origin, irrespective of the ChIP-Seq chromatin source. Unforeseen was the finding that 30%-40% of unaligned reads were actually alignable. To validate these observations, we investigated the characteristics of the previously unaligned reads corresponding to TAL1, a human TF involved in lineage specification of hemopoietic cells. We show that, while unmapped ChIP-Seq read datasets contain foreign DNA sequences, additional TFBSs can be identified from the previously unaligned ChIP-Seq reads. Our results indicate that the re-evaluation of previously unaligned reads from ChIP-Seq experiments will significantly contribute to TF target identification and determination of emerging properties of GRNs. PMID:25727450

  2. Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry

    PubMed Central

    Engelen, Erik; Brandsma, Johannes H.; Moen, Maaike J.; Signorile, Luca; Dekkers, Dick H. W.; Demmers, Jeroen; Kockx, Christel E. M.; Ozgür, Zehila; van IJcken, Wilfred F. J.; van den Berg, Debbie L. C.; Poot, Raymond A.

    2015-01-01

    The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type. PMID:25990348

  3. Analysis of TGFβ1 and IL-10 transcriptional regulation in CTCL cells by chromatin immunoprecipitation.

    PubMed

    Chang, Tzu-Pei; Kim, Myra; Vancurova, Ivana

    2014-01-01

    The immunosuppressive cytokines transforming growth factor β1 (TGFβ1) and interleukin-10 (IL-10) regulate a variety of biological processes including differentiation, proliferation, tissue repair, tumorigenesis, inflammation, and host defense. Aberrant expression of TGFβ1 and IL-10 has been associated with many types of autoimmune and inflammatory disorders, as well as with many types of cancer and leukemia. Patients with cutaneous T cell lymphoma (CTCL) have high levels of malignant CD4+ T cells expressing IL-10 and TGFβ1 that suppress the immune system and diminish the antitumor responses. The transcriptional regulation of TGFβ1 and IL-10 expression is orchestrated by several transcription factors, including NFκB. However, while the transcriptional regulation of pro-inflammatory and anti-apoptotic genes by NFκB has been studied extensively, much less is known about the NFκB regulation of immunosuppressive genes. In this chapter, we describe a protocol that uses chromatin immunoprecipitation (ChIP) to analyze the transcriptional regulation of TGFβ1 and IL-10 by measuring recruitment of NFκB p65, p50, c-Rel, Rel-B, and p52 subunits to TGFβ1 and IL-10 promoters in human CTCL Hut-78 cells. PMID:24908319

  4. Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data

    PubMed Central

    Kawakami, Eiryo; Nakaoka, Shinji; Ohta, Tazro; Kitano, Hiroaki

    2016-01-01

    Predicting responsible transcription regulators on the basis of transcriptome data is one of the most promising computational approaches to understanding cellular processes and characteristics. Here, we present a novel method employing vast amounts of chromatin immunoprecipitation (ChIP) experimental data to address this issue. Global high-throughput ChIP data was collected to construct a comprehensive database, containing 8 578 738 binding interactions of 454 transcription regulators. To incorporate information about heterogeneous frequencies of transcription factor (TF)-binding events, we developed a flexible framework for gene set analysis employing the weighted t-test procedure, namely weighted parametric gene set analysis (wPGSA). Using transcriptome data as an input, wPGSA predicts the activities of transcription regulators responsible for observed gene expression. Validation of wPGSA with published transcriptome data, including that from over-expressed TFs, showed that the method can predict activities of various TFs, regardless of cell type and conditions, with results totally consistent with biological observations. We also applied wPGSA to other published transcriptome data and identified potential key regulators of cell reprogramming and influenza virus pathogenesis, generating compelling hypotheses regarding underlying regulatory mechanisms. This flexible framework will contribute to uncovering the dynamic and robust architectures of biological regulation, by incorporating high-throughput experimental data in the form of weights. PMID:27131787

  5. Physicochemical characterization of C3b receptors isolated from human erythrocytes by immunoprecipitation.

    PubMed Central

    Gerdes, J; Stein, H

    1980-01-01

    A high yield of active C3b receptors was obtained by solubilizing human erythrocyte membranes with 2 M KBr, whereas other solubilization agents yielded no, or significantly less activity. Gel filtration of the KBr lysates revealed that the apparent molecular wieght of biologically active C3b receptor molecules was greater than 1 x 10(6). Immunoprecipitates prepared with radio-iodinated KBr lysates and anti-C3 receptor sera (AC3RS) were subjected to sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) or sodium dodecyl gel filtration. Unreduced SDS-PAGE and gel filtration profiles showed three predominant peaks with apparent mol. wts of 1--1.3 x 10(6), 80,000 and 60,000. Whereas the high mol. wt component decreased only slightly after reduction, the 80,000 and 60,000 mol. wt components disappeared and two new peaks with apparent mol. wts of 38,000 and 18,000 appeared in SDS-PAGE profiles. Although the high mol. wt component present in reduced SDS-PAGE profiles was detectable in some of the control experiments, none of the other peaks could be precipitated with control sera, and these components could be demonstrated only when KBr lysates of C3b receptor-positive erythrocytes and AC3RS that were able to inhibit ligand binding of the C3b receptors were used for precipitation. These findings suggest that (a) the C3b receptor of human erythrocytes in its biologically active state is a macromolecule with an apparent mol. wt higher than 1 x 10(6) and (b) the protein moiety consists predominantly of non-covalently linked protein molecules with apparent mol wts of 80,000 and 60,000. These protein molecules are composed of disulphide-bridged polypeptide chains with apparent mol. wts of 38,000 and 18,000. PMID:7461716

  6. Identification of Lysine Acetylation in Mycobacterium abscessus Using LC-MS/MS after Immunoprecipitation.

    PubMed

    Guo, Jintao; Wang, Changwei; Han, Yi; Liu, Zhiyong; Wu, Tian; Liu, Yan; Liu, Yang; Tan, Yaoju; Cai, Xinshan; Cao, Yuanyuan; Wang, Bangxing; Zhang, Buchang; Liu, Chunping; Tan, Shouyong; Zhang, Tianyu

    2016-08-01

    Mycobacterium abscessus (MAB), which manifests in the pulmonary system, is one of the neglected causes of nontuberculous mycobacteria (NTM) infection. Treatment against MAB is difficult, characterized by its intrinsic antibiotic drug resistance. Lysine acetylation can alter the physiochemical property of proteins in living organisms. This study aimed to determine if this protein post-translational modification (PTM) exists in a clinical isolate M. abscessus GZ002. We used the antiacetyl-lysine immunoprecipitation to enrich the low-abundant PTM proteins, followed by the LC-MS/MS analysis. The lysine acetylome of M. abscessus GZ002 was determined. There were 459 lysine acetylation sites found in 289 acetylated proteins. Lysine acetylation occurred in 5.87% of the M. abscessus GZ002 proteome, and at least 25% of them were growth essential. Aerobic respiration and carbohydrate metabolic pathways of M. abscessus GZ002 were enriched with lysine acetylation. Through bioinformatics analysis, we identified four major acetyl motif logos (K(ac)Y, K(ac)F, K(ac)H, and DK(ac)). Further comparison of the reported M. tuberculosis (MTB) acetylomes and that of MAB GZ002 revealed several common features between these two species. The lysine residues of several antibiotic-resistance, virulence, and persistence-related proteins were acetylated in both MAB GZ002 and MTB. There were 51 identical acetylation sites in 37 proteins found in common between MAB GZ002 and MTB. Overall, we demonstrate a profile of lysine acetylation in MAB GZ002 proteome that shares similarities with MTB. Interventions that target at these conserved sections may be valuable as anti-NTM or anti-TB therapies. PMID:27323652

  7. Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP)

    PubMed Central

    Fujita, Toshitsugu; Asano, Yoshinori; Ohtsuka, Junko; Takada, Yoko; Saito, Kazunobu; Ohki, Rieko; Fujii, Hodaka

    2013-01-01

    Biochemical analysis of molecular interactions in specific genomic regions requires their isolation while retaining molecular interactions in vivo. Here, we report isolation of telomeres by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using a transcription activator-like (TAL) protein recognizing telomere repeats. Telomeres recognized by the tagged TAL protein were immunoprecipitated with an antibody against the tag and subjected to identification of telomere-binding molecules. enChIP-mass spectrometry (enChIP-MS) targeting telomeres identified known and novel telomere-binding proteins. The data have been deposited to the ProteomeXchange with identifier PXD000461. In addition, we showed that RNA associated with telomeres could be isolated by enChIP. Identified telomere-binding molecules may play important roles in telomere biology. enChIP using TAL proteins would be a useful tool for biochemical analysis of specific genomic regions of interest. PMID:24201379

  8. Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9)

    PubMed Central

    Sun, Ningning; Sun, Wanchun; Li, Shuiming; Yang, Jingbo; Yang, Longfei; Quan, Guihua; Gao, Xiang; Wang, Zijian; Cheng, Xin; Li, Zehui; Peng, Qisheng; Liu, Ning

    2015-01-01

    Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other species. In order to replicate efficiently in the new host, influenza viruses have to interact with a variety of host factors. In the present study, H7N9 nucleoprotein was transfected into human HEK293T cells, followed by immunoprecipitated and analyzed by proteomics approaches. A series of host proteins co-immunoprecipitated were identified with high confidence, some of which were found to be acetylated at their lysine residues. Bioinformatics analysis revealed that spliceosome might be the most relevant pathway involved in host response to nucleoprotein expression, increasing our emerging knowledge of host proteins that might be involved in influenza virus replication activities. PMID:26528969

  9. Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9).

    PubMed

    Sun, Ningning; Sun, Wanchun; Li, Shuiming; Yang, Jingbo; Yang, Longfei; Quan, Guihua; Gao, Xiang; Wang, Zijian; Cheng, Xin; Li, Zehui; Peng, Qisheng; Liu, Ning

    2015-01-01

    Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other species. In order to replicate efficiently in the new host, influenza viruses have to interact with a variety of host factors. In the present study, H7N9 nucleoprotein was transfected into human HEK293T cells, followed by immunoprecipitated and analyzed by proteomics approaches. A series of host proteins co-immunoprecipitated were identified with high confidence, some of which were found to be acetylated at their lysine residues. Bioinformatics analysis revealed that spliceosome might be the most relevant pathway involved in host response to nucleoprotein expression, increasing our emerging knowledge of host proteins that might be involved in influenza virus replication activities. PMID:26528969

  10. Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres.

    PubMed Central

    Nagaki, Kiyotaka; Talbert, Paul B; Zhong, Cathy Xiaoyan; Dawe, R Kelly; Henikoff, Steven; Jiang, Jiming

    2003-01-01

    The centromeres of Arabidopsis thaliana chromosomes contain megabases of complex DNA consisting of numerous types of repetitive DNA elements. We developed a chromatin immunoprecipitation (ChIP) technique using an antibody against the centromeric H3 histone, HTR12, in Arabidopsis. ChIP assays showed that the 180-bp centromeric satellite repeat was precipitated with the antibody, suggesting that this repeat is the key component of the centromere/kinetochore complex in Arabidopsis. PMID:12663558

  11. Investigation of histone H4 hyperacetylation dynamics in the 5S rRNA genes family by chromatin immunoprecipitation assay.

    PubMed

    Burlibașa, Liliana; Suciu, Ilinca

    2015-12-01

    Oogenesis is a critical event in the formation of female gamete, whose role in development is to transfer genomic information to the next generation. During this process, the gene expression pattern changes dramatically concomitant with genome remodelling, while genomic information is stably maintained. The aim of the present study was to investigate the presence of H4 acetylation of the oocyte and somatic 5S rRNA genes in Triturus cristatus, using chromatin immunoprecipitation assay (ChIP). Our findings suggest that some epigenetic mechanisms such as histone acetylation could be involved in the transcriptional regulation of 5S rRNA gene families. PMID:25315165

  12. ReCLIP (Reversible Cross-Link Immuno-Precipitation): An Efficient Method for Interrogation of Labile Protein Complexes

    PubMed Central

    Smith, Andrew L.; Friedman, David B.; Yu, Huapeng; Carnahan, Robert H.; Reynolds, Albert B.

    2011-01-01

    The difficulty of maintaining intact protein complexes while minimizing non-specific background remains a significant limitation in proteomic studies. Labile interactions, such as the interaction between p120-catenin and the E-cadherin complex, are particularly challenging. Using the cadherin complex as a model-system, we have developed a procedure for efficient recovery of otherwise labile protein-protein interactions. We have named the procedure “ReCLIP” (Reversible Cross-Link Immuno-Precipitation) to reflect the primary elements of the method. Using cell-permeable, thiol-cleavable crosslinkers, normally labile interactions (i.e. p120 and E-cadherin) are stabilized in situ prior to isolation. After immunoprecipitation, crosslinked binding partners are selectively released and all other components of the procedure (i.e. beads, antibody, and p120 itself) are discarded. The end result is extremely efficient recovery with exceptionally low background. ReCLIP therefore appears to provide an excellent alternative to currently available affinity-purification approaches, particularly for studies of labile complexes. PMID:21283770

  13. Sensitive detection of C-reactive protein in serum by immunoprecipitation-microchip capillary gel electrophoresis.

    PubMed

    Herwig, Ela; Marchetti-Deschmann, Martina; Wenz, Christian; Rüfer, Andreas; Redl, Heinz; Bahrami, Soheyl; Allmaier, Günter

    2015-06-01

    Sepsis represents a significant cause of mortality in intensive care units. Early diagnosis of sepsis is essential to increase the survival rate of patients. Among others, C-reactive protein (CRP) is commonly used as a sepsis marker. In this work we introduce immune precipitation combined with microchip capillary gel electrophoresis (IP-MCGE) for the detection and quantification of CRP in serum samples. First high-abundance proteins (HSA, IgG) are removed from serum samples using affinity spin cartridges, and then the remaining proteins are labeled with a fluorescence dye and incubated with an anti-CRP antibody, and the antigen/antibody complex is precipitated with protein G-coated magnetic beads. After precipitation the complex is eluted from the beads and loaded onto the MCGE system. CRP could be reliably detected and quantified, with a detection limit of 25 ng/μl in serum samples and 126 pg/μl in matrix-free samples. The overall sensitivity (LOQ = 75 ng/μl, R(2) = 0.9668) of the method is lower than that of some specially developed methods (e.g., immune radiometric assay) but is comparable to those of clinically accepted ELISA methods. The straightforward sample preparation (not prone to mistakes), reduced sample and reagent volumes (including the antibodies), and high throughput (10 samples/3 h) are advantages and therefore IP-MCGE bears potential for point-of-care diagnosis. PMID:25778394

  14. ChIPseq in Yeast Species: From Chromatin Immunoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses.

    PubMed

    Lelandais, Gaëlle; Blugeon, Corinne; Merhej, Jawad

    2016-01-01

    Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIPseq) is a powerful technique for the genome-wide location of protein DNA-binding sites. The ChIP experiment consists in treating living cells with a cross-linking agent to bind proteins to their DNA substrates. After fragmentation of DNA, specific fractions associated with a particular protein of interest are purified by immunoaffinity. They are next sequenced and identified on the reference genome using dedicated bioinformatics programs. Several technical aspects are important to obtain high-quality ChIPseq results. This includes the quality of antibodies, the sequencing protocols, the use of accurate controls and the careful choice of bioinformatics tools. We present here a general protocol to perform ChIPseq analyses in yeast species. This protocol has been optimized to identify target genes of specific transcription factors but can be used for any other DNA binding proteins. PMID:26483023

  15. The brain as immunoprecipitator of serum autoantibodies against N-Methyl-D-aspartate receptor subunit NR1.

    PubMed

    Castillo-Gomez, Esther; Kästner, Anne; Steiner, Johann; Schneider, Anja; Hettling, Bilke; Poggi, Giulia; Ostehr, Kristin; Uhr, Manfred; Asif, Abdul R; Matzke, Mike; Schmidt, Ulrike; Pfander, Viktoria; Hammer, Christian; Schulz, Thomas F; Binder, Lutz; Stöcker, Winfried; Weber, Frank; Ehrenreich, Hannelore

    2016-01-01

    Autoantibodies (AB) against N-methyl-D-aspartate receptor subunit NR1 (NMDAR1) are highly seroprevalent in health and disease. Symptomatic relevance may arise upon compromised blood-brain barrier (BBB). However, it remained unknown whether circulating NMDAR1 AB appear in the cerebrospinal fluid (CSF). Of n = 271 subjects with CSF-serum pairs, 26 were NMDAR1 AB seropositive, but only 1 was CSF positive. Contrariwise, tetanus AB (non-brain-binding) were present in serum and CSF of all subjects, with CSF levels higher upon BBB dysfunction. Translational mouse experiments proved the hypothesis that the brain acts as an 'immunoprecipitator'; simultaneous injection of NMDAR1 AB and the non-brain-binding green fluorescent protein AB resulted in high detectability of the former in brain and the latter in CSF. PMID:26505629

  16. Rabbit antisera against three different bacteria which can induce reactive arthritis: analysis by ELISA, immunoprecipitation and Western Blot.

    PubMed Central

    Ogasawara, M; Kobayashi, S; Hill, J L; Kono, D H; Yu, D T

    1985-01-01

    Three strains of bacteria which induce reactive arthritis were collected: a Shigella flexneri, designated 7060; another Sh. flexneri, designated 316; and a Yersinia enterocolitica of serotype 03. Rabbit antisera were generated against each of them to test for the extent and nature of cross-reactivity among these strains. When analysed by the ELISA technique, antisera against 7060 and 316 showed strong cross-reactivity with Y. enterocolitica. In contrast, the reaction of antisera prepared against putatively non-arthritis-causing bacteria reacted several-folds less. Using immunoprecipitation, sodium dodecyl sulphate-polyacrylamide gel electrophoresis and Western Blot procedures, a 92,000 MW cross-reactive antigen on the Yersinia was identified. The antigen was present on the outer membranes of the Y. enterocolitica, and enzyme digestion experiments showed that this antigen was protein in nature. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:3884493

  17. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures.

    PubMed

    Thomson, John P; Fawkes, Angie; Ottaviano, Raffaele; Hunter, Jennifer M; Shukla, Ruchi; Mjoseng, Heidi K; Clark, Richard; Coutts, Audrey; Murphy, Lee; Meehan, Richard R

    2015-01-01

    Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets. PMID:25985418

  18. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures

    PubMed Central

    Thomson, John P.; Fawkes, Angie; Ottaviano, Raffaele; Hunter, Jennifer M.; Shukla, Ruchi; Mjoseng, Heidi K.; Clark, Richard; Coutts, Audrey; Murphy, Lee; Meehan, Richard R.

    2015-01-01

    Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; “DIP-SC-seq”) on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets. PMID:25985418

  19. Novel in vivo targets of ΔNp63 in keratinocytes identified by a modified chromatin immunoprecipitation approach

    PubMed Central

    Birkaya, Barbara; Ortt, Kori; Sinha, Satrajit

    2007-01-01

    Background p63 is a transcription factor that plays an important role in skin epidermal development and differentiation. The p63 gene encodes for two major protein isoforms, those containing an amino-terminal trans-activation domain (TAp63) and those lacking this domain (ΔNp63). Both the TA and ΔN transcripts are also alternatively spliced at the 3' end producing proteins with unique C-termini that are designated as α, β and γ isoforms. Recent research has suggested that ΔNp63 is the predominant isoform expressed and active in keratinocytes. Results To better elucidate the biological role of p63 in regulating gene expression in keratinocytes we performed chromatin immunoprecipitation (ChIP) experiments with ΔNp63-specific antibodies. We included an additional step in the ChIP procedure to enrich for ΔNp63 targets by screening the library of immunoprecipitated DNA for its ability to bind recombinant GST-ΔNp63. Cloning of ΔNp63-ChIP-derived DNA fragments identified more than 60 potential ΔNp63 target loci that were located close to or embedded within known or predicted genes. Identity of these target genes suggests that they may participate in a myriad of cellular processes including transcriptional regulation, signaling and metabolism. Here we confirm the binding of ΔNp63 to several of these genomic loci both by EMSA and replicate ChIP assays. Finally we show that the expression of many of these target genes is altered when ΔNp63 levels in keratinocytes are reduced by siRNA, further confirming that these are bona fide targets. Conclusion This unbiased genomic approach has allowed us to uncover functional targets of ΔNp63 and serves as the initial step in further analysis of the transcriptional regulatory mechanisms that are governed by p63 in keratinocytes. PMID:17521434

  20. Cloning and Characterization of a New Site-Specific Methyl-Directed ElmI Endonuclease Recognizing and Cleaving C5-methylated DNA Sequence 5'-G(5mC)^NG(5mC)-3'.

    PubMed

    Chernukhin, V A; Gonchar, D A; Abdurashitov, M A; Belichenko, O A; Dedkov, V S; Mikhnenkova, N A; Lomakovskaya, E N; Udal'yeva, S G; Degtyarev, S Kh

    2016-01-01

    Putative open reading frames of MD-endonucleases have been identified in Enterobacteria genomes as a result of the search for amino acid sequences homologous to MD-endonuclease BisI. A highly conserved DNA primary structure of these open reading frames in different genera of Enterobacteria (Escherichia, Klebsiella and Cronobacter) has allowed researchers to create primers for PCR screening, which was carried out on Enterobacteria DNA collected from natural sources. The DNA fragment, about 440 bp in length, was amplified by use of the genomic DNA of a wild E.coli LM N17 strain as a template and was inserted into the pMTL22 vector. Endonuclease activity was detected in an E.coli ER 2267 strain transformed with the obtained construction. A new enzyme named ElmI was purified by chromatographic techniques from the recombinant strain biomass. It was discovered that similarly to BisI this enzyme specifically cleaves the methylated DNA sequence 5'-GCNGC- 3' before the central nucleotide "N" if this sequence contains two 5-methylcytosines. However, unlike BisI, ElmI more efficiently cleaves this sequence if more than two cytosine residues are methylated. PMID:27099792

  1. Cloning and Characterization of a New Site-Specific Methyl-Directed ElmI Endonuclease Recognizing and Cleaving C5-methylated DNA Sequence 5’-G(5mC)^NG(5mC)-3’

    PubMed Central

    Chernukhin, V. A.; Gonchar, D. A.; Abdurashitov, M. A.; Belichenko, O. A.; Dedkov, V. S.; Mikhnenkova, N. A.; Lomakovskaya, E. N.; Udal’yeva, S. G.; Degtyarev, S. Kh.

    2016-01-01

    Putative open reading frames of MD-endonucleases have been identified in Enterobacteria genomes as a result of the search for amino acid sequences homologous to MD-endonuclease BisI. A highly conserved DNA primary structure of these open reading frames in different genera of Enterobacteria (Escherichia, Klebsiella and Cronobacter) has allowed researchers to create primers for PCR screening, which was carried out on Enterobacteria DNA collected from natural sources. The DNA fragment, about 440 bp in length, was amplified by use of the genomic DNA of a wild E.coli LM N17 strain as a template and was inserted into the pMTL22 vector. Endonuclease activity was detected in an E.coli ER 2267 strain transformed with the obtained construction. A new enzyme named ElmI was purified by chromatographic techniques from the recombinant strain biomass. It was discovered that similarly to BisI this enzyme specifically cleaves the methylated DNA sequence 5’-GCNGC- 3’ before the central nucleotide “N” if this sequence contains two 5-methylcytosines. However, unlike BisI, ElmI more efficiently cleaves this sequence if more than two cytosine residues are methylated. PMID:27099792

  2. Identification of cross-reactive promastigote cell surface antigens of some leishmanial stocks by 125I labeling and immunoprecipitation.

    PubMed Central

    Gardiner, P R; Jaffe, C L; Dwyer, D M

    1984-01-01

    Externally oriented surface membrane constituents of promastigotes from several Leishmania species were radiolabeled with 125I. Autoradiographs of cell surface-labeled and sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated proteins of the stocks revealed distinctive patterns of bands in the molecular weight range of 6,000 to 240,000. Immunoprecipitation of detergent extracts of the labeled promastigote stocks with anti-Leishmania donovani membrane serum demonstrated that each of the stocks contained some antigenically cross-reactive determinants. The electrophoretic patterns of these determinants serve both to distinguish the parasite stocks (by unique, species-specific patterns) and to indicate antigenic similarities in stocks thought to be different by other biochemical criteria. At least 12 cross-reactive cell surface antigens in two New World leishmanias are recognized by polyvalent anti-L. donovani serum, suggesting that these common leishmanial antigens may account for the documented serological cross-reactivities among various Leishmania species. In all stocks tested, an iodinated protein was identified which had a relative molecular weight of 65,000 under reducing conditions but which demonstrated an increase in relative mobility in sodium dodecyl sulfate-polyacrylamide gels under nonreducing conditions. Distinctive patterns of the antigens common to the several stocks were also demonstrated with the use of monoclonal antibodies. Images PMID:6363295

  3. MOBE-ChIP: a large-scale chromatin immunoprecipitation assay for cell type-specific studies.

    PubMed

    Lau, On Sun; Bergmann, Dominique C

    2015-10-01

    Cell type-specific transcriptional regulators play critical roles in the generation and maintenance of multicellularity. As they are often expressed at low levels, in vivo DNA-binding studies of these regulators by standard chromatin immunoprecipitation (ChIP) assays are technically challenging. We describe here an optimized ChIP protocol termed Maximized Objects for Better Enrichment (MOBE)-ChIP, which enhances the sensitivity of ChIP assays for detecting cell type-specific signals. The protocol, which is based on the disproportional increase of target signals over background at higher scales, uses substantially greater volume of starting materials than conventional ChIPs to achieve high signal enrichment. This technique can capture weak binding events that are ambiguous in standard ChIP assays, and is useful both in gene-specific and whole-genome analysis. This protocol has been optimized for Arabidopsis, but should be applicable to other model systems with minor modifications. The full procedure can be completed within 3 days. PMID:26332947

  4. Encapsulation of Adenovirus Serotype 5 in Anionic Lecithin Liposomes using a Bead-Based Immunoprecipitation Technique Enhances Transfection Efficiency

    PubMed Central

    Mendez, N.; Herrera, V.; Zhang, L.; Hedjran, F.; Feuer, R.; Blair, S.; Trogler, W.; Reid, T.

    2014-01-01

    Oncolytic viruses (OVs) constitute a promising class of cancer therapeutics which exploit validated genetic pathways known to be deregulated in many cancers. To overcome an immune response and to enhance its potential use to treat primary and metastatic tumors, a method for liposomal encapsulation of adenovirus has been developed. The encapsulation of adenovirus in non-toxic anionic lecithin-cholesterol-PEG liposomes ranging from 140–180nm in diameter have been prepared by self-assembly around the viral capsid. The encapsulated viruses retain their ability to infect cancer cells. Furthermore, an immunoprecipitation (IP) technique has shown to be a fast and effective method to extract non-encapsulated viruses and homogenize the liposomes remaining in solution. 78% of adenovirus plaque forming units were encapsulated and retained infectivity after IP processing. Additionally, encapsulated viruses have shown enhanced transfection efficiency up to 4× higher compared to non-encapsulated Ads. Extracting non-encapsulated viruses from solution may prevent an adverse in vivo immune response and may enhance treatment for multiple administrations. PMID:25154663

  5. Specific detection of peste des petits ruminants virus antibodies in sheep and goat sera by the luciferase immunoprecipitation system.

    PubMed

    Berguido, Francisco J; Bodjo, Sanne Charles; Loitsch, Angelika; Diallo, Adama

    2016-01-01

    Peste des petits ruminants (PPR) is a contagious and often fatal transboundary animal disease affecting mostly sheep, goats and wild small ruminants. This disease is endemic in most of Africa, the Middle, Near East, and large parts of Asia. The causal agent is peste des petits ruminants virus (PPRV), which belongs to the genus Morbillivirus in the family Paramyxoviridae. This genus also includes measles virus (MV), canine distemper virus (CDV) and rinderpest virus (RPV). All are closely related viruses with serological cross reactivity. In this study, we have developed a Luciferase Immunoprecipitation System (LIPS) for the rapid detection of antibodies against PPRV in serum samples and for specific differentiation from antibodies against RPV. PPR and rinderpest (RP) serum samples were assayed by PPR-LIPS and two commercially available PPR cELISA tests. The PPR-LIPS showed high sensitivity and specificity for the samples tested and showed no cross reactivity with RPV unlike the commercial PPR cELISA tests which did cross react with RPV. Based on the results shown in this study, PPR-LIPS is presented as a good candidate for the specific serosurveillance of PPR. PMID:26506137

  6. Characterization of the Escherichia coli σS core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis

    PubMed Central

    Peano, Clelia; Wolf, Johannes; Demol, Julien; Rossi, Elio; Petiti, Luca; De Bellis, Gianluca; Geiselmann, Johannes; Egli, Thomas; Lacour, Stephan; Landini, Paolo

    2015-01-01

    In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with σ factors, accessory subunits able to direct RNA polymerase “core enzyme” (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the σS-associated RNA polymerase form (EσS) during transition from exponential to stationary phase. We identified 63 binding sites for EσS overlapping known or putative promoters, often located upstream of genes (encoding either ORFs or non-coding RNAs) showing at least some degree of dependence on the σS-encoding rpoS gene. EσS binding did not always correlate with an increase in transcription level, suggesting that, at some σS-dependent promoters, EσS might remain poised in a pre-initiation state upon binding. A large fraction of EσS-binding sites corresponded to promoters recognized by RNA polymerase associated with σ70 or other σ factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, EσS appears to contribute significantly to transcription of genes encoding proteins involved in LPS biosynthesis and in cell surface composition. Finally, our results highlight a direct role of EσS in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC. PMID:26020590

  7. Development of microLIPS (Luciferase Immunoprecipitation Systems): a novel microfluidic assay for rapid serum antibody detection

    NASA Astrophysics Data System (ADS)

    Chandrangsu, Matt; Burbelo, Peter D.; Iadarola, Michael J.; Smith, Paul D.; Morgan, Nicole Y.

    2012-06-01

    There is considerable interest in the development of rapid, point-of-care antibody detection for the diagnosis of infectious and auto-immune diseases. In this paper, we present work on the development of a self-contained microfluidic format for the Luciferase Immunoprecipitation Systems (LIPS) assay. Whereas the majority of immunoassays for antigen-specific antibodies employ either bacteria- or yeast-expressed proteins and require the use of secondary antibodies, the LIPS technique uses a fusion protein comprised of a Renilla luciferase reporter and the antigen of interest produced via mammalian cell culture, ensuring the addition of mammalian post-translational modifications. Patient serum is mixed with the fusion protein and passed over immobilized Protein A/G; after washing, the only remaining luciferase-tagged antigens are those retained by specific antibodies. These can be quantitatively measured using chemiluminescence upon the introduction of coelenterazine. The assay has been successfully employed for a wide variety of diseases in a microwell format. We report on a recent demonstration of rapid HSV-2 diagnosis with the LIPS assay in a microfluidic format, using one microliter of serum and obtaining results in under ten minutes. We will also discuss recent progress on two fronts, both aimed at the deployment of this technology in the field: first, simplifying assay operation through the automation of flow control using power-free means; and second, efforts to increase signal levels, primarily through strategies to increase antibody binding capacity, in order to move towards portable battery powered electronics.

  8. OVINE PROGRESSIVE PNEUMONIA VIRUS CAPSID IS B-CELL IMMUNODOMINANT USING WESTERN BLOT ANALYSIS: A COMPARISON OF SENSITIVITY BETWEEN WESTERN BLOT ANALYSIS AND IMMUNOPRECIPITATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A western blot assay (WB) was developed and analyzed against the comparable standard, immunoprecipitation of 35[S] methionine/cysteine-labeled ovine progressive pneumonia virus (OPPV) proteins (IP), for its ability to detect anti-OPPV antibodies using endpoint titers. WB is 12-fold more sensitive i...

  9. Deregulated Direct Targets of the Hepatitis B Virus (HBV) Protein, HBx, Identified through Chromatin Immunoprecipitation and Expression Microarray Profiling*

    PubMed Central

    Sung, Wing-Kin; Lu, Yiwei; Lee, Charlie W. H.; Zhang, Dongwei; Ronaghi, Mostafa; Lee, Caroline G. L.

    2009-01-01

    The hepatitis B-X (HBx) protein is strongly associated with hepatocellular carcinoma. It is implicated not to directly cause cancer but to play a role in hepatocellular carcinoma as a co-factor. The oncogenic potential of HBx primarily lies in its interaction with transcriptional regulators resulting in aberrant gene expression and deregulated cellular pathways. Utilizing ultraviolet irradiation to simulate a tumor-initiating event, we integrated chip-based chromatin immunoprecipitation (ChIP-chip) with expression microarray profiling and identified 184 gene targets directly deregulated by HBx. One-hundred forty-four transcription factors interacting with HBx were computationally inferred. We experimentally validated that HBx interacts with some of the predicted transcription factors (pTF) as well as the promoters of the deregulated target genes of these pTFs. Significantly, we demonstrated that the pTF interacts with the promoters of the deregulated HBx target genes and that deregulation by HBx of these HBx target genes carrying the pTF consensus sequences can be reversed using pTF small interfering RNAs. The roles of these deregulated direct HBx target genes and their relevance in cancer was inferred via querying against biogroup/cancer-related microarray databases using web-based NextBioTM software. Six pathways, including the Jak-STAT pathway, were predicted to be significantly deregulated when HBx binds indirectly to direct target gene promoters. In conclusion, this study represents the first ever demonstration of the utilization of ChIP-chip to identify deregulated direct gene targets from indirect protein-DNA binding as well as transcriptional factors directly interacting with HBx. Increased knowledge of the gene/transcriptional factor targets of HBx will enhance our understanding of the role of HBx in hepatocellular carcinogenesis and facilitate the design of better strategies in combating hepatitis B virus-associated hepatocellular carcinoma. PMID:19439406

  10. Deregulated direct targets of the hepatitis B virus (HBV) protein, HBx, identified through chromatin immunoprecipitation and expression microarray profiling.

    PubMed

    Sung, Wing-Kin; Lu, Yiwei; Lee, Charlie W H; Zhang, Dongwei; Ronaghi, Mostafa; Lee, Caroline G L

    2009-08-14

    The hepatitis B-X (HBx) protein is strongly associated with hepatocellular carcinoma. It is implicated not to directly cause cancer but to play a role in hepatocellular carcinoma as a co-factor. The oncogenic potential of HBx primarily lies in its interaction with transcriptional regulators resulting in aberrant gene expression and deregulated cellular pathways. Utilizing ultraviolet irradiation to simulate a tumor-initiating event, we integrated chip-based chromatin immunoprecipitation (ChIP-chip) with expression microarray profiling and identified 184 gene targets directly deregulated by HBx. One-hundred forty-four transcription factors interacting with HBx were computationally inferred. We experimentally validated that HBx interacts with some of the predicted transcription factors (pTF) as well as the promoters of the deregulated target genes of these pTFs. Significantly, we demonstrated that the pTF interacts with the promoters of the deregulated HBx target genes and that deregulation by HBx of these HBx target genes carrying the pTF consensus sequences can be reversed using pTF small interfering RNAs. The roles of these deregulated direct HBx target genes and their relevance in cancer was inferred via querying against biogroup/cancer-related microarray databases using web-based NextBio(TM) software. Six pathways, including the Jak-STAT pathway, were predicted to be significantly deregulated when HBx binds indirectly to direct target gene promoters. In conclusion, this study represents the first ever demonstration of the utilization of ChIP-chip to identify deregulated direct gene targets from indirect protein-DNA binding as well as transcriptional factors directly interacting with HBx. Increased knowledge of the gene/transcriptional factor targets of HBx will enhance our understanding of the role of HBx in hepatocellular carcinogenesis and facilitate the design of better strategies in combating hepatitis B virus-associated hepatocellular carcinoma. PMID

  11. Chromatin immunoprecipitation assays revealed CREB and serine 133 phospho-CREB binding to the CART gene proximal promoter

    PubMed Central

    Rogge, George A; Shen, Li-Ling; Kuhar, Michael J.

    2010-01-01

    Both over expression of cyclic AMP response element binding protein (CREB) in the nucleus accumbens (NAc), and intra-accumbal injection of cocaine- and amphetamine-regulated transcript (CART) peptides, have been shown to decrease cocaine reward. Also, over expression of CREB in the rat NAc increased CART mRNA and peptide levels, but it is not known if this was due to a direct action of P-CREB on the CART gene promoter. The goal of this study was to test if CREB and P-CREB bound directly to the CRE site in the CART promoter, using chromatin immunoprecipitation (ChIP) assays. ChIP assay with anti-CREB antibodies showed an enrichment of the CART promoter fragment containing the CRE region over IgG precipitated material, a non-specific control. Forskolin, which was known to increase CART mRNA levels in GH3 cells, was utilized to show that the drug increased levels of P-CREB protein and P-CREB binding to the CART promoter CRE-containing region. A region of the c-Fos promoter containing a CRE cis-regulatory element was previously shown to bind P-CREB, and it was used here as a positive control. These data suggest that the effects of CREB over expression on blunting cocaine reward could be, at least in part, attributed to the increased expression of the CART gene by direct interaction of P-CREB with the CART promoter CRE site, rather than by some indirect action. PMID:20451507

  12. Simultaneous Detection of 3-Nitrotyrosine and 3-Nitro-4-hydroxyphenylacetic Acid in Human Urine by Online SPE LC-MS/MS and Their Association with Oxidative and Methylated DNA Lesions.

    PubMed

    Chao, Mu-Rong; Hsu, Yu-Wen; Liu, Hung-Hsin; Lin, Jia-Hong; Hu, Chiung-Wen

    2015-05-18

    Reactive nitrogen species (RNS) can modify proteins at tyrosine and tryptophan residues, and they are involved in the pathogenesis of various human diseases. In this study, we present the first liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based method that enables the simultaneous measurement of urinary 3-nitrotyrosine (3-NTYR) and its metabolite 3-nitro-4-hydroxyphenylacetic acid (NHPA). After the addition of stable isotope-labeled internal standards, urine samples were purified and enriched using manual solid-phase extraction (SPE) and HPLC fractionation followed by online SPE LC-MS/MS analysis. The limits of quantification in urine were 3.1 and 2.5 pg/mL for 3-NTYR and NHPA, respectively. Inter- and intraday imprecision was <15%. The mean relative recoveries of 3-NTYR and NHPA in urine were 89-98% and 90-98%, respectively. We further applied this method to 65 urinary samples from healthy subjects. Urinary samples were also analyzed for N-nitrosodimethylamine (NDMA) as well as oxidative and methylated DNA lesions, namely, 8-oxo-7,8-dihydroguanine (8-oxoGua), 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo), N7-methylguanine (N7-MeG), and N3-methyladenine (N3-MeA), using reported LC-MS/MS methods. Urinary 3-NTYR and NHPA levels were measured at concentrations of 63.2 ± 51.5 and 77.4 ± 60.8 pg/mL, respectively. Urinary 3-NTYR and NHPA levels were highly correlated with each other and with 8-oxoGua and 8-oxodGuo. Our findings demonstrated that a relationship exists between oxidative and nitrative stress. However, 3-NTYR and NHPA were correlated with N7-MeG and N3-MeA but not with NDMA, suggesting that NDMA may not be a representative biomarker of N-nitroso compounds that are induced by RNS. PMID:25825822

  13. Genomic response to Wnt signalling is highly context-dependent - Evidence from DNA microarray and chromatin immunoprecipitation screens of Wnt/TCF targets

    SciTech Connect

    Railo, Antti; Pajunen, Antti; Itaeranta, Petri; Naillat, Florence; Vuoristo, Jussi; Kilpelaeinen, Pekka; Vainio, Seppo

    2009-10-01

    Wnt proteins are important regulators of embryonic development, and dysregulated Wnt signalling is involved in the oncogenesis of several human cancers. Our knowledge of the downstream target genes is limited, however. We used a chromatin immunoprecipitation-based assay to isolate and characterize the actual gene segments through which Wnt-activatable transcription factors, TCFs, regulate transcription and an Affymetrix microarray analysis to study the global transcriptional response to the Wnt3a ligand. The anti-{beta}-catenin immunoprecipitation of DNA-protein complexes from mouse NIH3T3 fibroblasts expressing a fusion protein of {beta}-catenin and TCF7 resulted in the identification of 92 genes as putative TCF targets. GeneChip assays of gene expression performed on NIH3T3 cells and the rat pheochromocytoma cell line PC12 revealed 355 genes in NIH3T3 and 129 genes in the PC12 cells with marked changes in expression after Wnt3a stimulus. Only 2 Wnt-regulated genes were shared by both cell lines. Surprisingly, Disabled-2 was the only gene identified by the chromatin immunoprecipitation approach that displayed a marked change in expression in the GeneChip assay. Taken together, our approaches give an insight into the complex context-dependent nature of Wnt pathway transcriptional responses and identify Disabled-2 as a potential new direct target for Wnt signalling.

  14. Co-immunoprecipitation with Tau Isoform-specific Antibodies Reveals Distinct Protein Interactions and Highlights a Putative Role for 2N Tau in Disease.

    PubMed

    Liu, Chang; Song, Xiaomin; Nisbet, Rebecca; Götz, Jürgen

    2016-04-01

    Alternative splicing generates multiple isoforms of the microtubule-associated protein Tau, but little is known about their specific function. In the adult mouse brain, three Tau isoforms are expressed that contain either 0, 1, or 2 N-terminal inserts (0N, 1N, and 2N). We generated Tau isoform-specific antibodies and performed co-immunoprecipitations followed by tandem mass tag multiplexed quantitative mass spectrometry. We identified novel Tau-interacting proteins of which one-half comprised membrane-bound proteins, localized to the plasma membrane, mitochondria, and other organelles. Tau was also found to interact with proteins involved in presynaptic signal transduction. MetaCore analysis revealed one major Tau interaction cluster that contained 33 Tau pulldown proteins. To explore the pathways in which these proteins are involved, we conducted an ingenuity pathway analysis that revealed two significant overlapping pathways, "cell-to-cell signaling and interaction" and "neurological disease." The functional enrichment tool DAVID showed that in particular the 2N Tau-interacting proteins were specifically associated with neurological disease. Finally, for a subset of Tau interactions (apolipoprotein A1 (apoA1), apoE, mitochondrial creatine kinase U-type, β-synuclein, synaptogyrin-3, synaptophysin, syntaxin 1B, synaptotagmin, and synapsin 1), we performed reverse co-immunoprecipitations, confirming the preferential interaction of specific isoforms. For example, apoA1 displayed a 5-fold preference for the interaction with 2N, whereas β-synuclein showed preference for 0N. Remarkably, a reverse immunoprecipitation with apoA1 detected only the 2N isoform. This highlights distinct protein interactions of the different Tau isoforms, suggesting that they execute different functions in brain tissue. PMID:26861879

  15. Co-immunoprecipitation with Tau Isoform-specific Antibodies Reveals Distinct Protein Interactions and Highlights a Putative Role for 2N Tau in Disease*

    PubMed Central

    Liu, Chang; Song, Xiaomin; Nisbet, Rebecca

    2016-01-01

    Alternative splicing generates multiple isoforms of the microtubule-associated protein Tau, but little is known about their specific function. In the adult mouse brain, three Tau isoforms are expressed that contain either 0, 1, or 2 N-terminal inserts (0N, 1N, and 2N). We generated Tau isoform-specific antibodies and performed co-immunoprecipitations followed by tandem mass tag multiplexed quantitative mass spectrometry. We identified novel Tau-interacting proteins of which one-half comprised membrane-bound proteins, localized to the plasma membrane, mitochondria, and other organelles. Tau was also found to interact with proteins involved in presynaptic signal transduction. MetaCore analysis revealed one major Tau interaction cluster that contained 33 Tau pulldown proteins. To explore the pathways in which these proteins are involved, we conducted an ingenuity pathway analysis that revealed two significant overlapping pathways, “cell-to-cell signaling and interaction” and “neurological disease.” The functional enrichment tool DAVID showed that in particular the 2N Tau-interacting proteins were specifically associated with neurological disease. Finally, for a subset of Tau interactions (apolipoprotein A1 (apoA1), apoE, mitochondrial creatine kinase U-type, β-synuclein, synaptogyrin-3, synaptophysin, syntaxin 1B, synaptotagmin, and synapsin 1), we performed reverse co-immunoprecipitations, confirming the preferential interaction of specific isoforms. For example, apoA1 displayed a 5-fold preference for the interaction with 2N, whereas β-synuclein showed preference for 0N. Remarkably, a reverse immunoprecipitation with apoA1 detected only the 2N isoform. This highlights distinct protein interactions of the different Tau isoforms, suggesting that they execute different functions in brain tissue. PMID:26861879

  16. Detection of anti-U3-RNP/fibrillarin IgG antibodies by line immunoblot assay has comparable clinical significance to immunoprecipitation testing in systemic sclerosis.

    PubMed

    Peterson, Lisa K; Jaskowski, Troy D; Mayes, Maureen D; Tebo, Anne E

    2016-04-01

    The aim of this study was to evaluate the performance and clinical relevance of a commercially available line immunoblot assay (LIA) for detecting anti-U3-RNP/fibrillarin (anti-U3-RNP), against immunoprecipitation (gold standard). This study involved a multi-ethnic cohort of 1000 American systemic sclerosis (SSc) patients and 50 healthy controls. Antinuclear antibodies and centromere antibodies were detected by indirect immunofluorescent antibody test, anti-topo I by immunodiffusion and anti-RNAP III by ELISA. The presence of anti-U3-RNP in select serum samples was detected by immunoprecipitation (IP) and LIA. By IP, U3-RNP antibody was detected in 75 (7.5 %) patients with SSc. Overall agreement between LIA and IP was very good (κ = 0.966). Analytic sensitivity and specificity of the U3-RNP LIA was 100 and 94.7 %, respectively. Clinical features associated with positivity for the anti-U3-RNP antibody include diffuse cutaneous SSc and increased prevalence of renal crisis, consistent with previous studies that used IP. Testing for U3-RNP antibodies is only performed by a small number of laboratories due to the complexity of both performance and interpretation of the IP. LIA is faster and less complex than IP. Excellent agreement between IP and LIA demonstrates that LIA is an acceptable and attractive alternative to IP for anti-U3-RNP detection. PMID:26467972

  17. Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies

    PubMed Central

    Gasper, William C.; Marinov, Georgi K.; Pauli-Behn, Florencia; Scott, Max T.; Newberry, Kimberly; DeSalvo, Gilberto; Ou, Susan; Myers, Richard M.; Vielmetter, Jost; Wold, Barbara J.

    2014-01-01

    Chromatin immunoprecipitation coupled with DNA sequencing (ChIP-seq) is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It identifies sites of transcription factor, cofactor and RNA polymerase occupancy, as well as the distribution of histone marks. Consortia such as the ENCyclopedia Of DNA Elements (ENCODE) have produced large datasets using manual protocols. However, future measurements of hundreds of additional factors in many cell types and physiological states call for higher throughput and consistency afforded by automation. Such automation advances, when provided by multiuser facilities, could also improve the quality and efficiency of individual small-scale projects. The immunoprecipitation process has become rate-limiting, and is a source of substantial variability when performed manually. Here we report a fully automated robotic ChIP (R-ChIP) pipeline that allows up to 96 reactions. A second bottleneck is the dearth of renewable ChIP-validated immune reagents, which do not yet exist for most mammalian transcription factors. We used R-ChIP to screen new mouse monoclonal antibodies raised against p300, a histone acetylase, well-known as a marker of active enhancers, for which ChIP-competent monoclonal reagents have been lacking. We identified, validated for ChIP-seq, and made publicly available a monoclonal reagent called ENCITp300-1. PMID:24919486

  18. Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis of the Penicillium chrysogenum Velvet Protein PcVelA Identifies Methyltransferase PcLlmA as a Novel Downstream Regulator of Fungal Development.

    PubMed

    Becker, Kordula; Ziemons, Sandra; Lentz, Katharina; Freitag, Michael; Kück, Ulrich

    2016-01-01

    molecular level. To address this issue, we performed ChIP-seq (chromatin immunoprecipitation in combination with next-generation sequencing) on and follow-up analysis of PcVelA, the core component of the velvet complex in P. chrysogenum. We demonstrate direct involvement of velvet in transcriptional control and present the putative methyltransferase PcLlmA as a new downstream factor and interaction partner of PcVelA. PMID:27570838

  19. Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis of the Penicillium chrysogenum Velvet Protein PcVelA Identifies Methyltransferase PcLlmA as a Novel Downstream Regulator of Fungal Development

    PubMed Central

    Becker, Kordula; Ziemons, Sandra; Lentz, Katharina; Freitag, Michael

    2016-01-01

    the molecular level. To address this issue, we performed ChIP-seq (chromatin immunoprecipitation in combination with next-generation sequencing) on and follow-up analysis of PcVelA, the core component of the velvet complex in P. chrysogenum. We demonstrate direct involvement of velvet in transcriptional control and present the putative methyltransferase PcLlmA as a new downstream factor and interaction partner of PcVelA. PMID:27570838

  20. Dynamic chromatin remodelling of ciliate macronuclear DNA as determined by an optimized chromatin immunoprecipitation (ChIP) method for Paramecium tetraurelia.

    PubMed

    Cheaib, Miriam; Simon, Martin

    2013-03-01

    We report the detailed evaluation of crucial parameters for chromatin immunoprecipitation (ChIP) of macronuclear DNA in the unicellular eukaryote Paramecium tetraurelia. Optimized parameters include crosslinking conditions, chromatin sonication and antibody titration thus providing a detailed protocol for successful ChIP in P. tetraurelia. As this ciliate is bacterivorous and RNAi by feeding represents a powerful tool for analysis of gene function, we moreover determined the effects of ingested nucleic acids by food bacteria. Feasibility of our protocol is demonstrated by characterisation of chromatin remodelling at promoters of cytosolic HSP70 isoforms during transcriptional activation under heat shock conditions by analyzing RNA abundance, nucleosome occupancy and levels of H3 lysine 9 acetylation. PMID:23385475

  1. Equivalence of Visual Immunoprecipitate Assay (VIP) for Salmonella for the detection of motile and nonmotile Salmonella in all foods to AOAC culture method: collaborative study.

    PubMed

    Feldsine, P T; Mui, L A; Forgey, R L; Kerr, D E

    2000-01-01

    Six foods representative of a wide variety of processed, dried powder processed, and raw food types were analyzed by the Visual Immunoprecipitate Assay (VIP) for Salmonella and AOAC INTERNATIONAL culture method. Paired samples of each food type were simultaneously analyzed; one sample by the VIP method and one by the AOAC culture method. A total of 24 laboratories representing federal government agencies and private industry, in the United States and Canada, participated in this collaborative study. Food types were inoculated with species of Salmonella with the exception of raw ground chicken, which was naturally contaminated. No statistical differences (p < 0.05) were observed between VIP for Salmonella interpretation and the AOAC culture method for any inoculation level of any food type or naturally contaminated food. The method was adopted Official First Action status by AOAC INTERNATIONAL. PMID:10995114

  2. Identification of C/EBPβ Target Genes in ALK+ Anaplastic Large Cell Lymphoma (ALCL) by Gene Expression Profiling and Chromatin Immunoprecipitation

    PubMed Central

    Bonzheim, Irina; Irmler, Martin; Klier-Richter, Margit; Steinhilber, Julia; Anastasov, Nataša; Schäfer, Sabine; Adam, Patrick; Beckers, Johannes; Raffeld, Mark; Fend, Falko; Quintanilla-Martinez, Leticia

    2013-01-01

    C/EBPβ (CCAAT enhancer binding protein) is a transcription factor that plays a crucial role in survival and transformation of ALK+ anaplastic large cell lymphoma (ALCL). The aim of this study was to identify the downstream targets of C/EBPβ responsible for ALK-mediated oncogenesis. C/EBPβ was knocked down in ALK+ ALCL cell lines with a C/EBPβ-shRNA, followed by gene expression profiling (GEP). GEP analysis revealed a reproducible signature of genes that were significantly regulated by C/EBPβ. Classification into biological categories revealed overrepresentation of genes involved in the immune response, apoptosis and cell proliferation. Transcriptional regulation by C/EBPβ was found in 6 of 11 (BCL2A1, G0S2, TRIB1, S100A9, DDX21 and DDIT4) genes investigated by chromatin immunoprecipitation. We demonstrated that BCL2A1, G0S2 and DDX21 play a crucial role in survival and proliferation of ALK+ ALCL cells. DDX21, a gene involved in rRNA biogenesis, was found differentially overexpressed in primary ALK+ ALCL cases. All three candidate genes were validated in primary ALCL cases by either immunohistochemistry or RT-qPCR. In conclusion, we identified and validated several key C/EBPβ-regulated genes with major impact on survival and cell growth in ALK+ ALCL, supporting the central role of C/EBPβ in ALK-mediated oncogenesis. PMID:23741337

  3. Characterization and stability of transthyretin isoforms in cerebrospinal fluid examined by immunoprecipitation and high-resolution mass spectrometry of intact protein.

    PubMed

    Poulsen, Keld; Bahl, Justyna M C; Tanassi, Julia T; Simonsen, Anja H; Heegaard, Niels H H

    2012-02-01

    Post-translational modifications (PTMs) contribute significantly to the complexity of proteins. PTMs may vary in certain patterns according to diseases and microenviroments making them potential markers for pathological processes. Human transthyretin (TTR) is a transporter of thyroxine and retinol in blood and cerebrospinal fluid (CSF). A single free cysteine thiol group in TTR possesses the ability to form mixed disulfides potentially related to diseases such as TTR amyloidosis and Alzheimer's disease (AD). Additionally, TTR-Cys10 S-thiolations might mirror the oxidative stress and redox balance of CSF. Here we describe a quick and gentle method for immunoprecipitating (IP) TTR from CSF with minimal introduction of sample-handling artifacts. A high-resolution mass spectrometer (LTQ-Orbitrap XL) was used in a simple setup with direct infusion that generates data suitable for confident assignment of TTR isoforms and validation of the protocol. Moreover, we demonstrate how simple storage of CSF at 4°C induces major oxidative modifications of TTR. Using the optimized method, we show data from a limited number of mild cognitive impairment (MCI) and AD patients. The protocol controls and minimizes the introduction of sample-handling artifacts during purification of TTR isoforms for high-resolution MS analysis. PMID:22286025

  4. Chromatin immunoprecipitation analysis of bortezomib-mediated inhibition of NFκB recruitment to IL-1β and TNFα gene promoters in human macrophages.

    PubMed

    Sanacora, Shannon; Chang, Tzu-Pei; Vancurova, Ivana

    2014-01-01

    Interleukin-1β (IL-1) and tumor necrosis factor-α (TNF) are important pro-inflammatory cytokines involved in the mediation of the immune response, inflammation, tissue repair, and tumor progression. Regulation of IL-1 and TNF expression is mediated at the level of transcription by the transcription factor NFκB. Inhibition of NFκB activity by the proteasome inhibitor bortezomib (BZ) has been used as a frontline therapy in multiple myeloma and other hematological malignancies. In this chapter, we describe a protocol that uses chromatin immunoprecipitation (ChIP) to analyze the NFκB recruitment to endogenous IL-1 and TNF promoters in BZ-treated human macrophages. Corresponding to the BZ-suppressed mRNA levels of IL-1 and TNF, we show that BZ inhibits p65 NFκB recruitment to IL-1 and TNF promoters. This study specifically uses U937 macrophages, but the protocol could be easily modified to analyze the regulation of NFκB recruitment in other cell types. PMID:24908318

  5. Detection of antibodies to varicella-zoster virus in recipients of the varicella vaccine by using a luciferase immunoprecipitation system assay.

    PubMed

    Cohen, Jeffrey I; Ali, Mir A; Bayat, Ahmad; Steinberg, Sharon P; Park, Hosun; Gershon, Anne A; Burbelo, Peter D

    2014-09-01

    A high-throughput test to detect varicella-zoster virus (VZV) antibodies in varicella vaccine recipients is not currently available. One of the most sensitive tests for detecting VZV antibodies after vaccination is the fluorescent antibody to membrane antigen (FAMA) test. Unfortunately, this test is labor-intensive, somewhat subjective to read, and not commercially available. Therefore, we developed a highly quantitative and high-throughput luciferase immunoprecipitation system (LIPS) assay to detect antibody to VZV glycoprotein E (gE). Tests of children who received the varicella vaccine showed that the gE LIPS assay had 90% sensitivity and 70% specificity, a viral capsid antigen enzyme-linked immunosorbent assay (ELISA) had 67% and 87% specificity, and a glycoprotein ELISA (not commercially available in the United States) had 94% sensitivity and 74% specificity compared with the FAMA test. The rates of antibody detection by the gE LIPS and glycoprotein ELISA were not statistically different. Therefore, the gE LIPS assay may be useful for detecting VZV antibodies in varicella vaccine recipients. (This study has been registered at ClinicalTrials.gov under registration no. NCT00921999.). PMID:24990909

  6. Genome-wide mapping of the distribution of CarD, RNAP σA, and RNAP β on the Mycobacterium smegmatis chromosome using chromatin immunoprecipitation sequencing

    PubMed Central

    Landick, Robert; Krek, Azra; Glickman, Michael S.; Socci, Nicholas D.; Stallings, Christina L.

    2014-01-01

    CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis [6]. We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σA were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli [3], however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 [5] as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164). PMID:25089258

  7. Genome-Wide Mapping of the Distribution of CarD, RNAP σ(A), and RNAP β on the Mycobacterium smegmatis Chromosome using Chromatin Immunoprecipitation Sequencing.

    PubMed

    Landick, Robert; Krek, Azra; Glickman, Michael S; Socci, Nicholas D; Stallings, Christina L

    2014-12-01

    CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis (6). We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed Chromatin Immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σ(A) were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σ(A) would be predominantly enriched at promoters based on work in Escherichia coli (3), however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σ(A). The colocalization of σ(A) and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 (5) as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164). PMID:25089258

  8. Adenosine A1( )receptors are selectively coupled to Gα(i-3) in postmortem human brain cortex: Guanosine-5'-O-(3-[(35)S]thio)triphosphate ([(35)S]GTPγS) binding/immunoprecipitation study.

    PubMed

    Odagaki, Yuji; Kinoshita, Masakazu; Ota, Toshio; Meana, J Javier; Callado, Luis F; García-Sevilla, Jesús A

    2015-10-01

    By means of guanosine-5'-O-(3-[(35)S]thio)triphosphate ([(35)S]GTPγS) binding assay combined with immunoprecipitation using anti-Gα subunit antibody, we recently reported 5-HT2A receptor- and M1 muscarinic acetylcholine receptor-mediated Gαq activation in rat cerebral cortical membranes (Odagaki et al., 2014). In the present study, this method has been applied to postmortem human brains, with focusing on adenosine receptor-mediated G-protein activation. In the exploratory experiments using a series of agonists and the antibodies specific to each Gα subtypes in the presence of low (10 nM) or high (50 μM) concentration of GDP, the most prominent increases in specific [(35)S]GTPγS binding in the membranes prepared from human prefrontal cortex were obtained for the combinations of adenosine (1mM)/anti-Gαi-3 in the presence of 50 μM GDP as well as 5-HT (100 μM)/anti-Gαq and carbachol (1mM)/anti-Gαq in the presence of 10nM GDP. Adenosine-induced activation of Gαi-3 emerged only when GDP concentrations were increased higher than 10 μM, and the following experiments were performed in the presence of 300 μM GDP. Adenosine increased specific [(35)S]GTPγS binding to Gαi-3 in a concentration-dependent manner to 251.4% of the basal unstimulated binding, with an EC50 of 1.77 μM. The involvement of adenosine A1 receptor was verified by the experiments using selective agonists and antagonists at adenosine A1 or A3 receptor. Among the α subunits of Gi/o class (Gαi-1, Gαi-2, Gαi-3, and Gαo.), only Gαi-3 was activated by 1mM adenosine, indicating that human brain adenosine A1 receptor is coupled preferentially, if not exclusively, to Gαi-3. PMID:26213104

  9. Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma.

    PubMed

    Wang, Xiao; Björklund, Stefan; Wasik, Agata M; Grandien, Alf; Andersson, Patrik; Kimby, Eva; Dahlman-Wright, Karin; Zhao, Chunyan; Christensson, Birger; Sander, Birgitta

    2010-01-01

    The SRY (sex determining region Y)-box 11 (SOX11) gene, located on chromosome 2p25, encodes for a transcription factor that is involved in tissue remodeling during embryogenesis and is crucial for neurogenesis. The role for SOX11 in hematopoiesis has not yet been defined. Two genes under direct control of SOX11 are the class- III β-tubulin gene (TUBB3) in neural cells and the transcription factor TEA domain family member 2 (TEAD2) in neural and mesenchymal progenitor cells. Normal, mature lymphocytes lack SOX11 but express SOX4, another member of the same group of SOX transcription factors. We and others recently identified SOX11 as aberrantly expressed in mantle cell lymphoma (MCL). Since SOX11 is variably expressed in MCL it may not be essential for tumorigenesis, but may carry prognostic information. Currently, no specific functional effects have been linked to SOX11 expression in MCL and it is not known which genes are under influence of SOX11 in lymphoma. In this study we found variable expression of SOX11, SOX4 and SOX12 mRNA in mantle cell lymphoma cell lines. Downregulation of SOX11 expression by siRNA verified that SOX11 controlled the expression of the gene TUBB3 in the MCL cell line Granta 519. Furthermore we identified, by global gene expression analysis, 26 new target genes influenced by siRNA SOX11 downmodulation. Among these genes, DBN1, SETMAR and HIG2 were found to be significantly correlated to SOX11 expression in two cohorts of primary mantle cell lymphomas. Chromatin immunoprecipitation (ChIP) analysis showed that these genes are direct targets of the SOX11 protein. In spite of almost complete downregulation of the SOX11 protein no significant effects on Granta 519 cell proliferation or survival in short term in vitro experiments was found. In summary we have identified a number of genes influenced by SOX11 expression in MCL cell lines and primary MCL. Among these genes, DBN1, SETMAR and HIG2 are direct transcriptional targets of the SOX11

  10. Synergistic effects of combined DNA methyltransferase inhibition and MBD2 depletion on breast cancer cells; MBD2 depletion blocks 5-aza-2ʹ-deoxycytidine-triggered invasiveness

    PubMed Central

    Cheishvili, David; Chik, Flora; Li, Chen Chen; Bhattacharya, Bishnu; Suderman, Matthew; Arakelian, Ani; Hallett, Michael; Rabbani, Shafaat A.; Szyf, Moshe

    2014-01-01

    5-Aza-2ʹ-deoxycytidine (5-azaCdR) not only inhibits growth of non-invasive breast cancer cells but also increases their invasiveness through induction of pro-metastatic genes. Methylated DNA binding protein 2 (MBD2) is involved in silencing methylated tumor suppressor genes as well as activation of pro-metastatic genes. In this study, we show that a combination of MBD2 depletion and DNA methyltransferases (DNMT) inhibition in breast cancer cells results in a combined effect in vitro and in vivo, enhancing tumor growth arrest on one hand, while inhibiting invasiveness triggered by 5-azaCdR on the other hand. The combined treatment of MBD2 depletion and 5-azaCdR suppresses and augments distinct gene networks that are induced by DNMT inhibition alone. These data point to a potential new approach in targeting the DNA methylation machinery by combination of MBD2 and DNMT inhibitors. PMID:25178277

  11. PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a Step-By-Step Protocol to the Transcriptome-Wide Identification of Binding Sites of RNA-Binding Proteins

    PubMed Central

    Spitzer, Jessica; Hafner, Markus; Landthaler, Markus; Ascano, Manuel; Farazi, Thalia; Wardle, Greg; Nusbaum, Jeff; Khorshid, Mohsen; Burger, Lukas; Zavolan, Mihaela; Tuschl, Thomas

    2014-01-01

    We recently developed a protocol for the transcriptome-wide isolation of RNA recognition elements readily applicable to any protein or ribonucleoprotein complex directly contacting RNA (including RNA helicases, polymerases, or nucleases) expressed in cell culture models either naturally or ectopically (Hafner et al., 2010). Briefly, immunoprecipitation of the RNA-binding protein of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. In the course of lysate preparation and immunoprecipitation, the mRNAs are partially degraded using Ribonu-clease T1. The isolated crosslinked RNA fragments are converted into a cDNA library and deep-sequenced using Solexa technology (see Explanatory Chapter: Next Generation Sequencing). By introducing photoreactive nucleosides that generate characteristic sequence changes upon crosslinking (see below), our protocol allows one to separate RNA segments bound by the protein of interest from the background un-crosslinked RNAs. PMID:24581442

  12. Comparative validation study to demonstrate the equivalence of a minor modification to AOAC Method 996.09 Visual Immunoprecipitate (VIP) for E. coli O157:H7 method to the reference culture method.

    PubMed

    Feldsine, Philip T; Kerr, David E; Shen, George; Lienau, Andrew H

    2009-01-01

    The Visual Immunoprecipitate (VIP) for the Detection of Escherichia coli 0157:H7 in Foods, AOAC Official Method 996.09, has been modified to change the color of the test and control lines of the device. A methods comparison study was conducted to demonstrate the equivalence of this modification to the reference culture method. Three foods were analyzed. In total, there were valid results from 225 samples and controls. Results showed that the VIP Gold for E. coli O157:H7 is equivalent to the reference culture methods for the detection of E. coli O157:H7. PMID:19916379

  13. PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues

    PubMed Central

    Yamaguchi, Nobutoshi; Winter, Cara M.; Wu, Miin-Feng; Kwon, Chang Seob; William, Dilusha A.; Wagner, Doris

    2014-01-01

    The ability of proteins to associate with genomic DNA in the context of chromatin is critical for many nuclear processes including transcription, replication, recombination, and DNA repair. Chromatin immunoprecipication (ChIP) is a practical and useful technique for characterizing protein / DNA association in vivo. The procedure generally includes six steps: (1) crosslinking the protein to the DNA; (2) isolating the chromatin; (3) chromatin fragmentation; (4) imunoprecipitation with antibodies against the protein of interest; (5) DNA recovery; and (6) PCR identification of factor associated DNA sequences. In this protocol, we describe guidelines, experimental setup, and conditions for ChIP in intact Arabidopsis tissues. This protocol has been used to study association of histone modifications, of chromatin remodeling ATPases, as well as of sequence-specific transcription factors with the genomic DNA in various Arabidopsis thaliana tissues. The protocol described focuses on ChIP-qPCR, but can readily be adapted for use in ChIP-chip or ChIP-seq experiments. The entire procedure can be completed within 3 days. PMID:24653666

  14. Power combiner

    DOEpatents

    Arnold, Mobius; Ives, Robert Lawrence

    2006-09-05

    A power combiner for the combining of symmetric and asymmetric traveling wave energy comprises a feed waveguide having an input port and a launching port, a reflector for reflecting launched wave energy, and a final waveguide for the collection and transport of launched wave energy. The power combiner has a launching port for symmetrical waves which comprises a cylindrical section coaxial to the feed waveguide, and a launching port for asymmetric waves which comprises a sawtooth rotated about a central axis.

  15. Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis Shows that WhiB Is a Transcription Factor That Cocontrols Its Regulon with WhiA To Initiate Developmental Cell Division in Streptomyces

    PubMed Central

    Chandra, Govind; Bibb, Maureen J.; Findlay, Kim C.; Buttner, Mark J.

    2016-01-01

    ABSTRACT WhiB is the founding member of a family of proteins (the WhiB-like [Wbl] family) that carry a [4Fe-4S] iron-sulfur cluster and play key roles in diverse aspects of the biology of actinomycetes, including pathogenesis, antibiotic resistance, and the control of development. In Streptomyces, WhiB is essential for the process of developmentally controlled cell division that leads to sporulation. The biochemical function of Wbl proteins has been controversial; here, we set out to determine unambiguously if WhiB functions as a transcription factor using chromatin immunoprecipitation sequencing (ChIP-seq) in Streptomyces venezuelae. In the first demonstration of in vivo genome-wide Wbl binding, we showed that WhiB regulates the expression of key genes required for sporulation by binding upstream of ~240 transcription units. Strikingly, the WhiB regulon is identical to the previously characterized WhiA regulon, providing an explanation for the identical phenotypes of whiA and whiB mutants. Using ChIP-seq, we demonstrated that in vivo DNA binding by WhiA depends on WhiB and vice versa, showing that WhiA and WhiB function cooperatively to control expression of a common set of WhiAB target genes. Finally, we show that mutation of the cysteine residues that coordinate the [4Fe-4S] cluster in WhiB prevents DNA binding by both WhiB and WhiA in vivo. PMID:27094333

  16. High-throughput evaluation of aryl hydrocarbon receptor-binding sites selected via chromatin immunoprecipitation-based screening in Hepa-1c1c7 cells stimulated with 2,3,7,8-tetrachlorodibenzo-p-dioxin.

    PubMed

    Kinehara, Masaki; Fukuda, Itsuko; Yoshida, Ken-Ichi; Ashida, Hitoshi

    2008-12-01

    Upon binding to ligands such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AhR) is activated to form a heterodimer with an aryl hydrocarbon receptor nuclear translocator (Arnt) and binds to DNA. It has been shown that the binding of AhR to DNA depends on the dioxin response element (DRE) and controls xenobiotic-response genes. AhR-binding DNA fragments from mouse hepatoma Hepa-1c1c7 cells stimulated with TCDD were once enriched in a chromatin immunoprecipitation (ChIP) DNA library and screened through a high-throughput southwestern chemistry-based enzyme-linked immunosorbent assay (SW-ELISA). After screening 1700 fragments, the ChIP-SW-ELISA screening strategy allowed us to isolate 77 fragments tightly interacting with AhR in the presence of TCDD. Only 39 of the 77 fragments appeared to contain a typical DRE, indicating that in some cases the DRE was dispensable for AhR-binding, while 75 fragments were located within promoter-distal regions. Genomic mapping of the 77 fragments enabled us to estimate 121 potential AhR targets including known targets such as Cyp1A1 and Cyp1B1, but only a limited number exhibited an altered expression dependent on TCDD. This study revealed the fact that TCDD-activated AhR frequently binds to promoter-distal regions even without a DRE and is not always involved in transcriptional regulation, suggesting that within the genome DNA-binding of AhR could take place often in many regions without cis-regulatory elements and might not be a key determinant to establish its regulatory function. PMID:19282623

  17. Combinations Therapies.

    PubMed

    Reinmuth, Niels; Reck, Martin

    2015-01-01

    Immunotherapy of cancer encompasses different strategies that elicit or enhance the immune response against tumors. The first results from clinical studies have provided promising data for the treatment of lung cancer patients with immunomodulating monotherapies. To improve the potential benefit of cancer immunotherapy, synergistic combinations of the various immunotherapy approaches or of different elements within each of the immunotherapy approaches are being explored. The rationale typically involves different but complementary mechanisms of action, eventually impinging on more than one immune system mechanism. As a prominent example, the simultaneous blockade of PD-1 and CTLA-4 is giving rise to therapeutic synergy, while still offering room for efficacy improvement. Moreover, combinations of immunomodulating agents with chemotherapy or targeted molecules are being tested. Animal models suggest that immunotherapies in combination with these various options offer evidence for synergistic effects and are likely to radically change cancer treatment paradigms. However, data obtained so far indicate that toxic side effects are also potentiated, which may even restrict the selection of patients that are suitable for these combinational approaches. Advancing the field of combinatorial immunotherapy will require changes in the way investigational agents are clinically developed as well as novel experimental end-points for efficacy evaluation. However, this combined therapeutic manipulation of both tumor and stromal cells may lead to a dramatic change in the therapeutic options of lung cancer patients in any disease stage that can only grossly be appreciated by the current studies. PMID:26384009

  18. Combination Light

    NASA Technical Reports Server (NTRS)

    1990-01-01

    The Rayovac TANDEM is an advanced technology combination work light and general purpose flashlight that incorporates several NASA technologies. The TANDEM functions as two lights in one. It features a long range spotlight and wide angle floodlight; simple one-hand electrical switching changes the beam from spot to flood. TANDEM developers made particular use of NASA's extensive research in ergonomics in the TANDEM's angled handle, convenient shape and different orientations. The shatterproof, water resistant plastic casing also draws on NASA technology, as does the shape and beam distance of the square diffused flood. TANDEM's heavy duty magnet that permits the light to be affixed to any metal object borrows from NASA research on rare earth magnets that combine strong magnetic capability with low cost. Developers used a NASA-developed ultrasonic welding technique in the light's interior.

  19. Combined inhibition of DNA methyltransferase and histone deacetylase restores caspase-8 expression and sensitizes SCLC cells to TRAIL.

    PubMed

    Kaminskyy, Vitaliy O; Surova, Olga V; Vaculova, Alena; Zhivotovsky, Boris

    2011-10-01

    Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a promising drug for the treatment of tumors; however, a number of cancer cells are resistant to this cytokine. Among the mechanisms of resistance of small cell lung carcinomas (SCLCs) to TRAIL is the lack of caspase-8 expression. Although methylation of the caspase-8 promoter has been suggested as the main mechanism of caspase-8 silencing, we showed that reduction of the enzymes involved in DNA methylation, DNA methyltransferases (DNMT) 1, 3a and 3b, was not sufficient to significantly restore caspase-8 expression in SCLC cells, signifying that other mechanisms are involved in caspase-8 silencing. We found that combination of the DNMT inhibitor decitabine with an inhibitor of histone deacetylase (HDAC) significantly increased caspase-8 expression in SCLC cells at the RNA and protein levels. Among all studied HDAC inhibitors, valproic acid (VPA) and CI-994 showed prolonged effects on histone acetylation, while combination with decitabine produced the most prominent effects on caspase-8 re-expression. Moreover, a significant reduction of survivin and cIAP-1 proteins level was observed after treatment with VPA. The combination of two drugs sensitized SCLC cells to TRAIL-induced apoptosis, involving mitochondrial apoptotic pathway and was accompanied by Bid cleavage, activation of Bax, and release of cytochrome c. Both initiator caspase-8 and -9 were required for the sensitization of SCLC cells to TRAIL. Thus, efficient restoration of caspase-8 expression in SCLC cells is achieved when a combination of DNMT and HDAC inhibitors is used, suggesting a combination of decitabine and VPA or CI-994 as a potential treatment for sensitization of SCLC cells lacking caspase-8 to TRAIL. PMID:21771726

  20. Birth control pills - combination

    MedlinePlus

    The pill - combination; Oral contraceptives - combination; OCP - combination; Contraception - combination ... Birth control pills help keep you from getting pregnant. When taken daily, they are one of the most ...

  1. Griffithsin and Carrageenan Combination To Target Herpes Simplex Virus 2 and Human Papillomavirus

    PubMed Central

    Levendosky, Keith; Mizenina, Olga; Martinelli, Elena; Jean-Pierre, Ninochka; Kizima, Larisa; Rodriguez, Aixa; Kleinbeck, Kyle; Bonnaire, Thierry; Robbiani, Melissa; Zydowsky, Thomas M.; O'Keefe, Barry R.

    2015-01-01

    Extensive preclinical evaluation of griffithsin (GRFT) has identified this lectin to be a promising broad-spectrum microbicide. We set out to explore the antiviral properties of a GRFT and carrageenan (CG) combination product against herpes simplex virus 2 (HSV-2) and human papillomavirus (HPV) as well as determine the mechanism of action (MOA) of GRFT against both viruses. We performed the experiments in different cell lines, using time-of-addition and temperature dependence experiments to differentiate inhibition of viral attachment from entry and viral receptor internalization. Surface plasmon resonance (SPR) was used to assess GRFT binding to viral glycoproteins, and immunoprecipitation and immunohistochemistry were used to identify the specific glycoprotein involved. We determined the antiviral activity of GRFT against HSV-2 to be a 50% effective concentration (EC50) of 230 nM and provide the first evidence that GRFT has moderate anti-HPV activity (EC50 = 0.429 to 1.39 μM). GRFT blocks the entry of HSV-2 and HPV into target cells but not the adsorption of HSV-2 and HPV onto target cells. The results of the SPR, immunoprecipitation, and immunohistochemistry analyses of HSV-2 combined suggest that GRFT may block viral entry by binding to HSV-2 glycoprotein D. Cell-based assays suggest anti-HPV activity through α6 integrin internalization. The GRFT-CG combination product but not GRFT or CG alone reduced HSV-2 vaginal infection in mice when given an hour before challenge (P = 0.0352). While GRFT significantly protected mice against vaginal HPV infection when dosed during and after HPV16 pseudovirus challenge (P < 0.026), greater CG-mediated protection was afforded by the GRFT-CG combination for up to 8 h (P < 0.0022). These findings support the development of the GRFT-CG combination as a broad-spectrum microbicide. PMID:26369967

  2. Griffithsin and Carrageenan Combination To Target Herpes Simplex Virus 2 and Human Papillomavirus.

    PubMed

    Levendosky, Keith; Mizenina, Olga; Martinelli, Elena; Jean-Pierre, Ninochka; Kizima, Larisa; Rodriguez, Aixa; Kleinbeck, Kyle; Bonnaire, Thierry; Robbiani, Melissa; Zydowsky, Thomas M; O'Keefe, Barry R; Fernández-Romero, José A

    2015-12-01

    Extensive preclinical evaluation of griffithsin (GRFT) has identified this lectin to be a promising broad-spectrum microbicide. We set out to explore the antiviral properties of a GRFT and carrageenan (CG) combination product against herpes simplex virus 2 (HSV-2) and human papillomavirus (HPV) as well as determine the mechanism of action (MOA) of GRFT against both viruses. We performed the experiments in different cell lines, using time-of-addition and temperature dependence experiments to differentiate inhibition of viral attachment from entry and viral receptor internalization. Surface plasmon resonance (SPR) was used to assess GRFT binding to viral glycoproteins, and immunoprecipitation and immunohistochemistry were used to identify the specific glycoprotein involved. We determined the antiviral activity of GRFT against HSV-2 to be a 50% effective concentration (EC50) of 230 nM and provide the first evidence that GRFT has moderate anti-HPV activity (EC50 = 0.429 to 1.39 μM). GRFT blocks the entry of HSV-2 and HPV into target cells but not the adsorption of HSV-2 and HPV onto target cells. The results of the SPR, immunoprecipitation, and immunohistochemistry analyses of HSV-2 combined suggest that GRFT may block viral entry by binding to HSV-2 glycoprotein D. Cell-based assays suggest anti-HPV activity through α6 integrin internalization. The GRFT-CG combination product but not GRFT or CG alone reduced HSV-2 vaginal infection in mice when given an hour before challenge (P = 0.0352). While GRFT significantly protected mice against vaginal HPV infection when dosed during and after HPV16 pseudovirus challenge (P < 0.026), greater CG-mediated protection was afforded by the GRFT-CG combination for up to 8 h (P < 0.0022). These findings support the development of the GRFT-CG combination as a broad-spectrum microbicide. PMID:26369967

  3. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

    PubMed

    Harris, R Alan; Wang, Ting; Coarfa, Cristian; Nagarajan, Raman P; Hong, Chibo; Downey, Sara L; Johnson, Brett E; Fouse, Shaun D; Delaney, Allen; Zhao, Yongjun; Olshen, Adam; Ballinger, Tracy; Zhou, Xin; Forsberg, Kevin J; Gu, Junchen; Echipare, Lorigail; O'Geen, Henriette; Lister, Ryan; Pelizzola, Mattia; Xi, Yuanxin; Epstein, Charles B; Bernstein, Bradley E; Hawkins, R David; Ren, Bing; Chung, Wen-Yu; Gu, Hongcang; Bock, Christoph; Gnirke, Andreas; Zhang, Michael Q; Haussler, David; Ecker, Joseph R; Li, Wei; Farnham, Peggy J; Waterland, Robert A; Meissner, Alexander; Marra, Marco A; Hirst, Martin; Milosavljevic, Aleksandar; Costello, Joseph F

    2010-10-01

    Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression. PMID:20852635

  4. Next Generation Epigenetic Detection Technique: Identifying Methylated DNA using Graphene Nanopore

    NASA Astrophysics Data System (ADS)

    Ahmed, Towfiq; Haraldsen, Jason T.; Zhu, Jian-Xin; Balatsky, A. V.

    2014-03-01

    DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells.Unusual methylation on CPG islands are identified as the prime causes for silencing the tumor suppressant genes. Early detection of such methylation can diagnose the potentially harmful oncogenic evolution of cells, and provide a promising guideline for cancer prevention.We propose a detection technique and calculate the transport current through punctured graphene as the cytosine and methylated cytosine translocate through the nanopore. We also calculate the transport properties for uracil and cyano-cytosine to compare. Our calculations of transmission, current and tunneling conductance show distinct signatures in their spectrum for each molecular type. Our theoretical study provides a next generation detection technique for identifying DNA methylation using graphene based nanopore device. This work was supported by U.S. DOE Office of Basic Energy Sciences, and by VR 621-2012-2983 and ERC 321031-DM. This work was, in part, supported by the Center for Integrated Nanotechnologies, a U.S. DOE BES user facility.

  5. Methylated DNA and microRNA in Body Fluids as Biomarkers for Cancer Detection

    PubMed Central

    Ma, Yanning; Wang, Xian; Jin, Hongchuan

    2013-01-01

    Epigenetic alterations including DNA methylation and microRNAs (miRNAs) play important roles in the initiation and progression of human cancers. As the extensively studied epigenetic changes in tumors, DNA methylation and miRNAs are the most potential epigenetic biomarkers for cancer diagnosis. After the identification of circulating cell-free nuclear acids, increasing evidence demonstrated great potential of cell-free epigenetic biomarkers in the blood or other body fluids for cancer detection. PMID:23681012

  6. Actions of human DNA glycosylases on uracil-containing DNA, methylated DNA and their reconstituted chromatins.

    PubMed

    Ishiwata, K; Oikawa, A

    1979-07-26

    Extracts of human lymphoblastoid cells catalyzed complete release of uracil (Ura) from PBS1 DNA, which contains Ura instead of thymine as a normal component (Ura-DNA), and 3-methyladenine (3-MeAde) from DNA methylated with methyl methanesulfonate (Me-DNA). These two activities, Ura-DNA glycosylase and 3-MeAde-DNA glycosylase, differed in heat stability. Cell extracts released Ura more rapidly and 3-MeAde more slowly from alkali-denatured preparations of Ura- and Me-DNA, respectively, than from native DNA's. On incubation with reconstituted chromatins, prepared from Ura-DNA and Me-DNA, respectively, with calf thymus chromosomal protein by salt gradient dialysis, cell extracts released all the Ura but only about half of the 3-MeAde residues, although both these chromatins were degraded by micrococcal nuclease until about half of the nucleotides became acid soluble. The activities of Ura-DNA and 3-MeAde-DNA glycosylase of xeroderma pigmentosum cells were similar to those of normal cells. PMID:465495

  7. Towards an immuno-precipitated neurodevelopmental animal model of schizophrenia.

    PubMed

    Meyer, Urs; Feldon, Joram; Schedlowski, Manfred; Yee, Benjamin K

    2005-01-01

    Epidemiological studies have indicated an association between maternal bacterial and viral infections during pregnancy and the higher incidence of schizophrenia in the resultant offspring post-puberty. One hypothesis asserts that the reported epidemiological link is mediated by prenatal activation of the foetal immune system in response to the elevation of maternal cytokine level due to infection. Here, we report that pregnant mouse dams receiving a single exposure to the cytokine-releasing agent, polyriboinosinic-polyribocytidilic acid (PolyI:C; at 2.5, 5.0, or 10.0 mg/kg) on gestation day 9 produced offspring that subsequently exhibited multiple schizophrenia-related behavioural deficits in adulthood, in comparison to offspring from vehicle injected or non-injected control dams. The efficacy of the PolyI:C challenge to induce cytokine responses in naïve non-pregnant adult female mice and in foetal brain tissue when injected to pregnant mice were further ascertained in separate subjects: (i) a dose-dependent elevation of interleukin-10 was detected in the adult female mice at 1 and 6h post-injection, (ii) 12 h following prenatal PolyI:C challenge, the foetal levels of interleukin-1beta were elevated. The spectrum of abnormalities included impairments in exploratory behaviour, prepulse inhibition, latent inhibition, the US-pre-exposure effect, spatial working memory; and enhancement in the locomotor response to systemic amphetamine (2.5 mg/kg, i.p.) as well as in discrimination reversal learning. The neuropsychological parallels between prenatal PolyI:C treatment in mice and psychosis in humans, demonstrated here, leads us to conclude that prenatal PolyI:C treatment represents one of the most powerful environmental-developmental models of schizophrenia to date. The uniqueness of this model lies in its epidemiological and immunological relevance. It is, sui generis, ideally suited for the investigation of the neuropsychoimmunological mechanisms implicated in the developmental aetiology and disease processes of schizophrenia. PMID:15964075

  8. Birth control pills - combination

    MedlinePlus

    ... this page: //medlineplus.gov/ency/patientinstructions/000655.htm Birth control pills - combination To use the sharing features on ... frequency of your menstrual cycles. Types of Combination Birth Control Pills Birth control pills come in packages. You ...

  9. Combined environmental stresses

    NASA Technical Reports Server (NTRS)

    Murray, R. H.; Mccally, M.

    1973-01-01

    Tolerance levels, physiological effects, and performance degradation during simultaneous or sequential exposures to two environmental stresses, and also three or more simultaneous stresses are described. Environmental stress combinations are characterized by four descriptors: order of occurrence, duration of exposure, severity of exposure, and type of interaction. Combined stress data and facilities for combined stress study are briefly mentioned.

  10. Failure combination method

    SciTech Connect

    Hedin, F.; Le Coguiec, A.; Le Floch, C.; Llory, M.; Villemeur, A.

    1981-01-01

    The method described in this paper is an inductive method for combining failures (called the Failure Combination Method (FCM)). It is based on a preliminary analysis of the systems performed with an FMEA. As a study has been undertaken to test the method, the organization of the study as well as its first results from a methodological point of view are stressed. 8 refs.

  11. Embodied Conceptual Combination

    PubMed Central

    Lynott, Dermot; Connell, Louise

    2010-01-01

    Conceptual combination research investigates the processes involved in creating new meaning from old referents. It is therefore essential that embodied theories of cognition are able to explain this constructive ability and predict the resultant behavior. However, by failing to take an embodied or grounded view of the conceptual system, existing theories of conceptual combination cannot account for the role of perceptual, motor, and affective information in conceptual combination. In the present paper, we propose the embodied conceptual combination (ECCo) model to address this oversight. In ECCo, conceptual combination is the result of the interaction of the linguistic and simulation systems, such that linguistic distributional information guides or facilitates the combination process, but the new concept is fundamentally a situated, simulated entity. So, for example, a cactus beetle is represented as a multimodal simulation that includes visual (e.g., the shiny appearance of a beetle) and haptic (e.g., the prickliness of the cactus) information, all situated in the broader location of a desert environment under a hot sun, and with (at least for some people) an element of creepy-crawly revulsion. The ECCo theory differentiates interpretations according to whether the constituent concepts are destructively, or non-destructively, combined in the situated simulation. We compare ECCo to other theories of conceptual combination, and discuss how it accounts for classic effects in the literature. PMID:21833267

  12. Effective Nutritional Supplement Combinations

    NASA Astrophysics Data System (ADS)

    Cooke, Matt; Cribb, Paul J.

    Few supplement combinations that are marketed to athletes are supported by scientific evidence of their effectiveness. Quite often, under the rigor of scientific investigation, the patented combination fails to provide any greater benefit than a group given the active (generic) ingredient. The focus of this chapter is supplement combinations and dosing strategies that are effective at promoting an acute physiological response that may improve/enhance exercise performance or influence chronic adaptations desired from training. In recent years, there has been a particular focus on two nutritional ergogenic aids—creatine monohydrate and protein/amino acids—in combination with specific nutrients in an effort to augment or add to their already established independent ergogenic effects. These combinations and others are discussed in this chapter.

  13. Combination therapy with statins.

    PubMed

    Gylling, Helena; Miettinen, Tatu A

    2002-09-01

    Statins effectively inhibit cholesterol synthesis and are currently the most commonly used drugs for the treatment of hypercholesterolemia. However, patients with familial hypercholesterolemia and those unwilling to take, or who cannot tolerate statins, and patients with combined hyperlipidemia require a combination treatment. Statins combined with cholesterol malabsorption, caused, e.g., by plant stanol esters or ezetimibe (Schering-Plough Corp/Merck & Co Inc), or with bile acid malabsorption, caused by bile acid binding resins or guar gum, inhibit compensatory increases in cholesterol synthesis and effectively lower LDL cholesterol levels. Combination therapy of statins with fibrates should be controlled by lipidology experts. Recent information on indications and advantages of combining statins with n-3 fatty acids, hormone replacement therapy, or niacin, will also be discussed. PMID:12498007

  14. Optical Communications Channel Combiner

    NASA Technical Reports Server (NTRS)

    Quirk, Kevin J.; Quirk, Kevin J.; Nguyen, Danh H.; Nguyen, Huy

    2012-01-01

    NASA has identified deep-space optical communications links as an integral part of a unified space communication network in order to provide data rates in excess of 100 Mb/s. The distances and limited power inherent in a deep-space optical downlink necessitate the use of photon-counting detectors and a power-efficient modulation such as pulse position modulation (PPM). For the output of each photodetector, whether from a separate telescope or a portion of the detection area, a communication receiver estimates a log-likelihood ratio for each PPM slot. To realize the full effective aperture of these receivers, their outputs must be combined prior to information decoding. A channel combiner was developed to synchronize the log-likelihood ratio (LLR) sequences of multiple receivers, and then combines these into a single LLR sequence for information decoding. The channel combiner synchronizes the LLR sequences of up to three receivers and then combines these into a single LLR sequence for output. The channel combiner has three channel inputs, each of which takes as input a sequence of four-bit LLRs for each PPM slot in a codeword via a XAUI 10 Gb/s quad optical fiber interface. The cross-correlation between the channels LLR time series are calculated and used to synchronize the sequences prior to combining. The output of the channel combiner is a sequence of four-bit LLRs for each PPM slot in a codeword via a XAUI 10 Gb/s quad optical fiber interface. The unit is controlled through a 1 Gb/s Ethernet UDP/IP interface. A deep-space optical communication link has not yet been demonstrated. This ground-station channel combiner was developed to demonstrate this capability and is unique in its ability to process such a signal.

  15. [Advantages of fixed combinations].

    PubMed

    Lachkar, Y

    2008-07-01

    Fixed combinations are indicated in the treatment of glaucoma and ocular hypertension when monotherapy does not sufficiently reduce IOP. Fixed combinations show better efficacy than the instillation of each separate component and are at least equivalent to the administration of both components in a separate association. They simplify treatment, increase compliance and quality of life, and decrease exposure to preservatives. Although they are less aggressive for patients when a new drug needs to be added, the use of fixed combinations should not decrease the follow-up. PMID:18957922

  16. Hydrocodone Combination Products

    MedlinePlus

    ... Other hydrocodone combination products are used to relieve cough. Hydrocodone is in a class of medications called ... and nervous system respond to pain. Hydrocodone relieves cough by decreasing activity in the part of the ...

  17. Earth science: Deadly combination

    NASA Astrophysics Data System (ADS)

    Duncan, Robert

    2015-11-01

    New evidence suggests that seismic waves from the Chicxulub meteorite impact doubled the eruption rate of lavas on the opposite side of the planet -- a combination that led to the mass extinction at the end of the Cretaceous period.

  18. Optimally combined confidence limits

    NASA Astrophysics Data System (ADS)

    Janot, P.; Le Diberder, F.

    1998-02-01

    An analytical and optimal procedure to combine statistically independent sets of confidence levels on a quantity is presented. This procedure does not impose any constraint on the methods followed by each analysis to derive its own limit. It incorporates the a priori statistical power of each of the analyses to be combined, in order to optimize the overall sensitivity. It can, in particular, be used to combine the mass limits obtained by several analyses searching for the Higgs boson in different decay channels, with different selection efficiencies, mass resolution and expected background. It can also be used to combine the mass limits obtained by several experiments (e.g. ALEPH, DELPHI, L3 and OPAL, at LEP 2) independently of the method followed by each of these experiments to derive their own limit. A method to derive the limit set by one analysis is also presented, along with an unbiased prescription to optimize the expected mass limit in the no-signal-hypothesis.

  19. [Fixed-dose combination].

    PubMed

    Nagai, Yoshio

    2015-03-01

    Many patients with type 2 diabetes mellitus(T2DM) do not achieve satisfactory glycemic control by monotherapy alone, and often require multiple oral hypoglycemic agents (OHAs). Combining OHAs with complementary mechanisms of action is fundamental to the management of T2DM. Fixed-dose combination therapy(FDC) offers a method of simplifying complex regimens. Efficacy and tolerability appear to be similar between FDC and treatment with individual agents. In addition, FDC can enhance adherence and improved adherence may result in improved glycemic control. Four FDC agents are available in Japan: pioglitazone-glimepiride, pioglitazone-metformin, pioglitazone-alogliptin, and voglibose-mitiglinide. In this review, the advantages and disadvantages of these four combinations are identified and discussed. PMID:25812374

  20. Klystron-linac combination

    DOEpatents

    Stein, W.E.

    1980-04-24

    A combination klystron-linear accelerator which utilizes anti-bunch electrons generated in the klystron section as a source of electrons to be accelerated in the accelerator section. Electron beam current is controlled by second harmonic bunching, constrictor aperture size and magnetic focusing. Rf coupling is achieved by internal and external coupling.

  1. Introduction to combined cycles

    NASA Astrophysics Data System (ADS)

    Moore, M. J.

    Ideas and concepts underlying the technology of combined cycles including the scientific principles involved and the reasons these cycles are in fashion at the present time, are presented. A cycle is a steady flow process for conversion of heat energy into work, in which a working medium passes through a range of states, returning to its original state. Cycles for power production are the steam cycle, which is a closed cycle, and the gas turbine, which represents an open cycle. Combined cycle thermodynamic parameters, are discussed. The general arrangement of the plant is outlined and important features of their component parts described. The scope for future development is discussed. It is concluded that for the next few years the natural gas fired combined cycle will be the main type of plant installed for electricity generation and cogeneration. Whilst gas turbines may not increase substantially in unit size, there remains scope for further increase in firing temperature with consequent increase in cycle performance. However the larger global reserves of coal are providing an incentive to the development of plant for clean coal combustion using the inherent advantage of the combined cycle to attain high efficiencies.

  2. Interschool Production Training Combines

    ERIC Educational Resources Information Center

    Il'ina, L. A.; Fat'ianov, V. V.

    1977-01-01

    An educational program draws together students from several secondary schools in one region in a labor practicum which combines training shops, classroom work, and laboratory experience. Examples are presented of schools throughout the USSR which are training pupils to be computer and machine operators, construction workers, cooks, automotive…

  3. Coherently combining antennas

    NASA Technical Reports Server (NTRS)

    Dybdal, Robert B. (Inventor); Curry, Samuel J. (Inventor)

    2009-01-01

    An apparatus includes antenna elements configured to receive a signal including pseudo-random code, and electronics configured to use the pseudo-random code to determine time delays of signals incident upon the antenna elements and to compensate the signals to coherently combine the antenna elements.

  4. Sentence-Combining Practice

    ERIC Educational Resources Information Center

    Akin, Judy O'Neal

    1978-01-01

    Sample sentence-combining lessons developed to accompany the first-year A-LM German textbook are presented. The exercises are designed for language manipulation practice; they involve breaking down more complex sentences into simpler sentences and the subsequent recombination into complex sentences. All language skills, and particularly writing,…

  5. Sentence Combining and Reading.

    ERIC Educational Resources Information Center

    Ney, James W.

    Research on the effects of two modes of sentence combining instruction on writing skills was conducted from 22 September through 17 December 1976, at Evans School in Tempe, Arizona. Subjects were 40 students in two fifth grade classes designated the individualized class and the group class. The individualized class followed a sentence combining…

  6. Combination hand rejuvenation procedures.

    PubMed

    Shamban, Ava T

    2009-01-01

    Although the hands age at the same rate as the face, the aging process differs and requires a combination treatment approach for optimal rejuvenation. Photoaging causes epidermal changes such as lentigines, actinic keratoses, fine wrinkles, and crepe-like textural change. Thinning of the dermis and subcutaneous fat occurs as a result of both ultraviolet light exposure and intrinsic aging. This process can lead to a skeletal appearance of the hands, with prominent veins and bulging tendons. The combination approach addresses all of these issues, employing lasers, intense pulsed light devices, fractional devices, fillers, peels, vein sclerotherapy, and an effective at-home skin care program as indicated for individual needs and concerns. PMID:19825471

  7. Superconductive ceramic oxide combination

    SciTech Connect

    Chatterjee, D.K.; Mehrotra, A.K.; Mir, J.M.

    1991-03-05

    This patent describes the combination of a superconductive ceramic oxide which degrades in conductivity upon contact of ambient air with its surface and, interposed between the ceramic oxide surface and ambient air in the amount of at least 1 mg per square meter of surface area of the superconductive ceramic oxide, a passivant polymer selected from the group consisting of a polyester ionomer and an alkyl cellulose.

  8. Combining modules for movement.

    PubMed

    Bizzi, E; Cheung, V C K; d'Avella, A; Saltiel, P; Tresch, M

    2008-01-01

    We review experiments supporting the hypothesis that the vertebrate motor system produces movements by combining a small number of units of motor output. Using a variety of approaches such as microstimulation of the spinal cord, NMDA iontophoresis, and an examination of natural behaviors in intact and deafferented animals we have provided evidence for a modular organization of the spinal cord. A module is a functional unit in the spinal cord that generates a specific motor output by imposing a specific pattern of muscle activation. Such an organization might help to simplify the production of movements by reducing the degrees of freedom that need to be specified. PMID:18029291

  9. Monotherapy versus combination therapy.

    PubMed

    Patel, Shilpa M; Saravolatz, Louis D

    2006-11-01

    The science of antibiotic therapy for infectious diseases continues to evolve. In many instances where empiric coverage is necessary, treatment with more than one agent is considered prudent. If an etiology is identified, antibiotics are modified based on culture and susceptibility data. Even when the organism is known, more than one antibiotic may be needed. Decisions about antibiotics should be made after assessments of pertinent clinical information, laboratory and microbiology information, ease of administration, patient compliance, potential adverse effects, cost, and available evidence supporting various treatment options. Clinicians also need to consider synergy and local resistance patterns in selecting therapeutic options. In this article, the authors outline monotherapy and combination therapy options for several common infectious diseases. PMID:17116443

  10. Stove-hearth combinations

    SciTech Connect

    Nesje, A.

    1980-08-26

    Stove-hearth combinations are described that are comprised of a combustion chamber having a pair of side walls supported on a base in opposing relation and joined by a rear wall. A cover or hood defines with the base and front edges of the side walls an opening to the chamber. Two doors are each hingedly associated with upper and lower pivot pins which when the door is in a closed position are disposed adjacent but outside a respective side wall front edge. Along upper and lower side edges of each side wall are formed parallel grooves adapted to be engaged slidably by the upper and lower pivot pins. As the door is opened from a stove to a hearth position the pivot pins are displaced along the grooves causing the door to be led gradually into a position along the outer side of its side wall.

  11. Superconducting combined function magnets

    SciTech Connect

    Hahn, H.; Fernow, R.C.

    1983-01-01

    Superconducting accelerators and storage rings, presently under construction or in the design phase, are based on separate dipole and quadrupole magnets. It is here suggested that a hybrid lattice configuration consisting of dipoles and combined function gradient magnets would: (1) reduce the number of magnet units and their total cost; and (2) increase the filling factor and thus the energy at a given field. Coil cross sections are presented for the example of the Brookhaven Colliding Beam Accelerator. An asymmetric two-layer cable gradient magnet would have transfer functions of 10.42 G/A and 0.628 G cm/sup -1//A versus 15.77 G/A and 2.03 G cm/sup -1//A of the present separate dipoles and quadrupoles.

  12. Newberry Combined Gravity 2016

    DOE Data Explorer

    Kelly Rose

    2016-01-22

    Newberry combined gravity from Zonge Int'l, processed for the EGS stimulation project at well 55-29. Includes data from both Davenport 2006 collection and for OSU/4D EGS monitoring 2012 collection. Locations are NAD83, UTM Zone 10 North, meters. Elevation is NAVD88. Gravity in milligals. Free air and observed gravity are included, along with simple Bouguer anomaly and terrain corrected Bouguer anomaly. SBA230 means simple Bouguer anomaly computed at 2.30 g/cc. CBA230 means terrain corrected Bouguer anomaly at 2.30 g/cc. This suite of densities are included (g/cc): 2.00, 2.10, 2.20, 2.30, 2.40, 2.50, 2.67.

  13. Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1.

    PubMed

    Harrison, Joseph S; Cornett, Evan M; Goldfarb, Dennis; DaRosa, Paul A; Li, Zimeng M; Yan, Feng; Dickson, Bradley M; Guo, Angela H; Cantu, Daniel V; Kaustov, Lilia; Brown, Peter J; Arrowsmith, Cheryl H; Erie, Dorothy A; Major, Michael B; Klevit, Rachel E; Krajewski, Krzysztof; Kuhlman, Brian; Strahl, Brian D; Rothbart, Scott B

    2016-01-01

    The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. Collectively, our studies are the first demonstrations of a DNA-protein interaction and an epigenetic modification directly regulating E3 ubiquitin ligase activity. They also define an orchestrated epigenetic control mechanism involving modifications both to histones and DNA that facilitate UHRF1 chromatin targeting, H3 ubiquitylation, and DNA methylation inheritance. PMID:27595565

  14. Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1

    PubMed Central

    Harrison, Joseph S; Cornett, Evan M; Goldfarb, Dennis; DaRosa, Paul A; Li, Zimeng M; Yan, Feng; Dickson, Bradley M; Guo, Angela H; Cantu, Daniel V; Kaustov, Lilia; Brown, Peter J; Arrowsmith, Cheryl H; Erie, Dorothy A; Major, Michael B; Klevit, Rachel E; Krajewski, Krzysztof; Kuhlman, Brian; Strahl, Brian D; Rothbart, Scott B

    2016-01-01

    The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. Collectively, our studies are the first demonstrations of a DNA-protein interaction and an epigenetic modification directly regulating E3 ubiquitin ligase activity. They also define an orchestrated epigenetic control mechanism involving modifications both to histones and DNA that facilitate UHRF1 chromatin targeting, H3 ubiquitylation, and DNA methylation inheritance. DOI: http://dx.doi.org/10.7554/eLife.17101.001 PMID:27595565

  15. [Insulin combined with selenium inhibit p38MAPK/CBP pathway and suppresses cardiomyocyte apoptosis in rats with diabetic cardiomyopathy].

    PubMed

    Xu, Tianjiao; Liu, Yong; Deng, Yating; Meng, Jin; Li, Ping; Xu, Xiaoli; Zeng, Jurong

    2016-07-01

    Objective To investigate the effect of insulin in combination with selenium on p38-mitogen-activated protein kinase/CREB-binding protein (p38MAPK/CBP) pathway in rats with diabetic cardiomyopathy. Methods Fifty SD rats were randomly grouped into control group, diabetic cardiomyopathy (DCM) group, diabetic cardiomyopathy with insulin treatment (DCM-In) group, diabetic cardiomyopathy with selenium treatment (DCM-Se) group, and diabetic cardiomyopathy with insulin and selenium combination treatment (DCM-In-Se) group. Flow cytometry was used to analyze cell cycle. TUNEL staining was used to detect cardiomyocyte apoptosis. Western blotting was used to examine the levels of cyclin D1, cyclin E, Bax, Bcl-2, p38MAPK, p-p38MAPK, CBP and Ku70. Co-immunoprecipitation was used to examine the acetylation status of Ku70. Results Insulin in combination with selenium significantly inhibited cardiomyocyte apoptosis, increased Bcl-2 levels and decreased Bax, cyclin D1, cyclin E, p38MAPK, p-p38MAPK, CBP, Ku70 and acetylated Ku70 levels. Conclusion The combined treatment of insulin and selenium suppresses cardiomyocyte apoptosis by inhibiting p38MAPK/CBP pathway. PMID:27363274

  16. Combined approach for gynecomastia

    PubMed Central

    El-Sabbagh, Ahmed Hassan

    2016-01-01

    Background: Gynecomastia is a deformity of male chest. Treatment of gynecomastia varied from direct surgical excision to other techniques (mainly liposuction) to a combination of both. Skin excision is done according to the grade. In this study, experience of using liposuction adjuvant to surgical excision was described. Patients and methods: Between September 2012 and April 2015, a total of 14 patients were treated with liposuction and surgical excision through a periareolar incision. Preoperative evaluation was done in all cases to exclude any underlying cause of gynecomastia. Results: All fourteen patients were treated bilaterally (28 breast tissues). Their ages ranged between 13 and 33 years. Two patients were classified as grade I, and four as grade IIa, IIb or III, respectively. The first 3 patients showed seroma. Partial superficial epidermolysis of areola occurred in 2 cases. Superficial infection of incision occurred in one case and was treated conservatively. Conclusion: All grades of gynecomastia were managed by the same approach. Skin excision was added to a patient that had severe skin excess with limited activity and bad skin complexion. No cases required another setting or asked for 2nd opinion. PMID:26955509

  17. Consecutive combined response spectrum

    NASA Astrophysics Data System (ADS)

    Xu, Longjun; Zhao, Guochen; Liu, Qingyang; Xie, Yujian; Xie, Lili

    2014-12-01

    Appropriate estimates of earthquake response spectrum are essential for design of new structures, or seismic safety evaluation of existing structures. This paper presents an alternative procedure to construct design spectrum from a combined normalized response spectrum (NRSC) which is obtained from pseudo-velocity spectrum with the ordinate scaled by different peak ground amplitudes (PGA, PGV, PGD) in different period regions. And a consecutive function f( T) used to normalize the ordinates is defined. Based on a comprehensive study of 220 strong ground motions recorded during recent eleven large worldwide earthquakes, the features of the NRSC are discussed and compared with the traditional normalized acceleration, velocity and displacement response spectra (NRSA, NRSV, NRSD). And the relationships between ground amplitudes are evaluated by using a weighted mean method instead of the arithmetic mean. Then the NRSC is used to define the design spectrum with given peak ground amplitudes. At last, the smooth spectrum is compared with those derived by the former approaches, and the accuracy of the proposed spectrum is tested through an analysis of the dispersion of ground motion response spectra.

  18. Combination vehicle assembly

    SciTech Connect

    Silverman, M.J. Sr.

    1987-03-17

    A combination recreational vehicle assembly is described comprising: two vehicles of a different type, the vehicles comprising a first, leading vehicle having a steering mechanism for maneuvering the assembly and a drivable axle mechanism for propelling the assembly; an independently drivable second vehicle trailing the first vehicle comprising a standard road vehicle having a motor, and an axle mechanism for connecting the motor to the wheels of the second vehicle for providing power to the wheels of the vehicle. A gear means for selectively disconnecting the motor from the axle mechanism to place the vehicle in neutral, and a steering means for maneuvering the second vehicle when driven independently of the first vehicle are included; and a releasable mechanical drive connection between the second vehicle motor and the first vehicle axle mechanism to provide power for driving the assembly. The drive connection comprises a drive pinion projecting from the second vehicle motor to the front of the second vehicle, and a drive shaft projecting from the first vehicle axle mechanism to the rear of the first vehicle.

  19. Electrode/workpiece combinations

    NASA Astrophysics Data System (ADS)

    Benedict, J. J.

    1989-10-01

    Of the many machine tool operations available in the shop today, plunge cut Electrical Discharge Machining (EDM) has become an increasingly useful method of materials fabrication. It is a necessary tool for the research and development type of work performed at the Lawrence Livermore National Laboratory (LLNL). With advancing technology, plunge cut EDMs are more efficient, faster, have greater accuracy and are able to produce better surface finishes. They have been in the past and will continue to be an important part of the production of quality parts in both the Precision and NC Shop. It should be kept in mind that as a non-traditional machining process, EDMing is a time consuming process that can be a very expensive method of producing parts. For this reason, it must be used in the most efficient manner in order to make it a cost-effective means of fabrication, although technology has advanced to the point of state-of-the-art equipment, there is currently a void in available technical information needed for use with this process. The type of information sought after concerns the area of electrode/workpiece combinations. This is in reference to the task of choosing the correct electrode material for the specific workpiece material encountered. A brief description of the EDM process will help in understanding the electrode/workpiece relationship.

  20. Biomass Gasification Combined Cycle

    SciTech Connect

    Judith A. Kieffer

    2000-07-01

    Gasification combined cycle continues to represent an important defining technology area for the forest products industry. The ''Forest Products Gasification Initiative'', organized under the Industry's Agenda 2020 technology vision and supported by the DOE ''Industries of the Future'' program, is well positioned to guide these technologies to commercial success within a five-to ten-year timeframe given supportive federal budgets and public policy. Commercial success will result in significant environmental and renewable energy goals that are shared by the Industry and the Nation. The Battelle/FERCO LIVG technology, which is the technology of choice for the application reported here, remains of high interest due to characteristics that make it well suited for integration with the infrastructure of a pulp production facility. The capital cost, operating economics and long-term demonstration of this technology area key input to future economically sustainable projects and must be verified by the 200 BDT/day demonstration facility currently operating in Burlington, Vermont. The New Bern application that was the initial objective of this project is not currently economically viable and will not be implemented at this time due to several changes at and around the mill which have occurred since the inception of the project in 1995. The analysis shows that for this technology, and likely other gasification technologies as well, the first few installations will require unique circumstances, or supportive public policies, or both to attract host sites and investors.

  1. Combined dyslipidemia in childhood.

    PubMed

    Kavey, Rae-Ellen W

    2015-01-01

    Combined dyslipidemia (CD) is now the predominant dyslipidemic pattern in childhood, characterized by moderate-to-severe elevation in triglycerides and non-high-density lipoprotein cholesterol (non-HDL-C), minimal elevation in low-density lipoprotein cholesterol (LDL-C), and reduced HDL-C. Nuclear magnetic resonance spectroscopy shows that the CD pattern is represented at the lipid subpopulation level as an increase in small, dense LDL and in overall LDL particle number plus a reduction in total HDL-C and large HDL particles, a highly atherogenic pattern. In youth, CD occurs almost exclusively with obesity and is highly prevalent, seen in more than 40% of obese adolescents. CD in childhood predicts pathologic evidence of atherosclerosis and vascular dysfunction in adolescence and young adulthood, and early clinical cardiovascular events in adult life. There is a tight connection between CD, visceral adiposity, insulin resistance, nonalcoholic fatty liver disease, and the metabolic syndrome, suggesting an integrated pathophysiological response to excessive weight gain. Weight loss, changes in dietary composition, and increases in physical activity have all been shown to improve CD significantly in children and adolescents in short-term studies. Most importantly, even small amounts of weight loss are associated with significant decreases in triglyceride levels and increases in HDL-C levels with improvement in lipid subpopulations. Diet change focused on limitation of simple carbohydrate intake with specific elimination of all sugar-sweetened beverages is very effective. Evidence-based recommendations for initiating diet and activity change are provided. Rarely, drug therapy is needed, and the evidence for drug treatment of CD in childhood is reviewed. PMID:26343211

  2. Combining multiple altimeter missions

    NASA Astrophysics Data System (ADS)

    Jacobs, G. A.; Mitchell, J. L.

    1997-10-01

    Viewing altimeter data only at the points where separate altimeter missions' ground tracks cross provides a method to observe long time period sea surface height (SSH) variations and avoids many of the problems inherent in combining separate altimeter data sets through an independently determined geoid. TOPEX/POSEIDON (T/P) data over the time period from January 1, 1993, to December 31, 1995, form a mean SSH that is used as a reference by other altimeter data sets. A least squares analysis of the mean T/P SSH determines the portion of the Geographically Correlated Orbit Error (GCOE) that may be observed through crossover differences and removes this portion of the GCOE. The analysis removes errors of 0.86 cm RMS at 1 cycle per orbit revolution (cpr) and indicates negligible errors at higher frequencies. After the GCOE removal, the accuracy of the T/P reference mean is better than 1 cm RMS as measured by crossover differences. The GCOE contained in the Geosat-Exact Repeat Mission (ERM) and ERS 1 data with orbit solutions using the Joint Gravity Model (JGM) 3 is evaluated through an adjustment to the T/P reference mean surface. The Geosat-ERM data indicate a bias of about 28 cm averaged over the globe, and the ERS 1 bias is 44 cm. The T/P data used here is not corrected for the oscillator drift correction error so that the actual bias is less by about 13 cm. Both the Geosat-ERM and ERS 1 GCOE are mainly 1 cpr. GCOE estimates at frequencies above 1 cpr indicate little actual orbit error but are more correlated to instrument correction errors (particularly water vapor). Simultaneous T/P and ERS 1 SSH anomalies to the T/P mean indicate good correlation.

  3. Combining Cooperative Education and Placement.

    ERIC Educational Resources Information Center

    Lentz, Glenda F.

    1984-01-01

    Suggests that placement, like cooperative education, can function better in academic affairs rather than student affairs. Describes the combination of the two departments at the University of South Florida and discusses advantages and disadvantages of a combined program. (JAC)

  4. Belladonna Alkaloid Combinations and Phenobarbital

    MedlinePlus

    Belladonna alkaloid combinations and phenobarbital are used to relieve cramping pains in conditions such as irritable bowel syndrome and ... Belladonna alkaloid combinations and phenobarbital come as a regular tablet, a slow-acting tablet, capsule, and liquid to take ...

  5. Tigecycline: Alone or in combination?

    PubMed

    Cai, Yun; Bai, Nan; Liu, Xu; Liang, Beibei; Wang, Jin; Wang, Rui

    2016-07-01

    Background The broad spectrum antibiotic tigecyline has promising efficacy against many multidrug-resistant (MDR) pathogens. However, when used clinically, many reports about treatment failures of tigecycline monotherapy indicate that it might not be sufficient to control severe infections. Combination therapy has become an option to treat infection with MDR bacteria because of the distinct advantage in terms of broad coverage, synergistic effect and prevention of drug resistance development. Methods Search terms 'tigecycline', 'GAR-936' and 'glycylcycline' combined with the term 'combination' were applied to retrieve the available in vitro and in vivo studies on tigecycline combination therapy from PubMed database (January 1993-August 2015). Results Colistin-tigecycline was the most studied combination and showed promising efficacy. Other combination regimens, such as tigecycline plus sulbactam, carbapenem or rifampicin, also showed synergistic effects against different bacteria. However, most of the data was from in vitro and animal studies. Only some case reports indicated that tigecycline containing combination therapy had favourable outcomes. Conclusions Although this study could not conclude that combination therapy with tigecycline was superior to monotherapy, when severe infection leaves no other choice, selection of combination drugs according to infection status and in vitro susceptibility testing is recommended. There is a great need for well-designed studies to evaluate the effectiveness and safety of combination therapy compared to tigecyline monotherapy. PMID:26982103

  6. New combination therapies for asthma.

    PubMed

    Donohue, J F; Ohar, J A

    2001-03-01

    Combination products often have useful clinical benefits in asthma. The scientific rationale for combination therapy includes the fact that different agents have complimentary modes of action. Long-acting beta(2)-agonists have effects on airway smooth muscle, and inhaled corticosteroids have potent topical antiinflammatory effect. This combination has been shown to effectively reduce exacerbations and improve symptoms. Substantial clinical trial data provide a rationale for dual-control therapy supported by basic scientific data. Another combined therapy is inhaled steroids plus leukotriene-receptor antagonists, which provides the patient with two effective therapies. Leukotriene-receptor antagonist can also be combined with antihistamines for improved asthma control. Older therapies including theophylline and controlled release albuterol have been effectively added to inhaled corticosteroids, enabling a reduction in the dose of the inhaled steroids. Many other combination therapies are presently being tested. PMID:11224725

  7. Combined oral contraceptive synergistically activates mineralocorticoid receptor through histone code modifications.

    PubMed

    Igunnu, Adedoyin; Seok, Young-Mi; Olatunji, Lawrence A; Kang, Seol-Hee; Kim, Inkyeom

    2015-12-15

    Clinical studies have shown that the use of combined oral contraceptive in pre-menopausal women is associated with fluid retention. However, the molecular mechanism is still elusive. We hypothesized that combined oral contraceptive (COC) ethinyl estradiol (EE) and norgestrel (N) synergistically activates mineralocorticoid receptor (MR) through histone code modifications. Twelve-week-old female Sprague-Dawley rats were treated with olive oil (control), a combination of 0.1µg EE and 1.0µg N (low COC) or 1.0µg EE and 10.0µg N (high COC) as well as 0.1 or 1.0µg EE and 1.0 or 10.0µg N daily for 6 weeks. Expression of MR target genes in kidney cortex was determined by quantitative real-time polymerase chain reaction. MR was quantified by western blot. Recruitment of MR and RNA polymerase II (Pol II) on promoters of target genes as well as histone code modifications was analyzed by chromatin immunoprecipitation assay. Treatment with COC increased renal cortical expression of MR target genes such as serum and glucocorticoid-regulated kinase 1 (Sgk-1), glucocorticoid-induced leucine zipper (Gilz), epithelial Na(+)channel (Enac) and Na(+)-K(+)-ATPase subunit α1 (Atp1a1). Although COC increased neither serum aldosterone nor MR expression in kidney cortex, it increased recruitment of MR and Pol II in parallel with increased H3Ac and H3K4me3 on the promoter regions of MR target genes. However, treatment with EE or N alone did not affect renal cortical expression of Sgk-1, Gilz, Enac or Atp1a1. These results indicate that COC synergistically activates MR through histone code modifications. PMID:26506558

  8. Computer Instruction on Sentence Combining.

    ERIC Educational Resources Information Center

    Humes, Ann

    This description of an interactive instructional computer program in sentence combining for upper elementary and middle school students begins by summarizing the content of the program, which focuses on the instructional technique in which students are given two or more short simple sentences to combine into one longer, complex and/or compound…

  9. Combination moisture and hydrogen getter

    DOEpatents

    Harrah, L.A.; Mead, K.E.; Smith, H.M.

    1983-09-20

    A combination moisture and hydrogen getter comprises (a) a moisture getter comprising a readily oxidizable metal; and (b) a hydrogen getter comprising (1) a solid acetylenic compound and (2) a hydrogenation catalyst. A method of scavenging moisture from a closed container uses the combination moisture and hydrogen getter to irreversibly chemically reduce the moisture and chemically bind the resultant hydrogen.

  10. Revised Accounting for Business Combinations

    ERIC Educational Resources Information Center

    Wilson, Arlette C.; Key, Kimberly

    2008-01-01

    The Financial Accounting Standards Board (FASB) has recently issued Statement of Financial Accounting Standards No. 141 (Revised 2007) Business Combinations. The object of this Statement is to improve the relevance, representational faithfulness, and comparability of reported information about a business combination and its effects. This Statement…

  11. Combination moisture and hydrogen getter

    DOEpatents

    Not Available

    1982-04-29

    A combination moisture and hydrogen getter comprises (a) a moisture getter comprising a readily oxidizable metal; and (b) a hydrogen getter comprising (i) a solid acetylenic compound and (ii) a hydrogenation catalyst. A method of scavenging moisture from a closed container uses the combination moisture and hydrogen getter to irreversibly chemically reduce the moisture and chemically bind the reusltant hydrogen.

  12. Combination moisture and hydrogen getter

    DOEpatents

    Harrah, Larry A.; Mead, Keith E.; Smith, Henry M.

    1983-01-01

    A combination moisture and hydrogen getter comprises (a) a moisture getter comprising a readily oxidizable metal; and (b) a hydrogen getter comprising (i) a solid acetylenic compound and (ii) a hydrogenation catalyst. A method of scavenging moisture from a closed container uses the combination moisture and hydrogen getter to irreversibly chemically reduce the moisture and chemically bind the resultant hydrogen.

  13. Combined deficiency of factor V and factor VIII is due to mutations in either LMAN1 or MCFD2

    PubMed Central

    Zhang, Bin; McGee, Beth; Yamaoka, Jennifer S.; Guglielmone, Hugo; Downes, Katharine A.; Minoldo, Salvador; Jarchum, Gustavo; Peyvandi, Flora; de Bosch, Norma B.; Ruiz-Saez, Arlette; Chatelain, Bernard; Olpinski, Marian; Bockenstedt, Paula; Sperl, Wolfgang; Kaufman, Randal J.; Nichols, William C.; Tuddenham, Edward G. D.; Ginsburg, David

    2006-01-01

    Mutations in LMAN1 (ERGIC-53) or MCFD2 cause combined deficiency of factor V and factor VIII (F5F8D). LMAN1 and MCFD2 form a protein complex that functions as a cargo receptor ferrying FV and FVIII from the endoplasmic reticulum to the Golgi. In this study, we analyzed 10 previously reported and 10 new F5F8D families. Mutations in the LMAN1 or MCFD2 genes accounted for 15 of these families, including 3 alleles resulting in no LMAN1 mRNA accumulation. Combined with our previous reports, we have identified LMAN1 or MCFD2 mutations as the causes of F5F8D in 71 of 76 families. Among the 5 families in which no mutations were identified, 3 were due to misdiagnosis, with the remaining 2 likely carrying LMAN1 or MCFD2 mutations that were missed by direct sequencing. Our results suggest that mutations in LMAN1 and MCFD2 may account for all cases of F5F8D. Immunoprecipitation and Western blot analysis detected a low level of LMAN1-MCFD2 complex in lymphoblasts derived from patients with missense mutations in LMAN1 (C475R) or MCFD2 (I136T), suggesting that complete loss of the complex may not be required for clinically significant reduction in FV and FVIII. PMID:16304051

  14. Combination pharmacotherapy for adult ADHD.

    PubMed

    Adler, Lenard A; Reingold, Lisa S; Morrill, Melinda S; Wilens, Timothy E

    2006-10-01

    Attention-deficit/hyperactivity disorder (ADHD) is one of the most prevalent neuropsychiatric disorders of adulthood. Although clinical guidelines recommend monotherapy with stimulants or atomoxetine, combination pharmacotherapy is a common practice among clinicians. There are four main situations in which combination medications may be necessary: partial response, dose-limiting side effects, associated disorders, and comorbid diagnoses. We present data from two chart reviews that support existing research on combination pharmacotherapy. Adjunct treatment of d-methylphenidate to stimulant medications extended the duration of therapeutic effect. Adjunct treatment of mirtazapine to stimulant medications reduced associated insomnia. These data support previous research that validates the use of combination pharmacotherapy for adults with ADHD. PMID:16968624

  15. New combinations in Odontostemma (Caryophyllaceae)

    PubMed Central

    Rabeler, Richard K.; Wagner, Warren L.

    2016-01-01

    Abstract Sixty-three new combinations in Odontostemma (Alsineae, Caryophyllaceae) are made to accommodate placement of all currently recognized taxa of Arenaria subg. Odontostemma within the genus Odontostemma. PMID:27489480

  16. Autonomous grain combine control system

    SciTech Connect

    Hoskinson, Reed L.; Kenney, Kevin L.; Lucas, James R.; Prickel, Marvin A.

    2013-06-25

    A system for controlling a grain combine having a rotor/cylinder, a sieve, a fan, a concave, a feeder, a header, an engine, and a control system. The feeder of the grain combine is engaged and the header is lowered. A separator loss target, engine load target, and a sieve loss target are selected. Grain is harvested with the lowered header passing the grain through the engaged feeder. Separator loss, sieve loss, engine load and ground speed of the grain combine are continuously monitored during the harvesting. If the monitored separator loss exceeds the selected separator loss target, the speed of the rotor/cylinder, the concave setting, the engine load target, or a combination thereof is adjusted. If the monitored sieve loss exceeds the selected sieve loss target, the speed of the fan, the size of the sieve openings, or the engine load target is adjusted.

  17. Atypical combinations and scientific impact.

    PubMed

    Uzzi, Brian; Mukherjee, Satyam; Stringer, Michael; Jones, Ben

    2013-10-25

    Novelty is an essential feature of creative ideas, yet the building blocks of new ideas are often embodied in existing knowledge. From this perspective, balancing atypical knowledge with conventional knowledge may be critical to the link between innovativeness and impact. Our analysis of 17.9 million papers spanning all scientific fields suggests that science follows a nearly universal pattern: The highest-impact science is primarily grounded in exceptionally conventional combinations of prior work yet simultaneously features an intrusion of unusual combinations. Papers of this type were twice as likely to be highly cited works. Novel combinations of prior work are rare, yet teams are 37.7% more likely than solo authors to insert novel combinations into familiar knowledge domains. PMID:24159044

  18. Diagnosis of severe combined immunodeficiency

    PubMed Central

    Gennery, A; Cant, A

    2001-01-01

    Early diagnosis of severe combined immunodeficiency (SCID) is important to enable prompt referral to a supraregional centre for bone marrow transplantation before the occurrence of end organ damage secondary to infective complications. This review outlines clinical, microbiological, and immunopathological clues that aid the diagnosis of SCID and emphasises the multidisciplinary approach needed to diagnose and treat these infants. Key Words: severe combined immunodeficiency • bone marrow transplantation • adenosine deaminase deficiency PMID:11253129

  19. Nonlinear combining of laser beams.

    PubMed

    Lushnikov, Pavel M; Vladimirova, Natalia

    2014-06-15

    We propose to combine multiple laser beams into a single diffraction-limited beam by beam self-focusing (collapse) in a Kerr medium. Beams with total power above critical are first combined in the near field and then propagated in the optical fiber/waveguide with Kerr nonlinearity. Random fluctuations during propagation eventually trigger a strong self-focusing event and produce a diffraction-limited beam carrying the critical power. PMID:24978503

  20. New combinations in Neotropical Thelypteridaceae

    PubMed Central

    Salino, Alexandre; Almeida, Thaís E.; Smith, Alan R.

    2015-01-01

    Abstract 288 new combinations of Neotropical Thelypteridaceae taxa are proposed in order to recognize monophyletic genera, based on the results of the most recent molecular phylogeny of the family, as well as the morphological uniformity of characters for each genus. The new nomenclatural combinations correspond to 186 Amauropelta taxa, 77 species of Goniopteris, and 25 Steiropteris taxa. A key to all native Neotropical genera of the family is also presented. PMID:26752025

  1. [Combination therapy for invasive aspergillosis].

    PubMed

    Ruiz-Camps, Isabel

    2011-03-01

    The frequency of invasive fungal infections, and specifically invasive aspergillosis, has increased in the last few decades. Despite the development of new antifungal agents, these infections are associated with high mortality, ranging from 40% to 80%, depending on the patient and the localization of the infection. To reduce these figures, several therapeutic strategies have been proposed, including combination therapy. Most of the available data on the efficacy of these combinations are from experimental models, in vitro data and retrospective observational studies or studies with a small number of patients that have included both patients in first-line treatment and those receiving rescue therapy; in addition there are many patients with possible forms of aspergillosis and few with demonstrated or probable forms. To date, there is no evidence that combination therapy has significantly higher efficacy than monotherapy; however, combination therapy could be indicated in severe forms of aspergillosis, or forms with central nervous involvement or extensive pulmonary involvement with respiratory insufficiency, etc. Among the combinations, the association of an echinocandin--the group that includes micafungin--with voriconazole or liposomal amphotericin B seems to show synergy. These combinations are those most extensively studied in clinical trials and therefore, although the grade of evidence is low, are recommended by the various scientific societies. PMID:21420576

  2. New antiretrovirals and new combinations.

    PubMed

    Havlir, D V; Lange, J M

    1998-01-01

    The appearance in the clinic of two to three new antiretroviral agents yearly since 1995 has permitted unprecedented advances in HIV treatment. This remarkable pace of drug development is a testimony to an extraordinary international effort involving scientists, clinicians, governments, community activists and industry dedicated to the rapid and safe development of novel therapies. New drugs present the opportunity to improve HIV therapy. They also create an enormous challenge to the clinician, who must constantly assimilate data on new drugs and incorporate this information into practical management strategies. Combination therapy has proven the most effective approach to treat HIV disease. The profound and sustained viral suppression achievable with combinations such as indinavir (IDV), lamivudine (3TC) and zidovudine (ZDV) have resulted in a dramatic shift in HIV treatment paradigms over the last year. The full potential of combination therapy with available drugs has yet to be realized as only a limited number of the possible combinations incorporating new drugs have been fully tested. Even drugs available for many years may have untapped potential. Didanosine (ddI) and stavudine (d4T), once thought to be contraindicated in combination because of their overlapping peripheral neuropathy toxicity, have proven well tolerated and effective. Combination therapy can increase antiviral suppression, prevent drug resistance, optimize drug exposure and simplify dosing, but it can also result in pharmacologic antagonism, subtherapeutic drug concentrations and unexpected toxicities. Clinical studies have confirmed in vitro studies showing pharmacologic antagonism for the combination of ZDV and d4T. Combining protease inhibitors with each other or with non-nucleoside reverse transcriptase inhibitors is complicated by effects both classes of drugs have on drug metabolism and clearance. These observations underline the importance of carefully conducted clinical studies to

  3. Understanding Resistance to Combination Chemotherapy

    PubMed Central

    Pritchard, Justin R.; Lauffenburger, Douglas A.; Hemann, Michael T.

    2014-01-01

    Summary The current clinical application of combination chemotherapy is guided by a historically successful set of practices that were developed by basic and clinical researchers 50-60 years ago. Thus, in order to understand how emerging approaches to drug development might aid the creation of new therapeutic combinations, it is critical to understand the defining principles underlying classic combination therapy and the original experimental rationales behind them. One such principle is that the use of combination therapies with independent mechanisms of action can minimize the evolution of drug resistance. Another is that in order to kill sufficient cancer cells to cure a patient, multiple drugs must be delivered at their maximum tolerated dose – a condition that allows for enhanced cancer cell killing with manageable toxicity. In light of these models, we aim to explore recent genomic evidence underlying the mechanisms of resistance to the combination regimens constructed on these principles. Interestingly, we find that emerging genomic evidence contradicts some of the rationales of early practitioners in developing commonly used drug regimens. However, we also find that the addition of recent targeted therapies has yet to change the current principles underlying the construction of anti-cancer combinatorial regimens, nor have they made substantial inroads into the treatment of most cancers. We suggest that emerging systems/network biology approaches have an immense opportunity to impact the rational development of successful drug regimens. Specifically, by examining drug combinations in multivariate ways, next generation combination therapies can be constructed with a clear understanding of how mechanisms of resistance to multi-drug regimens differ from single agent resistance. PMID:23164555

  4. Combination vaccines against diarrheal diseases

    PubMed Central

    Venkatesan, Malabi M; Van de Verg, Lillian L

    2015-01-01

    Abstract Diarrheal diseases remain a leading cause of global childhood mortality and morbidity. Several recent epidemiological studies highlight the rate of diarrheal diseases in different parts of the world and draw attention to the impact on childhood growth and survival. Despite the well-documented global burden of diarrheal diseases, currently there are no combination diarrheal vaccines, only licensed vaccines for rotavirus and cholera, and Salmonella typhi-based vaccines for typhoid fever. The recognition of the impact of diarrheal episodes on infant growth, as seen in resource-poor countries, has spurred action from governmental and non-governmental agencies to accelerate research toward affordable and effective vaccines against diarrheal diseases. Both travelers and children in endemic countries will benefit from a combination diarrheal vaccine, but it can be argued that the greater proportion of any positive impact will be on the public health status of the latter. The history of combination pediatric vaccines indicate that monovalent or single disease vaccines are typically licensed first prior to formulation in a combination vaccine, and that the combinations themselves undergo periodic revision in response to need for improvement in safety or potential for wider coverage of important pediatric pathogens. Nevertheless combination pediatric vaccines have proven to be an effective tool in limiting or eradicating communicable childhood diseases worldwide. The landscape of diarrheal vaccine candidates indicates that there now several in active development that offer options for potential testing of combinations to combat those bacterial and viral pathogens responsible for the heaviest disease burden—rotavirus, ETEC, Shigella, Campylobacter, V. cholera and Salmonella. PMID:25891647

  5. COMBINE Archive Specification Version 1.

    PubMed

    Bergmann, Frank T; Rodriguez, Nicolas; Le Novère, Nicolas

    2015-01-01

    Several standard formats have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. The Open Modeling EXchange format (OMEX) supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, an optional metadata file, and the files describing the model. The manifest is an XML file listing all files included in the archive and their type. The metadata file provides additional information about the archive and its content. Although any format can be used, we recommend an XML serialization of the Resource Description Framework. Together with the other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. PMID:26528559

  6. Highly scalable coherent fiber combining

    NASA Astrophysics Data System (ADS)

    Antier, M.; Bourderionnet, J.; Larat, C.; Lallier, E.; Brignon, A.

    2015-10-01

    An architecture for active coherent fiber laser beam combining using an interferometric measurement is demonstrated. This technique allows measuring the exact phase errors of each fiber beam in a single shot. Therefore, this method is a promising candidate toward very large number of combined fibers. Our experimental system, composed of 16 independent fiber channels, is used to evaluate the achieved phase locking stability in terms of phase shift error and bandwidth. We show that only 8 pixels per fiber on the camera is required for a stable close loop operation with a residual phase error of λ/20 rms, which demonstrates the scalability of this concept. Furthermore we propose a beam shaping technique to increase the combining efficiency.

  7. Combined magnetic and gravity analysis

    NASA Technical Reports Server (NTRS)

    Hinze, W. J.; Braile, L. W.; Chandler, V. W.; Mazella, F. E.

    1975-01-01

    Efforts are made to identify methods of decreasing magnetic interpretation ambiguity by combined gravity and magnetic analysis, to evaluate these techniques in a preliminary manner, to consider the geologic and geophysical implications of correlation, and to recommend a course of action to evaluate methods of correlating gravity and magnetic anomalies. The major thrust of the study was a search and review of the literature. The literature of geophysics, geology, geography, and statistics was searched for articles dealing with spatial correlation of independent variables. An annotated bibliography referencing the Germane articles and books is presented. The methods of combined gravity and magnetic analysis techniques are identified and reviewed. A more comprehensive evaluation of two types of techniques is presented. Internal correspondence of anomaly amplitudes is examined and a combined analysis is done utilizing Poisson's theorem. The geologic and geophysical implications of gravity and magnetic correlation based on both theoretical and empirical relationships are discussed.

  8. Printed sectoral horn power combiner

    NASA Astrophysics Data System (ADS)

    Boccia, Luigi; Emanuele, Antonio; Shamsafar, Alireza; Arnieri, Emilio; Amendola, Giandomenico

    2015-02-01

    In this work, it is presented a new configuration of planar power combiner/divider based on an H-plane sectoral horn antenna. This component is proposed to realise the basic building blocks of printed power-combining amplifiers. It will be shown how the sectoral horn elements can be implemented on substrate integrated waveguide and multilayer printed circuit board technologies, thus obtaining a high integration level. In the following, the design procedure will be described reporting an example of an 11-stage power divider/combiner in C-band. A prototype has been fabricated, and the measured results compared with the numerical model. Experimental results are in good agreement with theoretical expectations showing a single-stage efficiency of about 90% and a bandwidth of 40%.

  9. Combined MTOR and autophagy inhibition

    PubMed Central

    Rangwala, Reshma; Chang, Yunyoung C; Hu, Janice; Algazy, Kenneth M; Evans, Tracey L; Fecher, Leslie A; Schuchter, Lynn M; Torigian, Drew A; Panosian, Jeffrey T; Troxel, Andrea B; Tan, Kay-See; Heitjan, Daniel F; DeMichele, Angela M; Vaughn, David J; Redlinger, Maryann; Alavi, Abass; Kaiser, Jonathon; Pontiggia, Laura; Davis, Lisa E; O’Dwyer, Peter J; Amaravadi, Ravi K

    2014-01-01

    The combination of temsirolimus (TEM), an MTOR inhibitor, and hydroxychloroquine (HCQ), an autophagy inhibitor, augments cell death in preclinical models. This phase 1 dose-escalation study evaluated the maximum tolerated dose (MTD), safety, preliminary activity, pharmacokinetics, and pharmacodynamics of HCQ in combination with TEM in cancer patients. In the dose escalation portion, 27 patients with advanced solid malignancies were enrolled, followed by a cohort expansion at the top dose level in 12 patients with metastatic melanoma. The combination of HCQ and TEM was well tolerated, and grade 3 or 4 toxicity was limited to anorexia (7%), fatigue (7%), and nausea (7%). An MTD was not reached for HCQ, and the recommended phase II dose was HCQ 600 mg twice daily in combination with TEM 25 mg weekly. Other common grade 1 or 2 toxicities included fatigue, anorexia, nausea, stomatitis, rash, and weight loss. No responses were observed; however, 14/21 (67%) patients in the dose escalation and 14/19 (74%) patients with melanoma achieved stable disease. The median progression-free survival in 13 melanoma patients treated with HCQ 1200mg/d in combination with TEM was 3.5 mo. Novel 18-fluorodeoxyglucose positron emission tomography (FDG-PET) measurements predicted clinical outcome and provided further evidence that the addition of HCQ to TEM produced metabolic stress on tumors in patients that experienced clinical benefit. Pharmacodynamic evidence of autophagy inhibition was evident in serial PBMC and tumor biopsies only in patients treated with 1200 mg daily HCQ. This study indicates that TEM and HCQ is safe and tolerable, modulates autophagy in patients, and has significant antitumor activity. Further studies combining MTOR and autophagy inhibitors in cancer patients are warranted. PMID:24991838

  10. Combined microwave science and propulsion

    SciTech Connect

    Palaszewski, B.

    1989-01-01

    The combined use of high-power active science instruments and high-power electric propulsion is investigated with a view to new science opportunities and measurements on future planetary missions. An example of a comet rendezvous mission that could benefit from this combination is discussed. It was found that, with electric propulsion, the launch mass of the comet spacecraft could be reduced by 61-68 percent over the chemical propulsion baseline mission. This high-power spacecraft is also capable of delivering a significant high-power radar science payload to the comet. 28 references.

  11. Subwavelength diffractive color beam combiner.

    PubMed

    Petrov, Nikolai I; Nikitin, Vladislav G; Danilov, Viktor A; Popov, Vladimir V; Usievich, Boris A

    2014-09-01

    A high-efficiency subwavelength diffractive beam combiner operating in a visible spectral range is designed, fabricated, and demonstrated. Such a device combines red, green, and blue color beams into one output light beam. Diffraction efficiencies of different types of gratings are calculated for various materials, incidence angles, and polarizations of light. It is shown that the plasmon resonance via a grating coupling occurs at the determined conditions. Subwavelength gratings with a period of 400 nm are fabricated and tested using laser and laser diode sources. PMID:25321371

  12. Sentence Combining: A Literature Review.

    ERIC Educational Resources Information Center

    Phillips, Sylvia E.

    Sentence combining--a technique of putting strings of sentence kernels together in a variety of ways so that completed sentences possess greater syntactic maturity--is a method offering much promise in the teaching of writing and composition. The purpose of this document is to provide a literature review of this procedure. After defining the term…

  13. Property attribution in combined concepts.

    PubMed

    Spalding, Thomas L; Gagné, Christina L

    2015-05-01

    Recent research shows that the judged likelihood of properties of modified nouns (baby ducks have webbed feet) is reduced relative to judgments for unmodified nouns (ducks have webbed feet). This modification effect has been taken as evidence both for and against the idea that combined concepts automatically inherit properties from their constituent concepts. Experiments 1 and 2 replicate this effect and demonstrate a reversed modification effect with false properties. That is, false properties are judged more likely with modification (e.g., purple candles have teeth is judged more likely than candles have teeth). These experiments also show that properties that are neither generically true nor false are unaffected by modification. Experiments 3 and 4 manipulate participants' expectation of contrast by showing modified and unmodified nouns that either match or mismatch in terms of a property and show that the judged likelihood of properties depends on the expectations of contrast set up by the manipulation. These results show that the modification effect is primarily driven by participants' understanding of the relation of subcategories to categories, rather than by the features of the concepts being combined, suggesting that the process of property attribution in combined concepts is strongly affected by pragmatic factors and is less strongly dependent on conceptual content than most theories of conceptual combination would suggest. PMID:25419816

  14. H gas turbine combined cycle

    SciTech Connect

    Corman, J.

    1995-10-01

    A major step has been taken in the development of the Next Power Generation System - {open_quotes}H{close_quotes} Technology Combined Cycle. This new gas turbine combined-cycle system increases thermal performance to the 60% level by increasing gas turbine operating temperature to 1430 C (2600 F) at a pressure ratio of 23 to 1. Although this represents a significant increase in operating temperature for the gas turbine, the potential for single digit NOx levels (based upon 15% O{sub 2}, in the exhaust) has been retained. The combined effect of performance increase and environmental control is achieved by an innovative closed loop steam cooling system which tightly integrates the gas turbine and steam turbine cycles. The {open_quotes}H{close_quotes} Gas Turbine Combined Cycle System meets the goals and objectives of the DOE Advanced Turbine System Program. The development and demonstration of this new system is being carried out as part of the Industrial/Government cooperative agreement under the ATS Program. This program will achieve first commercial operation of this new system before the end of the century.

  15. Property Attribution in Combined Concepts

    ERIC Educational Resources Information Center

    Spalding, Thomas L.; Gagné, Christina L.

    2015-01-01

    Recent research shows that the judged likelihood of properties of modified nouns ("baby ducks have webbed feet") is reduced relative to judgments for unmodified nouns ("ducks have webbed feet"). This modification effect has been taken as evidence both for and against the idea that combined concepts automatically inherit…

  16. Combination Effects of Antimicrobial Peptides

    PubMed Central

    Yu, Guozhi; Baeder, Desiree Y.; Regoes, Roland R.

    2016-01-01

    Antimicrobial peptides (AMPs) are ancient and conserved across the tree of life. Their efficacy over evolutionary time has been largely attributed to their mechanisms of killing. Yet, the understanding of their pharmacodynamics both in vivo and in vitro is very limited. This is, however, crucial for applications of AMPs as drugs and also informs the understanding of the action of AMPs in natural immune systems. Here, we selected six different AMPs from different organisms to test their individual and combined effects in vitro. We analyzed their pharmacodynamics based on the Hill function and evaluated the interaction of combinations of two and three AMPs. Interactions of AMPs in our study were mostly synergistic, and three-AMP combinations displayed stronger synergism than two-AMP combinations. This suggests synergism to be a common phenomenon in AMP interaction. Additionally, AMPs displayed a sharp increase in killing within a narrow dose range, contrasting with those of antibiotics. We suggest that our results could lead a way toward better evaluation of AMP application in practice and shed some light on the evolutionary consequences of antimicrobial peptide interactions within the immune system of organisms. PMID:26729502

  17. Assessing "Combining Forms" in Science.

    ERIC Educational Resources Information Center

    Floriani, Bernard P.; Cairns, Jack C.

    1982-01-01

    Since there appears to be a direct relationship between reading comprehension and vocabulary, an inventory is offered which assesses students' knowledge of the meaning of "combining forms" (automobile, aero-dynamics, etc.) and not words themselves. The inventory can serve as a model to develop additional inventories for Latin/Greek roots.…

  18. Sentence Combining: A Rhetorical Perspective.

    ERIC Educational Resources Information Center

    Daiker, Donald A., Ed.; And Others

    The 23 original essays on sentence combining in this volume range in focus from classroom methodology and effectiveness, through theoretical issues and syntactic constructions, to current issues in the field. The essays and their authors are as follows: (1) "The Role of the Elaborated Dominant Nominal in the Measurement of Conceptual and Syntactic…

  19. Combining Clozapine and Talk Therapies.

    ERIC Educational Resources Information Center

    Mulroy, Kevin

    Clozapine is an antipsychotic medication used in the treatment of schizophrenia. This paper reviews articles concerning clozapine therapy. It considers its benefits and dangers in various situations, and how it can be successfully combined with talk therapies. Studies are reviewed concerning patients in outpatient clinics, partial hospitalization…

  20. Isolation of Human Genomic DNA Sequences with Expanded Nucleobase Selectivity.

    PubMed

    Rathi, Preeti; Maurer, Sara; Kubik, Grzegorz; Summerer, Daniel

    2016-08-10

    We report the direct isolation of user-defined DNA sequences from the human genome with programmable selectivity for both canonical and epigenetic nucleobases. This is enabled by the use of engineered transcription-activator-like effectors (TALEs) as DNA major groove-binding probes in affinity enrichment. The approach provides the direct quantification of 5-methylcytosine (5mC) levels at single genomic nucleotide positions in a strand-specific manner. We demonstrate the simple, multiplexed typing of a variety of epigenetic cancer biomarker 5mC with custom TALE mixes. Compared to antibodies as the most widely used affinity probes for 5mC analysis, i.e., employed in the methylated DNA immunoprecipitation (MeDIP) protocol, TALEs provide superior sensitivity, resolution and technical ease. We engineer a range of size-reduced TALE repeats and establish full selectivity profiles for their binding to all five human cytosine nucleobases. These provide insights into their nucleobase recognition mechanisms and reveal the ability of TALEs to isolate genomic target sequences with selectivity for single 5-hydroxymethylcytosine and, in combination with sodium borohydride reduction, single 5-formylcytosine nucleobases. PMID:27429302

  1. Methylome analysis using MeDIP-seq with low DNA concentrations.

    PubMed

    Taiwo, Oluwatosin; Wilson, Gareth A; Morris, Tiffany; Seisenberger, Stefanie; Reik, Wolf; Pearce, Daniel; Beck, Stephan; Butcher, Lee M

    2012-04-01

    DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a technique that balances accuracy, genome coverage, resolution and cost, yet is low in DNA input in order to minimize the drain on precious samples. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) fulfils these criteria, combining MeDIP with massively parallel DNA sequencing. Here we report an improved protocol using 100-fold less genomic DNA than that commonly used. We show comparable results for specificity (>97%) and enrichment (>100-fold) over a wide range of DNA concentrations (5,000-50 ng) and demonstrate the utility of the protocol for the generation of methylomes from rare bone marrow cells using 160-300 ng of starting DNA. The protocol described here, i.e., DNA extraction to generation of MeDIP-seq library, can be completed within 3-5 d. PMID:22402632

  2. Whole genome DNA methylation analysis based on high throughput sequencing technology.

    PubMed

    Li, Ning; Ye, Mingzhi; Li, Yingrui; Yan, Zhixiang; Butcher, Lee M; Sun, Jihua; Han, Xu; Chen, Quan; Zhang, Xiuqing; Wang, Jun

    2010-11-01

    There are numerous approaches to decipher a whole genome DNA methylation profile ("methylome"), each varying in cost, throughput and resolution. The gold standard of these methods, whole genome bisulfite-sequencing (BS-seq), involves treatment of DNA with sodium bisulfite combined with subsequent high throughput sequencing. Using BS-seq, we generated a single-base-resolution methylome in human peripheral blood mononuclear cells (in press). This BS-seq map was then used as the reference methylome to compare two alternative sequencing-based methylome assays (performed on the same donor of PBMCs): methylated DNA immunoprecipitation (MeDIP-seq) and methyl-binding protein (MBD-seq). In our analysis, we found that MeDIP-seq and MBD-seq are complementary strategies, with MeDIP-seq more sensitive to highly methylated, high-CpG densities and MDB-seq more sensitive to highly methylated, moderate-CpG densities. Taking into account the size of a mammalian genome and the current expense of sequencing, we feel 3gigabases (Gbp) 45bp paired-end MeDIP-seq or MBD-seq uniquely mapped reads is the minimum requirement and cost-effective strategy for methylome pattern analysis. PMID:20430099

  3. Gestational stress induces depressive-like and anxiety-like phenotypes through epigenetic regulation of BDNF expression in offspring hippocampus.

    PubMed

    Zheng, Yu; Fan, Weidong; Zhang, Xianquan; Dong, Erbo

    2016-01-01

    Exposure to stressful life events during pregnancy exerts profound effects on neurodevelopment and increases the risk for several neurodevelopmental disorders including major depression. The mechanisms underlying the consequences of gestational stress are complex and remain to be elucidated. This study investigated the effects of gestational stress on depressive-like behavior and epigenetic modifications in young adult offspring. Gestational stress was induced by a combination of restraint and 24-hour light disturbance to pregnant dams throughout gestation. Depressive-like and anxiety-like behaviors of young adult offspring were examined. The expression and promoter methylation of brain derived neurotrophic factor (BDNF) were measured using RT-qPCR, Western blot, methylated DNA immunoprecipitation (MeDIP) and chromatin immunoprecipitation (ChIP). In addition, the expressions of histone deacetylases (HDACs) and acetylated histone H3 lysine 14 (AcH3K14) were also analyzed. Our results show that offspring from gestational stress dams exhibited depressive-like and anxiety-like behaviors. Biochemically, stress-offspring showed decreased expression of BDNF, increased expression of DNMT1, HDAC1, and HDAC2, and decreased expression of AcH3K14 in the hippocampus as compared to non-stress offspring. Data from MeDIP and ChIP assays revealed an increased methylation as well as decreased binding of AcH3K14 on specific BDNF promoters. Pearson analyses indicated that epigenetic changes induced by gestational stress were correlated with depressive-like and anxiety-like behaviors. These data suggest that gestational stress may be a suitable model for understanding the behavioral and molecular epigenetic changes observed in patients with depression. PMID:26890656

  4. Towards an operational IDS combination

    NASA Astrophysics Data System (ADS)

    Valette, J.; Soudarin, L.; Willis, P.; Govind, R.; Stepanek, P.; Lemoine, F.; Altamimi, Z.; Le Bail, K.

    2007-12-01

    The International DORIS Service is in operation since 2003. Over the last four years, five instruments on the SPOT 2-4-5, ENVISAT and the JASON-1 satellites have provided DORIS Doppler data collected from a global network of about 50 stations. The number of Analysis Centers (AC) who have processed the data and have high level experience has progressively risen. Among them, two ACs : IGN/JPL using GYPSY/OASIS software and LEGOS/CLS using GINS/DYNAMO software now provide solutions of station coordinates and EOPs on a routine basis to the IGN and NASA CDDIS data centers. INASAN also processes DORIS data using GYPSY/OASIS software and submitted SINEX files to the ITRF2005 solution. The two newest DORIS analysis centers, include Geoscience Australia (GA) using the NASA GEODYN software and the Geodetic Observatory Pecny (GOP) using the BERNESE software. The GOP has adapted software not originally designed to process DORIS data. The performance reached by the new analysis centers in orbit and station positions determination is very encouraging. The availability of geodetic solutions from different algorithms and software packages allows us to efficiently contribute to cross-comparison of the solutions and to the improvement of the DORIS technique. The operational combinations of SINEX solutions contributed by the DORIS analysis centers will have to perform at least two functions. The first one is an internal validation of each individual AC time series. The second is a combination of all the AC weekly solutions in order to generate IDS combined products for station coordinates and EOPs. The paper presents the status of each AC processing (strategy, results, organization and future plan) and the combinations of solutions for the period of several years (2002-2006 as an objective). The combinations are realized with the IGN/LAREG CATREF software. Essential to the analysts, the station network event file (discontinuities, poor data span) will be updated and listed. The

  5. Rifamycins, Alone and in Combination.

    PubMed

    Rothstein, David M

    2016-01-01

    Rifamycins inhibit RNA polymerase of most bacterial genera. Rifampicin remains part of combination therapy for treating tuberculosis (TB), and for treating Gram-positive prosthetic joint and valve infections, in which biofilms are prominent. Rifabutin has use for AIDS patients in treating mycobacterial infections TB and Mycobacterium avium complex (MAC), having fewer drug-drug interactions that interfere with AIDS medications. Rifabutin is occasionally used in combination to eradicate Helicobacter pylori (peptic ulcer disease). Rifapentine has yet to fulfill its potential in reducing time of treatment for TB. Rifaximin is a monotherapeutic agent to treat gastrointestinal (GI) disorders, such as hepatic encephalopathy, irritable bowel syndrome, and travelers' diarrhea. Rifaximin is confined to the GI tract because it is not systemically absorbed on oral dosing, achieving high local concentrations, and showing anti-inflammatory properties in addition to its antibacterial activity. Resistance issues are unavoidable with all the rifamycins when the bioburden is high, because of mutations that modify RNA polymerase. PMID:27270559

  6. [Familial combined hyperlipidemia: consensus document].

    PubMed

    Mata, Pedro; Alonso, Rodrigo; Ruíz-Garcia, Antonio; Díaz-Díaz, Jose L; González, Noemí; Gijón-Conde, Teresa; Martínez-Faedo, Ceferino; Morón, Ignacio; Arranz, Ezequiel; Aguado, Rocío; Argueso, Rosa; Perez de Isla, Leopoldo

    2014-10-01

    Familial combined hyperlipidemia (FCH) is a frequent disorder associated with premature coronary artery disease. It is transmitted in an autosomal dominant manner, although there is not a unique gene involved. The diagnosis is performed using clinical criteria, and variability in lipid phenotype and family history of hyperlipidemia are necessaries. Frequently, the disorder is associated with type2 diabetes mellitus, arterial hypertension and central obesity. Patients with FCH are considered as high cardiovascular risk and the lipid target is an LDL-cholesterol <100mg/dL, and <70mg/dL if cardiovascular disease or type 2 diabetes are present. Patients with FCH require lipid lowering treatment using potent statins and sometimes, combined lipid-lowering treatment. Identification and management of other cardiovascular risk factors as type 2 diabetes and hypertension are fundamental to reduce cardiovascular disease burden. This document gives recommendations for the diagnosis and global treatment of patients with FCH directed to specialists and general practitioners. PMID:25131181

  7. [Familial combined hyperlipidemia: consensus document].

    PubMed

    Mata, Pedro; Alonso, Rodrigo; Ruíz-Garcia, Antonio; Díaz-Díaz, Jose L; González, Noemí; Gijón-Conde, Teresa; Martínez-Faedo, Ceferino; Morón, Ignacio; Arranz, Ezequiel; Aguado, Rocío; Argueso, Rosa; Perez de Isla, Leopoldo

    2014-10-01

    Familial combined hyperlipidemia (FCH) is a frequent disorder associated with premature coronary artery disease. It is transmitted in an autosomal dominant manner, although there is not a unique gene involved. The diagnosis is performed using clinical criteria, and variability in lipid phenotype and family history of hyperlipidemia are necessaries. Frequently, the disorder is associated with type2 diabetes mellitus, arterial hypertension and central obesity. Patients with FCH are considered as high cardiovascular risk and the lipid target is an LDL-cholesterol <100mg/dL, and <70mg/dL if cardiovascular disease or type 2 diabetes are present. Patients with FCH require lipid lowering treatment using potent statins and sometimes, combined lipid-lowering treatment. Identification and management of other cardiovascular risk factors as type 2 diabetes and hypertension are fundamental to reduce cardiovascular disease burden. This document gives recommendations for the diagnosis and global treatment of patients with FCH directed to specialists and general practitioners. PMID:25034722

  8. [Management of combined thoracoabdominal wounds].

    PubMed

    Solov'ev, G M; Bagdasarov, V V

    1998-01-01

    Last years in the country gace rise to the problem of treatment of fire-arm's wounds in civil population. The results of treatment of victims with firearm thoracoabdominal wounds have evidenced unprepareness of surgeons for rendering specialized aid in conditions of "military-urban" surgery. The study performed by the authors has shown that there are substantial and principal differences between many postulates of war-field surgery and "military-urban" surgery. It consists in early hospitalization of victims with combined thoraco-abdominal injuries, prevalence of bullet wounds over fire-mine explosive injuries which have an effect on the extent of surgical intervention, results of treatment and development of complications. The proposed treatment modalities in victims with combined penetrated thoracoabdominal injuries in great measure may contribute to optimization of surgical aid in conditions of "military-urban" surgery. PMID:9791984

  9. Airbreathing combined cycle engine systems

    NASA Technical Reports Server (NTRS)

    Rohde, John

    1992-01-01

    The Air Force and NASA share a common interest in developing advanced propulsion systems for commercial and military aerospace vehicles which require efficient acceleration and cruise operation in the Mach 4 to 6 flight regime. The principle engine of interest is the turboramjet; however, other combined cycles such as the turboscramjet, air turborocket, supercharged ejector ramjet, ejector ramjet, and air liquefaction based propulsion are also of interest. Over the past months careful planning and program implementation have resulted in a number of development efforts that will lead to a broad technology base for those combined cycle propulsion systems. Individual development programs are underway in thermal management, controls materials, endothermic hydrocarbon fuels, air intake systems, nozzle exhaust systems, gas turbines and ramjet ramburners.

  10. Combined docking and grasping device

    NASA Technical Reports Server (NTRS)

    Burch, J. L.; Johnston, J. D. (Inventor)

    1977-01-01

    A combined docking and grasping device for use with a manipulator arm on a docking vehicle and the like for mechanically connecting a docking vehicle with an orbital payload having a receptacle for receiving the device is described. The device includes a pair of opposing jaw members having opposing serrated surfaces for grasping an object and a triangular cam portion on an outer surface for insertion and interlocking with an orbital payload.

  11. Combined buoyancy-thermocapillary convection

    NASA Technical Reports Server (NTRS)

    Homsy, G. M.

    1990-01-01

    Combined buoyancy-thermocapillary convection was studied in 2D and 3D. Fluid motion caused by thermally induced tension gradients on the free surface of a fluid is termed thermocapillary convection. It is well-known that in containerless processing of materials in space, thermocapillary convection is a dominant mechanism of fluid flow. Welding and crystal growth processes are terrestrial applications where thermocapillary convection has direct relevance.

  12. Combined-cycle power tower

    SciTech Connect

    Bohn, M S; Williams, T A; Price, H W

    1994-10-01

    This paper evaluates a new power tower concept that offers significant benefits for commercialization of power tower technology. The concept uses a molten nitrate salt centralreceiver plant to supply heat, in the form of combustion air preheat, to a conventional combined-cycle power plant. The evaluation focused on first commercial plants, examined three plant capacities (31, 100, and 300 MWe), and compared these plants with a solar-only 100-MWe plant and with gas-only combined-cycle plants in the same three capacities. Results of the analysis point to several benefits relative to the solar-only plant including low energy cost for first plants, low capital cost for first plants, reduced risk with respect to business uncertainties, and the potential for new markets. In addition, the concept appears to have minimal technology development requirements. Significantly, the results show that it is possible to build a first plant with this concept that can compete with existing gas-only combined-cycle plants.

  13. Imagining a Stata / Python Combination

    NASA Technical Reports Server (NTRS)

    Fiedler, James

    2012-01-01

    There are occasions when a task is difficult in Stata, but fairly easy in a more general programming language. Python is a popular language for a range of uses. It is easy to use, has many high ]quality packages, and programs can be written relatively quickly. Is there any advantage in combining Stata and Python within a single interface? Stata already offers support for user-written programs, which allow extensive control over calculations, but somewhat less control over graphics. Also, except for specifying output, the user has minimal programmatic control over the user interface. Python can be used in a way that allows more control over the interface and graphics, and in so doing provide a roundabout method for satisfying some user requests (e.g., transparency levels in graphics and the ability to clear the results window). My talk will explore these ideas, present a possible method for combining Stata and Python, and give examples to demonstrate how this combination might be useful.

  14. Combination chemoprevention with grape antioxidants.

    PubMed

    Singh, Chandra K; Siddiqui, Imtiaz A; El-Abd, Sabah; Mukhtar, Hasan; Ahmad, Nihal

    2016-06-01

    Antioxidant ingredients present in grape have been extensively investigated for their cancer chemopreventive effects. However, much of the work has been done on individual ingredients, especially focusing on resveratrol and quercetin. Phytochemically, whole grape represents a combination of numerous phytonutrients. Limited research has been done on the possible synergistic/additive/antagonistic interactions among the grape constituents. Among these phytochemical constituents of grapes, resveratrol, quercetin, kaempferol, catechin, epicatechin, and anthocyanins (cyanidin and malvidin) constitute more than 70% of the grape polyphenols. Therefore, these have been relatively well studied for their chemopreventive effects against a variety of cancers. While a wealth of information is available individually on cancer chemopreventive/anti-proliferative effects of resveratrol and quercetin, limited information is available regarding the other major constituents of grape. Studies have also suggested that multiple grape antioxidants, when used in combination, alone or with other agents/drugs show synergistic or additive anti-proliferative response. Based on strong rationale emanating from published studies, it seems probable that a combination of multiple grape ingredients alone or together with other agents could impart 'additive synergism' against cancer. PMID:26829056

  15. Combining Psychodynamic Psychotherapy and Pharmacotherapy.

    PubMed

    Gorman, Jack M

    2016-01-01

    Many patients with depression, anxiety disorders, and other psychiatric disorders are treated with combinations of psychodynamic psychotherapy and medication. Whether this is better than monotherapy is an empirical question that requires much more extensive research than is currently available. When medications were first introduced to treat psychiatric illnesses, some psychopharmacologists insisted that it heralded a new area of "biological psychiatry" that would ultimately render psychotherapy obsolete. Psychodynamic theorists and practitioners, on the other hand, argued that psychopharmacology offered only a superficial approach to treatment. Fortunately, these battles are now largely supplanted by the belief that whatever treatment offers the patient the best outcome should be employed, regardless of the therapist's theoretical outlook. This should motivate more extensive study of the value of combination treatment. So far, the few studies that have been done suggest that the combination of psychodynamic psychotherapy and medication may be superior for the treatment of mood and anxiety disorders, but most of these studies have small sample sizes and involve only short-term psychotherapy. An examination of the neuroscience of mood and anxiety disorders and of the mechanism of action of psychodynamic psychotherapy and of antidepressant medication suggests several routes by which the two treatment modalities could be synergistic: stimulation of hippocampal neurogenesis; epigenetic regulation of gene expression; dendritic remodeling; enhanced prefrontal cortical control of limbic system activity; and action at specific neurohormonal and neurotransmitter targets. The evidence for each of these mechanisms is reviewed with an eye toward potential experiments that might be relevant to them. PMID:27200462

  16. Combined acoustic and optical trapping

    PubMed Central

    Thalhammer, G.; Steiger, R.; Meinschad, M.; Hill, M.; Bernet, S.; Ritsch-Marte, M.

    2011-01-01

    Combining several methods for contact free micro-manipulation of small particles such as cells or micro-organisms provides the advantages of each method in a single setup. Optical tweezers, which employ focused laser beams, offer very precise and selective handling of single particles. On the other hand, acoustic trapping with wavelengths of about 1 mm allows the simultaneous trapping of many, comparatively large particles. With conventional approaches it is difficult to fully employ the strengths of each method due to the different experimental requirements. Here we present the combined optical and acoustic trapping of motile micro-organisms in a microfluidic environment, utilizing optical macro-tweezers, which offer a large field of view and working distance of several millimeters and therefore match the typical range of acoustic trapping. We characterize the acoustic trapping forces with the help of optically trapped particles and present several applications of the combined optical and acoustic trapping, such as manipulation of large (75 μm) particles and active particle sorting. PMID:22025990

  17. Evidence of normal functional levels of activated protein C inhibitor in combined Factor V/VIII deficiency disease.

    PubMed Central

    Canfield, W M; Kisiel, W

    1982-01-01

    Human activated protein C (APC) is a plasma serine protease that possesses amidolytic and anticoagulant activity. The rate at which the amidolytic and anticoagulant activity of APC was neutralized in normal plasma was essentially identical to that observed in plasma obtained from four individuals with combined Factor V/VIII deficiency disease. Incubation of radioiodinated APC with either normal human plasma or the combined Factor V/VIII-deficient plasmas resulted in the formation of a stable complex (Mr = 96,000) of the enzyme and a plasma protein as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Pretreatment of the radiolabeled APC with diisopropyl fluorophosphate prevented the formation of the enzyme-protein complex. On the basis of its ability to form a complex with radiolabeled APC, the APC-binding protein was purified to homogeneity from normal human plasma by ammonium sulfate fractionation, heparin-agarose chromatography, and QAE-Sephadex A-50 chromatography. The APC-binding protein (Mr = 54,000) is a glycoprotein, and possesses an amino-terminal sequence of Gly-Arg-Thr-Cys-Pro-Lys-Pro-Asp. The amino-terminal sequence of the APC-binding protein exhibited considerable homology with bovine colostrum inhibitor and pancreatic trypsin inhibitor, but no apparent sequence homology with the plasma serine protease inhibitors. Affinity-purified antibody against APC-binding protein immunoprecipitated a complex of radiolabeled APC and native APC-binding protein from normal human plasma. Complex formation was virtually eliminated in plasma immunodepleted of the APC-binding protein. Quantitative electroimmunoassay indicated essentially equal levels of APC-binding protein antigen in normal plasma compared with plasma from four patients with combined Factor V/VIII deficiency disease. Images PMID:6294139

  18. Insights into the polerovirus-plant interactome revealed by co-immunoprecipitation and mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The identification of host proteins that interact with virus proteins is a major challenge for the field of virology. Phloem-limited viruses pose extraordinary challenges for in vivo protein interaction experiments because these viruses are localized in very few and highly specialized host cells. ...

  19. Preparation of Gap Junctions in Membrane Microdomains for Immunoprecipitation and Mass Spectrometry Interactome Analysis.

    PubMed

    Fowler, Stephanie; Akins, Mark; Bennett, Steffany A L

    2016-01-01

    Protein interaction networks at gap junction plaques are increasingly implicated in a variety of intracellular signaling cascades. Identifying protein interactions of integral membrane proteins is a valuable tool for determining channel function. However, several technical challenges exist. Subcellular fractionation of the bait protein matrix is usually required to identify less abundant proteins in complex homogenates. Sufficient solvation of the lipid environment without perturbation of the protein interactome must also be achieved. The present chapter describes the flotation of light and heavy liver tissue membrane microdomains to facilitate the identification and analysis of endogenous gap junction proteins and includes technical notes for translation to other integral membrane proteins, tissues, or cell culture models. These procedures are valuable tools for the enrichment of gap junction membrane compartments and for the identification of gap junction signaling interactomes. PMID:27207290

  20. Assays to Measure PTEN Lipid Phosphatase Activity In Vitro from Purified Enzyme or Immunoprecipitates.

    PubMed

    Spinelli, Laura; Leslie, Nicholas R

    2016-01-01

    PTEN is a one of the most frequently mutated tumor suppressors in human cancers. It is essential for regulating diverse biological processes and through its lipid phosphatase activity regulates the PI 3-Kinase signaling pathway. Sensitive phosphatase assays are employed to study the catalytic activity of PTEN against phospholipid substrates. Here we describe protocols to assay PTEN lipid phosphatase activity using either purified enzyme (purified PTEN lipid phosphatase assay) or PTEN immunopurified from tissues or cultured cells (cellular IP PTEN lipid phosphatase assay) against vesicles containing radiolabeled PIP3 substrate. PMID:27514802

  1. Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data

    PubMed Central

    wa Maina, Ciira; Honkela, Antti; Matarese, Filomena; Grote, Korbinian; Stunnenberg, Hendrik G.; Reid, George; Lawrence, Neil D.; Rattray, Magnus

    2014-01-01

    Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2). The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ER) and FOXA1 binding in their proximal promoter regions. PMID:24830797

  2. NOVEL METHODS FOR TARGET PROTEIN IDENTIFICATION USING IMMUNOPRECIPITATION - LC/MS/MS

    EPA Science Inventory

    Proteomics provides a powerful approach to screen and analyze responses to environmental exposures which induce alterations in protein expression, phosphorylation. ubiquitinylation, oxidation. and modulation of general proteome function. Post-translational modifications (PTM) of ...

  3. Chemistry of combined residual chlorination

    SciTech Connect

    Leao, S.F.; Selleck, R.E.

    1982-01-01

    The decay of the combined chlorine residual was investigated in this work. Recent concerns about the formation of undesirable compounds such as chloroform with free residual chlorination have focused attention on the alternative use of combined residual chlorination. This work investigates the applicability of reactions proposed to describe the transformations and decay of the combined residual with time. Sodium hypochlorite was added to buffered solutions of ammonia with the chlorine residual being monitored over periods extending up to 10 days. The reaction was studied at four initial concentrations of hypochlorite of 100, 50, 25 and 10 mg/L as Cl/sub 2/ with molar application ratios of chlorine to ammonia, defined herein as M ratios, of 0.90, 0.50, 0.25 and 0.05 at each hypochlorite dose. Sixty-eight experiments were conducted at the pH of 6.6 and 7.2. The conclusions are: (1) in the absence of free chlorine, the concentration of NH/sub 3/ does not seem to affect the rate of disappearance of the residual other than through the formation of NHCl/sub 2/ by NH/sub 2/Cl hydrolysis; (2) the reaction between NHCl/sub 2/ and NH/sub 4//sup +/ to form NH/sub 2/Cl is either much slower than reported by Gray et. al. or the mechanism is different with a rate limiting step not involving NH/sub 3/ or NH/sub 4//sup +/; (3) a redox reaction in addition to the first-order decomposition of NHCl/sub 2/ appears necessary. Model simulation results indicated that a reaction of the type NH/sub 2/Cl + NHCl/sub 2/ ..-->.. P added to the first-order NHCl/sub 2/ decomposition can explain the results observed except at the higher chlorine doses.

  4. Combined autophagy and HDAC inhibition

    PubMed Central

    Mahalingam, Devalingam; Mita, Monica; Sarantopoulos, John; Wood, Leslie; Amaravadi, Ravi K; Davis, Lisa E; Mita, Alain C; Curiel, Tyler J; Espitia, Claudia M; Nawrocki, Steffan T; Giles, Francis J; Carew, Jennifer S

    2014-01-01

    We previously reported that inhibition of autophagy significantly augmented the anticancer activity of the histone deacetylase (HDAC) inhibitor vorinostat (VOR) through a cathepsin D-mediated mechanism. We thus conducted a first-in-human study to investigate the safety, preliminary efficacy, pharmacokinetics (PK), and pharmacodynamics (PD) of the combination of the autophagy inhibitor hydroxychloroquine (HCQ) and VOR in patients with advanced solid tumors. Of 27 patients treated in the study, 24 were considered fully evaluable for study assessments and toxicity. Patients were treated orally with escalating doses of HCQ daily (QD) (d 2 to 21 of a 21-d cycle) in combination with 400 mg VOR QD (d one to 21). Treatment-related adverse events (AE) included grade 1 to 2 nausea, diarrhea, fatigue, weight loss, anemia, and elevated creatinine. Grade 3 fatigue and/or myelosuppression were observed in a minority of patients. Fatigue and gastrointestinal AE were dose-limiting toxicities. Six-hundred milligrams HCQ and 400 mg VOR was established as the maximum tolerated dose and recommended phase II regimen. One patient with renal cell carcinoma had a confirmed durable partial response and 2 patients with colorectal cancer had prolonged stable disease. The addition of HCQ did not significantly impact the PK profile of VOR. Treatment-related increases in the expression of CDKN1A and CTSD were more pronounced in tumor biopsies than peripheral blood mononuclear cells. Based on the safety and preliminary efficacy of this combination, additional clinical studies are currently being planned to further investigate autophagy inhibition as a new approach to increase the efficacy of HDAC inhibitors. PMID:24991835

  5. Combining Speed Information Across Space

    NASA Technical Reports Server (NTRS)

    Verghese, Preeti; Stone, Leland S.

    1995-01-01

    We used speed discrimination tasks to measure the ability of observers to combine speed information from multiple stimuli distributed across space. We compared speed discrimination thresholds in a classical discrimination paradigm to those in an uncertainty/search paradigm. Thresholds were measured using a temporal two-interval forced-choice design. In the discrimination paradigm, the n gratings in each interval all moved at the same speed and observers were asked to choose the interval with the faster gratings. Discrimination thresholds for this paradigm decreased as the number of gratings increased. This decrease was not due to increasing the effective stimulus area as a control experiment that increased the area of a single grating did not show a similar improvement in thresholds. Adding independent speed noise to each of the n gratings caused thresholds to decrease at a rate similar to the original no-noise case, consistent with observers combining an independent sample of speed from each grating in both the added- and no-noise cases. In the search paradigm, observers were asked to choose the interval in which one of the n gratings moved faster. Thresholds in this case increased with the number of gratings, behavior traditionally attributed to an input bottleneck. However, results from the discrimination paradigm showed that the increase was not due to observers' inability to process these gratings. We have also shown that the opposite trends of the data in the two paradigms can be predicted by a decision theory model that combines independent samples of speed information across space. This demonstrates that models typically used in classical detection and discrimination paradigms are also applicable to search paradigms. As our model does not distinguish between samples in space and time, it predicts that discrimination performance should be the same regardless of whether the gratings are presented in two spatial intervals or two temporal intervals. Our last

  6. Gap and stripline combined monitor

    DOEpatents

    Yin, Y.

    1984-02-16

    A combined gap and stripline monitor device for measuring the intensity and position of a charged particle beam bunch in a beam pipe of a synchrotron radiation facility. The monitor has first and second beam pipe portions with an axial gap therebetween. An outer pipe cooperates with the first beam pipe portion to form a gap enclosure, while inner strips cooperate with the first beam pipe portion to form a stripline monitor, with the stripline length being the same as the gap enclosure length.

  7. Gap and stripline combined monitor

    DOEpatents

    Yin, Yan

    1986-01-01

    A combined gap and stripline monitor device (10) for measuring the intensity and position of a charged particle beam bunch in a beam pipe of a synchotron radiation facility. The monitor has first and second beam pipe portions (11a, 11b) with an axial gap (12) therebetween. An outer pipe (14) cooperates with the first beam pipe portion (11a) to form a gap enclosure, while inner strips (23a-d) cooperate with the first beam pipe portion (11a) to form a stripline monitor, with the stripline length being the same as the gap enclosure length.

  8. Combined Electrolysis Catalytic Exchange (CECE)

    SciTech Connect

    Ellis, R.E.; Mills, T.K.; Rogers, M.L.

    1980-09-30

    Starting from an effort to control airborne emissions, the Mound tritium containment program has evolved to include development of the Combined Electrolysis Catalytic Exchange (CECE) process. This process separates tritiated aqueous streams into detritiated water and an enriched hydrogen stream that is suitable for use by other tritium recovery processes. Experimentation has shown that the process performs as predicted by bench-scale measurements, and that available process components exhibit acceptable resistance to damage by radiation from tritium exposure. Planned future efforts are concentrated on finalizing automatic control of the process and on developing feed treatment methods for the protection of process components.

  9. Combining GRACE and GOCE for a new combined EIGEN model

    NASA Astrophysics Data System (ADS)

    Marty, J.; Bruinsma, S. L.; Balmino, G.; Biancale, R.; Foerste, C.; Flechtner, F.; Abrikosov, O.; Dahle, C.; Neumayer, H.; Koenig, R.; Raimondo, J.

    2010-12-01

    GOCE is equipped with a 3-axes gradiometer (approximately radial, along-track, normal to the orbit plane), which provides gravity gradients that are measured with high precision within the measurement bandwidth of approximately 200 to 10 seconds (0.005 to 0.1 Hz; this translates to a distance along the satellite track of about 80-1600 km), whereas outside this interval the noise increases rapidly (i.e., colored noise). Due to this instrumental behavior, the gravity gradient observation equations must be filtered in order to retain only the precise information that is contained in the measurement bandwidth, i.e. the medium and short wavelengths of the gravity field. The GRACE satellites are equipped with a very precise microwave ranging system, and the mission was designed to accurately measure the long wavelengths of the gravity field every 30 days. Hence, GRACE and GOCE are complementary in the spectral domain. When combining GRACE and GOCE data however, particular care must be taken not to degrade the lower degrees of the resulting solution due to a filter pass band that is too wide. The high accuracy of GRACE-only models such as ITG-GRACE2010S up to degree 120-140 (spatial resolution of 167-143 km) implies that the high-pass cut-off period of the optimum filter actually should not be 200 seconds, but much less. The GOCE GPS-SST data are used to geo-locate the gradients, and satellite-to-satellite tracking normal equations are generated equally and their impact on the combined solution is evaluated. The construction of an accurate satellite-only model to degree and order 200 is therefore only possible after a rigorous filter selection procedure, which entails computing as many complete gravity field solutions as there are filters to assess. The solutions are evaluated through comparison with EIGEN-51C and ITG-GRACE2010S, as well as orbit computation tests.

  10. [Combination therapy of hypopharyngeal cancer].

    PubMed

    Miyahara, H

    1987-06-01

    Between 1978 and 1983, ninety-three patients with cancer of the hypopharynx were treated. They were evaluated as to sex, age, primary site, TNM classification, stage, habits of smoking and drinking, past history of irradiation, treatment modality and end results. Eighty-seven percent of the patients visited us at as late a stage as advanced stage III or IV, and were treated mainly by combined therapy involving irradiation and pharyngolaryngoesophagectomy. The 3-year and 5-year survival rates were 38.6% and 33.3%, respectively. After December 1983, 14 new patients with advanced disease including three with coervical esophageal cancer were treated with neo-adjuvant combination chemotherapy which included cisplatin, peplomycin, methotrexate, and bleomycin over two courses of therapy. The response rate (CR + PR) was high, being 82% for the primary tumor and 78% for the metastatic node. Histopathological effects of neo-adjuvant chemotherapy were studied in the resected specimens. The evaluation was based on the Ohboshi-Shimosato classification. The histological effects did not agree with the clinical effects. Grade II b change was evaluated mostly in CR cases and grade II a change was seen in PR cases. It thus seems that neo-adjuvant chemotherapy prior to surgery and/or radiation including cisplatin and other agents is very useful as a multidisciplinary treatment for cancer of the hypopharynx. PMID:3592715

  11. VACUUM TRAP AND VALVE COMBINATION

    DOEpatents

    Milleron, N.; Levenson, L.

    1963-02-19

    This patent relates to a vacuum trap and valve combination suitable for use in large ultra-high vacuum systems. The vacuum trap is a chamber having an inlet and outlet opening which may be made to communicate with a chamber to be evacuated and a diffusion pump, respectively. A valve is designed to hermeticaliy seal with inlet opening and, when opened, block the line-of- sight'' between the inlet and outlet openings, while allowing a large flow path between the opened vaive and the side walls of the trap. The interior of the trap and the side of the valve facing the inlet opening are covered with an impurity absorbent, such as Zeolite or activated aluminum. Besides the advantage of combining two components of a vacuum system into one, the present invention removes the need for a baffle between the pump and the chamber to be evacuated. In one use of a specific embodiment of this invention, the transmission probability was 45 and the partial pressure of the pump fluid vapor in the vacuum chamber was at least 100 times lower than its vapor pressure. (AEC)

  12. Radiation tolerant combinational logic cell

    NASA Technical Reports Server (NTRS)

    Maki, Gary R. (Inventor); Gambles, Jody W. (Inventor); Whitaker, Sterling (Inventor)

    2009-01-01

    A system has a reduced sensitivity to Single Event Upset and/or Single Event Transient(s) compared to traditional logic devices. In a particular embodiment, the system includes an input, a logic block, a bias stage, a state machine, and an output. The logic block is coupled to the input. The logic block is for implementing a logic function, receiving a data set via the input, and generating a result f by applying the data set to the logic function. The bias stage is coupled to the logic block. The bias stage is for receiving the result from the logic block and presenting it to the state machine. The state machine is coupled to the bias stage. The state machine is for receiving, via the bias stage, the result generated by the logic block. The state machine is configured to retain a state value for the system. The state value is typically based on the result generated by the logic block. The output is coupled to the state machine. The output is for providing the value stored by the state machine. Some embodiments of the invention produce dual rail outputs Q and Q'. The logic block typically contains combinational logic and is similar, in size and transistor configuration, to a conventional CMOS combinational logic design. However, only a very small portion of the circuits of these embodiments, is sensitive to Single Event Upset and/or Single Event Transients.

  13. Phonological and Phonetic Asymmetries of Cw Combinations

    ERIC Educational Resources Information Center

    Suh, Yunju

    2009-01-01

    This thesis investigates the relationship between the phonological distribution of Cw combinations, and the acoustic/perceptual distinctiveness between syllables with plain C onsets and with Cw combination onsets. Distributional asymmetries of Cw combinations discussed in this thesis include the avoidance of Cw combinations in the labial consonant…

  14. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Standards for Grades of Apples Grades § 51.304 Combination grades. (a) Combinations of the above grades may... permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the higher grade in the combination....

  15. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Standards for Grades of Apples Grades § 51.304 Combination grades. (a) Combinations of the above grades may... permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the higher grade in the combination....

  16. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Standards for Grades of Apples Grades § 51.304 Combination grades. (a) Combinations of the above grades may... permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the higher grade in the combination....

  17. Combination drilling and skiving tool

    DOEpatents

    Stone, William J.

    1989-01-01

    A combination drilling and skiving tool including a longitudinally extending hollow skiving sleeve slidably and concentrically mounted on a right-handed twist drill. Dogs or pawls provided on the internal periphery of the skiving sleeve engage with the helical grooves of the drill. During a clockwise rotation of the tool, the drill moves downwardly and the sleeve translates upwardly, so that the drill performs a drilling operation on a workpiece. On the other hand, the drill moves upwardly and the sleeve translates downwardly, when the tool is rotated in a counter-clockwise direction, and the sleeve performs a skiving operation. The drilling and skiving operations are separate, independent and exclusive of each other.

  18. Combining Flavour and CP Symmetries

    NASA Astrophysics Data System (ADS)

    Feruglio, Ferruccio

    2013-07-01

    I shortly review the impact of the most recent neutrino oscillation data on our attempts to construct a realistic model for neutrino masses and mixing angles. Models based on anarchy and its variants remain an open possibility, reinforced by the latest experimental findings. Many models based on discrete symmetries no longer work in their simplest realizations. I illustrate several proposals that can rescue discrete symmetries. In particular I discuss the possibility of combining discrete flavour symmetries and CP, and I describe a recently proposed symmetry breaking pattern that allows to predict all mixing parameters, angles and phases, in terms of a single real unknown. I analyze several explicit examples of this construction, providing new realistic mixing patterns.

  19. Combined processing of lead concentrates

    NASA Astrophysics Data System (ADS)

    Kubasov, V. L.; Paretskii, V. M.; Sidorin, G. N.; Travkin, V. F.

    2013-06-01

    A combined scheme of processing of lead concentrates with the production of pure metallic lead and the important components containing in these concentrates is considered. This scheme includes sulfating roasting of the lead concentrates and two-stage leaching of the formed cinder with the formation of a sulfate solution and lead sulfate. When transformed into a carbonate form, lead sulfate is used for the production of pure metallic lead. Silver, indium, copper, cadmium, nickel, cobalt, and other important components are separately extracted from a solution. At the last stage, zinc is extracted by either extraction followed by electrolytic extraction of a metal or the return of the forming solution of sulfuric acid to cinder leaching.

  20. Combined Volumetric and Surface Registration

    PubMed Central

    Zöllei, Lilla; Fischl, Bruce

    2009-01-01

    In this paper, we propose a novel method for the registration of volumetric images of the brain that optimizes the alignment of both cortical and subcortical structures. In order to achieve this, relevant geometrical information is extracted from a surface-based morph and diffused into the volume using the Navier operator of elasticity, resulting in a volumetric warp that aligns cortical folding patterns. This warp field is then refined with an intensity driven optical flow procedure that registers noncortical regions, while preserving the cortical alignment. The result is a combined surface and volume morph (CVS) that accurately registers both cortical and subcortical regions, establishing a single coordinate system suitable for the entire brain. PMID:19273000

  1. [Combined orthodontic and restorative treatment].

    PubMed

    Kuijpers, M A R; Loomans, B

    2015-11-01

    In patients with agenesis or enamel anomalies in anterior teeth combined orthodontic and restorative treatment is often necessary to achieve an optimal aesthetic result. How both can best be achieved, but also how to maintain the result, requires communication between the dentist and the orthodontist. The orthodontic treatment plan needs to be established in cooperation with the dentist who will carry out the restorative treatment while the patient is at a young age. Since with these young patients, who are still growing craniofacially and whose teeth are still developing, possible future restorative and/or orthodontic treatment, as well as the means of orthodontic retention, need to be included in the treatment plan. In cleft palate patients, it is also important that methods of orthodontic retention of maxillary arch width are given timely attention in the restorative treatment plan because it is especially vulnerable to relapse. PMID:26568998

  2. Combined PET/MRI scanner

    DOEpatents

    Schlyer, David; Woody, Craig L.; Rooney, William; Vaska, Paul; Stoll, Sean; Pratte, Jean-Francois; O'Connor, Paul

    2007-10-23

    A combined PET/MRI scanner generally includes a magnet for producing a magnetic field suitable for magnetic resonance imaging, a radiofrequency (RF) coil disposed within the magnetic field produced by the magnet and a ring tomograph disposed within the magnetic field produced by the magnet. The ring tomograph includes a scintillator layer for outputting at least one photon in response to an annihilation event, a detection array coupled to the scintillator layer for detecting the at least one photon outputted by the scintillator layer and for outputting a detection signal in response to the detected photon and a front-end electronic array coupled to the detection array for receiving the detection signal, wherein the front-end array has a preamplifier and a shaper network for conditioning the detection signal.

  3. Combination syndrome symptomatology and treatment.

    PubMed

    Tolstunov, Len

    2011-04-01

    Combination syndrome (CS) is one of the most fascinating oral conditions yet is poorly understood and underappreciated in the literature and clinical practice. This article reviews the most important literature on this subject and analyzes the etiology, symptomatology, diagnosis, and current therapeutic modalities for treatment in an attempt to better understand CS. The syndrome represents an example ofa complex pathologic condition of the entire stomatognathic system with a multitude of hard-tissue, soft-tissue, and occlusal changes. These changes, initiated by a certain sequence of events, beginning with a prolonged period of tooth loss, can lead to severe bone atrophy in different regions of the jaws, loss of masticatory function, and the need for complex treatment. Implant rehabilitation of these patients in a preventative approach with cooperation of the entire dental team is emphasized. PMID:21560744

  4. How rats combine temporal cues.

    PubMed

    Guilhardi, Paulo; Keen, Richard; MacInnis, Mika L M; Church, Russell M

    2005-05-31

    The procedures for classical and operant conditioning, and for many timing procedures, involve the delivery of reinforcers that may be related to the time of previous reinforcers and responses, and to the time of onsets and terminations of stimuli. The behavior resulting from such procedures can be described as bouts of responding that occur in some pattern at some rate. A packet theory of timing and conditioning is described that accounts for such behavior under a wide range of procedures. Applications include the food searching by rats in Skinner boxes under conditions of fixed and random reinforcement, brief and sustained stimuli, and several response-food contingencies. The approach is used to describe how multiple cues from reinforcers and stimuli combine to determine the rate and pattern of response bouts. PMID:15845307

  5. Combined gluteoplasty: liposuction and lipoinjection.

    PubMed

    Cárdenas-Camarena, L; Lacouture, A M; Tobar-Losada, A

    1999-10-01

    From April of 1995 to August of 1998, 62 female and four male patients had gluteoplasties. To improve the gluteal region, two techniques that create excellent results in other parts of the body, liposuction and lipoinjection, were combined. The ages of the patients ranged from 18 to 52 years (mean, 31 years). Liposuction was done with a tumescent technique in the lumbosacral, trochanteric, and subgluteal region to improve gluteal shape. The amount of fat aspirated was only that necessary to obtain the desired contour. In all cases, liposuction was also performed in other areas. Lipoinjection was done with round-tip cannulas in different planes of the gluteal region, and the fat was applied in small strips. The quantity of fat infiltrated varied from 120 to 280 cc per gluteus, with a mean of 210 cc. The results were evaluated by the patients and the surgical team with preoperative and postoperative photographs. Follow-up ranged from 3 months to 3 years and 5 months, with a mean of 17 months. No patient was dissatisfied with the results, and more than 90 percent considered their results good or excellent. Liposuction complications consisted of four seromas, six visible irregularities, and two palpable irregularities. Lipoinjection complications occurred in 16 gluteus regions (12 percent); all had gluteal temporal hyperemia and erythema, which resolved with conservative treatment except in one case (4 cc of sterile material corresponding to fat necrosis was drained in that patient). No irregularities or depressions occurred in the gluteus. One case of probable fat embolism syndrome had a satisfactory evolution. This gluteoplasty technique is simple and low in cost, with minimal morbidity and very good results. It is important to note that a good result does not depend on a great amount of fat infiltration but rather on a harmonious way of combining both surgical procedures: fat elimination by liposuction and gluteus augmentation by lipoinjection. PMID:10513938

  6. Promising combination therapies with gemcitabine.

    PubMed

    Robinson, Blaine W; Ostruszka, Leo; Im, Michael M; Shewach, Donna S

    2004-04-01

    Because treatment regimens for breast cancer commonly include gemcitabine, we evaluated two promising combinations in preclinical studies: gemcitabine (Gemzar; Eli Lilly and Company, Indianapolis, IN) with either ionizing radiation or docetaxel (Taxotere; Aventis Pharmaceuticals, Inc, Parsippany, NJ). In breast cancer cell lines that expressed either wild-type p53 (MCF-7) or mutant p53 (MCF-7/Adr), sensitivity to the cytotoxic effects of gemcitabine during a 24-hour incubation was similar (IC(50) values 80 and 60 nmol/L in MCF-7 and MCF-7/Adr, respectively). Both cell lines were well radiosensitized by gemcitabine at the corresponding IC(50), with radiation enhancement ratios of 1.6 to 1.7. Although the MCF-7 cells accumulated nearly twice as much gemcitabine triphosphate compared with the MCF-7/Adr cells, a similar reduction in 2'-deoxyadenosine 5'-triphosphate pools was observed. While the number of dying cells, as measured by sub-G1 DNA content or S-phase cells unable to replicate DNA, differed between the wild-type p53 or mutant p53-expressing cell lines, neither parameter correlated with radiosensitization. Docetaxel was a more potent cytotoxic agent than gemcitabine in MCF-7 cells (IC(50) = 1 nmol/L). Strong synergistic cytotoxicity was observed in cells treated with gemcitabine (24 hours) followed by docetaxel (24 hours) or the reverse sequence. However, simultaneous addition of the two drugs was antagonistic. To determine whether synergy with radiation or docetaxel was mediated by increased DNA damage, DNA double-strand breaks (double-strand breaks) were measured by immunostaining for phosphorylated H2AX. Ionizing radiation produced more double-strand breaks than gemcitabine alone, while no significant double-strand breaks formed with docetaxel alone. The addition of docetaxel or ionizing radiation to gemcitabine-treated cells did not increase H2AX foci formation. These results show that the combination of gemcitabine with ionizing radiation or docetaxel

  7. [Keratoplasty combined with cataract surgery].

    PubMed

    Muraine, M; Gueudry, J; Retout, A; Genevois, O

    2012-09-01

    Corneal pathologies leading to keratoplasty are often associated with cataract and combined surgery is therefore mandatory. Triple procedure with penetrating keratoplasty and concurrent cataract extraction followed by intra ocular lens (IOL) implantation is usually the preferential choice because visual rehabilitation is theoretically more rapid. Surgeons have to be aware of surgical conditions during open-sky surgery because vitreous pressure is not counterbalanced by anterior chamber pressure. Today, many surgeons prefer non-simultaneous procedures with cataract surgery performed months after grafting because of the improvement in spherical refractive error. More recently, new triple procedures, Descemet's stripping automated keratoplasty and concurrent cataract surgery have gained popularity, especially in patients with Fuchs dystrophy associated with cataract. Surgery starts with phacoemulsification, followed by endothelium exchange through a 3 to 5 mm incision. Advantages against classic triple procedure are quick visual rehabilitation, fewer induced refractive errors, minimal postoperative discomfort and corneal integrity. Surgeons have to consider an eventual postoperative hyperopic shift secondary to corneal lenticule shape when choosing adequate intraocular lens. PMID:22921023

  8. Pulling Seton: Combination of mechanisms

    PubMed Central

    Izadpanah, Ahmad; Rezazadehkermani, Mohammad; Hosseiniasl, Seyed Mohammad; Farghadin, Afrouz; Ghahramani, Leila; Bananzadeh, Alimohammad; Roshanravan, Reza; Izadpanah, Ahad

    2016-01-01

    Background: Seton-based techniques are among popular methods for treating high type anal fistula. These techniques are categorized to cutting and noncutting regarding their mechanism of action. In this report we are about to describe a new technique, which is a combination of both mechanisms; we call it Pulling Seton. Materials and Methods: In this technique after determining internal and external orifice of fistula, fistulectomy is done from both ends to the level of external sphincteric muscle. Finally, a remnant of fistula, which remains beneath external sphincteric muscle is excised, and Seton is passed instead of it and tied externally. After the wound heals, patient is asked to pull down the Seton for 3–4 min, 4 times a day. We prospectively enrolled 201 patients with high type anal fistula in this study. Results: Seton gradually passes through external sphincteric muscle till it is displaced outwards or removed by a surgeon via a small incision. 94% of patients treated by this method accomplished their treatment completely without recurrence. None of the patients developed permanent fecal or gas incontinence. Only 5% of patients developed with recurrence of fistula. Since Seton traction is not permanent in this technique, Seton cuts external sphincter slowly, and minimal rate of incontinence is reported. Conclusion: Pulling Seton seems to be an efficient way in treating high type anal fistula with minimal rate of recurrence and complications such as incontinence and authors suggest further randomized studies to compare its efficacy with other Seton-based techniques. PMID:27169099

  9. Radiosensitive severe combined immunodeficiency disease.

    PubMed

    Dvorak, Christopher C; Cowan, Morton J

    2010-02-01

    Inherited defects in components of the nonhomologous end-joining DNA repair mechanism produce a T-B-NK+ severe combined immunodeficiency disease (SCID) characterized by heightened sensitivity to ionizing radiation. Patients with the radiosensitive form of SCID may also have increased short- and long-term sensitivity to the alkylator-based chemotherapy regimens that are traditionally used for conditioning before allogeneic hematopoietic cell transplantation (HCT). Known causes of radiosensitive SCID include deficiencies of Artemis, DNA ligase IV, DNA-dependent protein kinase catalytic subunit, and Cernunnos-XLF, all of which have been treated with HCT. Because of these patients' sensitivity to certain forms of chemotherapy, the approach to donor selection and the type of conditioning regimen used for a patient with radiosensitive SCID requires careful consideration. Significantly more research needs to be done to determine the long-term outcomes of patients with radiosensitive SCID after HCT and to discover novel nontoxic approaches to HCT that might benefit those patients with intrinsic radiosensitivity and chemosensitivity as well as potentially all patients undergoing an HCT. PMID:20113890

  10. Electrochromic variable transmission optical combiner

    NASA Astrophysics Data System (ADS)

    Draper, Russell S.; Wood, Michael V.; Radmard, Bijan; Mahmud, Ken; Schuler, Peter; Sotzing, Gregory A.; Seshadri, Venkataraman; Mino, Warren; Padilla, Javier; Otero, Tobibio F.

    2005-05-01

    Complementary coloring conducting polymer based electrochromic devices have been designed, fabricated and tested for possible application as a variable attenuation combiner element for a see-through head mounted display or a variable trasnsmissive sand wind dust goggle lens. Electrochromic cells fabricated on both glass and polycarbonate substrates have been demonstrated to meet closely the desired goals of low power consumption, wide transmission range, fast switching speeds and long lifetime. Photopic transmissions of 34% in colored state and 67% in bleached state were achieved in a reproducible manner. The measured switching times are 0.6 sec (colored to bleached state) and 1.9 sec (bleached to colored state). The life cycle testing showed stability up to 92,000 switches. The measured power consumption of the fabricated devices was < 1 mW/cm . The electrochromic technology design effort has identified processes for obtaining the optimum layer thickness and selecting polymers and gel electrolytes necessary to obtain the widest transmission range, fastest switching speed and longest lifetime. Early environmental testing has been performed by subjecting prototype electrochromic cells to temperatures varying from -30°C to + 40°C with the results reported herein. Follow on work includes further optimization of electronic drive schemes as well as field testing of electrochromic lens equipped sand, wind dust goggles.

  11. Externally fired combined cycle demonstration

    SciTech Connect

    Orozco, N.J.; Young, S.; LaHaye, P.G.; Strom-Olsen, J.; Seger, J.L.; Pickup, H.

    1995-11-01

    Externally Fired Combined Cycles (EFCCs) can increase the amount of electricity produced from ash bearing fuels up to 40%, with overall powerplant efficiencies in excess of 45%. Achieving such high efficiencies requires high temperature-high pressure air heaters capable of driving modern gas turbines from gas streams containing the products of coal combustion. A pilot plant has been constructed in Kennebunk, Maine to provide proof of concept and evaluation of system components. Tests using pulverized Western Pennsylvania bituminous coal have been carried out since April, 1995. The ceramic air heater extracts energy from the products of coal combustion to power a gas turbine. This air heater has operated at gas inlet temperatures over 1,095 C and pressures over 7.0 atm without damage to the ceramic tube string components. Stable gas turbine operation has been achieved with energy input from the air heater and a supplementary gas fired combustor. Efforts are underway to fire the cycle on coal only, and to increase the duration of the test runs. Air heater improvements are being implemented and evaluated. These improvements include installation of a second pass of ceramic tubes and evaluation of corrosion resistant coatings on the ceramic tubes.

  12. Combined control-structure optimization

    NASA Technical Reports Server (NTRS)

    Salama, M.; Milman, M.; Bruno, R.; Scheid, R.; Gibson, S.

    1989-01-01

    An approach for combined control-structure optimization keyed to enhancing early design trade-offs is outlined and illustrated by numerical examples. The approach employs a homotopic strategy and appears to be effective for generating families of designs that can be used in these early trade studies. Analytical results were obtained for classes of structure/control objectives with linear quadratic Gaussian (LQG) and linear quadratic regulator (LQR) costs. For these, researchers demonstrated that global optima can be computed for small values of the homotopy parameter. Conditions for local optima along the homotopy path were also given. Details of two numerical examples employing the LQR control cost were given showing variations of the optimal design variables along the homotopy path. The results of the second example suggest that introducing a second homotopy parameter relating the two parts of the control index in the LQG/LQR formulation might serve to enlarge the family of Pareto optima, but its effect on modifying the optimal structural shapes may be analogous to the original parameter lambda.

  13. Combined Panofsky Quadrupole & Corrector Dipole

    SciTech Connect

    George Biallas; Nathan Belcher; David Douglas; Tommy Hiatt; Kevin Jordan

    2007-07-02

    Two styles of Panofsky Quadrupoles with integral corrector dipole windings are in use in the electron beam line of the Free Electron Laser at Jefferson Lab. We combined steering and focusing functions into single magnets, adding hundreds of Gauss-cm dipole corrector capability to existing quadrupoles because space is at a premium along the beam line. Superposing a one part in 100 dipole corrector field on a 1 part in 1000, weak (600 to 1000 Gauss) quadrupole is possible because the parallel slab iron yoke of the Panofsky Quadrupole acts as a window frame style dipole yoke. The dipole field is formed when two electrically floating “current sources”, designed and made at JLab, add and subtract current from the two opposite quadrupole current sheet windings parallel to the dipole field direction. The current sources also drive auxiliary coils at the yoke’s inner corners that improve the dipole field. Magnet measurements yielded the control system field maps that characterize the two types of fields. Field analysis using TOSCA, construction and wiring details, magnet measurements and reference for the current source are presented.

  14. Radiosensitive Severe Combined Immunodeficiency Disease

    PubMed Central

    Dvorak, Christopher C.; Cowan, Morton J.

    2009-01-01

    Synopsis Inherited defects in components of the non-homologous end joining DNA repair mechanism produce a T-B-NK+ severe combined immunodeficiency disease (SCID) characterized by heightened sensitivity to ionizing radiation. Patients with the radiosensitive form of SCID may also have increased short- and long-term sensitivity to the alkylator-based chemotherapy regimens traditionally utilized for conditioning prior to allogeneic hematopoietic cell transplantation (HCT). Known etiologies of radiosensitive SCID include deficiencies of Artemis, DNA Ligase IV, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and Cernunnos-XLF, all of which have been treated with HCT. Because of their sensitivity to certain forms of chemotherapy, the approach to donor selection and type of conditioning regimen utilized for a radiosensitive SCID patient requires careful consideration. Significantly more research needs to be done in order to determine the long-term outcomes of radiosensitive SCID patients following HCT, as well as to discover novel non-toxic approaches to HCT that might benefit those with intrinsic radio- and chemo-sensitivity, as well as potentially all patients undergoing an HCT. PMID:20113890

  15. Efficient Web Services Policy Combination

    NASA Technical Reports Server (NTRS)

    Vatan, Farrokh; Harman, Joseph G.

    2010-01-01

    Large-scale Web security systems usually involve cooperation between domains with non-identical policies. The network management and Web communication software used by the different organizations presents a stumbling block. Many of the tools used by the various divisions do not have the ability to communicate network management data with each other. At best, this means that manual human intervention into the communication protocols used at various network routers and endpoints is required. Developing practical, sound, and automated ways to compose policies to bridge these differences is a long-standing problem. One of the key subtleties is the need to deal with inconsistencies and defaults where one organization proposes a rule on a particular feature, and another has a different rule or expresses no rule. A general approach is to assign priorities to rules and observe the rules with the highest priorities when there are conflicts. The present methods have inherent inefficiency, which heavily restrict their practical applications. A new, efficient algorithm combines policies utilized for Web services. The method is based on an algorithm that allows an automatic and scalable composition of security policies between multiple organizations. It is based on defeasible policy composition, a promising approach for finding conflicts and resolving priorities between rules. In the general case, policy negotiation is an intractable problem. A promising method, suggested in the literature, is when policies are represented in defeasible logic, and composition is based on rules for non-monotonic inference. In this system, policy writers construct metapolicies describing both the policy that they wish to enforce and annotations describing their composition preferences. These annotations can indicate whether certain policy assertions are required by the policy writer or, if not, under what circumstances the policy writer is willing to compromise and allow other assertions to take

  16. Combining Individual Psychodynamics with Structural Family Therapy.

    ERIC Educational Resources Information Center

    Melito, Richard

    1988-01-01

    Presents integrative framework for combining central aspects of individual psychodynamics with structural family therapy in meaningful way. Explains how framework derives from developmental perspective. Presents case example to illustrate combined approach and demonstrate its utility. (Author/NB)

  17. Improving Writing with Sentence Combining Exercises.

    ERIC Educational Resources Information Center

    Nutter, Norma; Safran, Joan

    1984-01-01

    Sentence-combining exercises, which require students to combine simple sentences in any way they wish, have helped learning disabled elementary children improve skills in writing, reading, and spelling. The exercises are flexible, motivating, and simple to design. (CL)

  18. Activating Transcription Factor 3 regulates in part the enhanced tumour cell cytotoxicity of the histone deacetylase inhibitor M344 and cisplatin in combination

    PubMed Central

    2010-01-01

    Background Activating Transcription Factor (ATF) 3 is a key regulator of the cellular integrated stress response whose expression has also been correlated with pro-apoptotic activities in tumour cell models. Combination treatments with chemotherapeutic drugs, such as cisplatin, and histone deacetylase (HDAC) inhibitors have been demonstrated to enhance tumour cell cytotoxicity. We recently demonstrated a role for ATF3 in regulating cisplatin-induced apoptosis and others have shown that HDAC inhibition can also induce cellular stress. In this study, we evaluated the role of ATF3 in regulating the co-operative cytotoxicity of cisplatin in combination with an HDAC inhibitor. Results The HDAC inhibitor M344 induced ATF3 expression at the protein and mRNA level in a panel of human derived cancer cell lines as determined by Western blot and quantitative RT-PCR analyses. Combination treatment with M344 and cisplatin lead to increased induction of ATF3 compared with cisplatin alone. Utilizing the MTT cell viability assay, M344 treatments also enhanced the cytotoxic effects of cisplatin in these cancer cell lines. The mechanism of ATF3 induction by M344 was found to be independent of MAPKinase pathways and dependent on ATF4, a known regulator of ATF3 expression. ATF4 heterozygote (+/-) and knock out (-/-) mouse embryonic fibroblast (MEF) as well as chromatin immunoprecipitation (ChIP) assays were utilized in determining the mechanistic induction of ATF3 by M344. We also demonstrated that ATF3 regulates the enhanced cytotoxicity of M344 in combination with cisplatin as evidenced by attenuation of cytotoxicity in shRNAs targeting ATF3 expressing cells. Conclusion This study identifies the pro-apoptotic factor, ATF3 as a novel target of M344, as well as a mediator of the co-operative effects of cisplatin and M344 induced tumour cell cytotoxicity. PMID:20828393

  19. 7 CFR 4280.193 - Combined funding.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Combined funding. 4280.193 Section 4280.193... Efficiency Improvements Program Section D. Combined Funding § 4280.193 Combined funding. The requirements for... if the project meets the requirements specified in § 4280.109. (b) Funding. Funding provided...

  20. 7 CFR 4280.193 - Combined funding.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Combined funding. 4280.193 Section 4280.193... Efficiency Improvements Program Section D. Combined Funding § 4280.193 Combined funding. The requirements for... if the project meets the requirements specified in § 4280.109. (b) Funding. Funding provided...

  1. 40 CFR 1506.4 - Combining documents.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Combining documents. 1506.4 Section 1506.4 Protection of Environment COUNCIL ON ENVIRONMENTAL QUALITY OTHER REQUIREMENTS OF NEPA § 1506.4 Combining documents. Any environmental document in compliance with NEPA may be combined with any...

  2. 38 CFR 3.323 - Combined ratings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Combined ratings. 3.323... Combined ratings. (a) Compensation—(1) Same type of service. When there are two or more service-connected compensable disabilities a combined evaluation will be made following the tables and rules prescribed in...

  3. 10 CFR 50.31 - Combining applications.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Combining applications. 50.31 Section 50.31 Energy NUCLEAR..., Certifications, and Regulatory Approvals; Form; Contents; Ineligibility of Certain Applicants § 50.31 Combining applications. An applicant may combine in one his several applications for different kinds of licenses...

  4. 10 CFR 50.52 - Combining licenses.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Combining licenses. 50.52 Section 50.52 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF PRODUCTION AND UTILIZATION FACILITIES Issuance, Limitations, and Conditions of Licenses and Construction Permits § 50.52 Combining licenses. The Commission may combine in...

  5. 12 CFR 602.16 - Combining requests.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 6 2010-01-01 2010-01-01 false Combining requests. 602.16 Section 602.16 Banks....16 Combining requests. You may not avoid paying fees by filing multiple requests at the same time... of requests to avoid fees, we will combine the requests and charge accordingly. We will assume...

  6. 19 CFR 191.93 - Combined applications.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Combined applications. 191.93 Section 191.93... § 191.93 Combined applications. An applicant for the procedures provided for in §§ 191.91 and 191.92 of... application package (see also § 191.195 of this part regarding combined applications for certification in...

  7. Early Combinations of Words and Actions.

    ERIC Educational Resources Information Center

    Shore, Cecilia

    Previous research has shown a similar starting time for early combinations of words and play actions in children and has suggested that similar cognitive processes underlie the transition to combining activities in language, symbolic play, and manipulative play. A study was undertaken to investigate combining activities in these three domains and…

  8. Power combining of semiconductor lasers: A review

    NASA Technical Reports Server (NTRS)

    Katz, J.

    1982-01-01

    Several methods of coherent power combining are described and compared. A comparison is also made between coherent and incoherent power combining, and important operational characteristics are considered. It is found that in communication links with demanding requirements coherent power combining is necessary.

  9. 49 CFR 387.305 - Combination vehicles.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 5 2011-10-01 2011-10-01 false Combination vehicles. 387.305 Section 387.305 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY... § 387.305 Combination vehicles. The following combinations will be regarded as one motor vehicle...

  10. 49 CFR 387.305 - Combination vehicles.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 5 2010-10-01 2010-10-01 false Combination vehicles. 387.305 Section 387.305 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY... § 387.305 Combination vehicles. The following combinations will be regarded as one motor vehicle...

  11. 49 CFR 387.305 - Combination vehicles.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 5 2013-10-01 2013-10-01 false Combination vehicles. 387.305 Section 387.305 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY... § 387.305 Combination vehicles. The following combinations will be regarded as one motor vehicle...

  12. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Apples Grades § 51.304 Combination grades...) Combinations other than these are not permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the...

  13. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Apples Grades § 51.304 Combination grades...) Combinations other than these are not permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the...

  14. [FIXED COMBINATION ATORVASTATIN-EZETIMIBE (ATOZET®)].

    PubMed

    Scheen, A J

    2016-01-01

    Cardiovascular prevention in subjects at high or very high risk requires a drastic reduction in LDL cholesterol according to the concept "the lower, the better". The combination of an inhibitor of cholesterol synthesis and a selective inhibitor of intestinal absorption results in a complementary and synergistic LDL-lowering activity. Besides a first fixed combination ezetimibe-simvastatin (Inegy®), a new fixed combination is presented, Atozet® that combines atorvastatin and ezetimibe. Because atorvastatin is more potent than simvastatin, this novel fixed combination should facilitate reaching therapeutic goals in terms of LDL cholesterol amongst patients with severe hypercholesterolaemia and/or at high or very high cardiovascular risk. PMID:26983314

  15. Molecular diagnosis of Prader-Willi syndrome: Comparison of cytogenetic and molecular genetic data including parent of origin dependent methylation DNA patterns

    SciTech Connect

    Butler, M.G.

    1996-01-11

    This letter to the editor discusses a recent study concerning the parent-of-origin methylation site at D15S63 and its application in molecular diagnostics confirming Prader-Willi syndrome (PWS). It concludes that more research is needed to clear up questions which remain regarding the causation of PWS. 20 refs., 1 tab.

  16. Overlap between differentially methylated DNA regions in blood B lymphocytes and genetic at-risk loci in primary Sjögren's syndrome

    PubMed Central

    Miceli-Richard, Corinne; Wang-Renault, Shu-Fang; Boudaoud, Saida; Busato, Florence; Lallemand, Céline; Bethune, Kevin; Belkhir, Rakiba; Nocturne, Gaétane; Mariette, Xavier; Tost, Jörg

    2016-01-01

    Background Beyond genetics, epigenetics alterations and especially those related to DNA methylation, play key roles in the pathogenesis of autoimmune diseases such as primary Sjögren's syndrome (pSS) and systemic lupus erythematosus. This study aimed to assess the role of methylation deregulation in pSS pathogeny through a genome-wide methylation approach. Patients and methods 26 female patients with pSS and 22 age-matched controls were included in this study. CD4+ T cells and CD19+ B cells were isolated from peripheral blood mononuclear cells by magnetic microbeads and their genome-wide DNA methylation profiles were analysed using Infinium Human Methylation 450 K BeadChips. Probes with a median DNA methylation difference of at least 7% and p<0.01 between patients and controls were considered significantly differentially methylated. Results Methylation alterations were mainly present in B cells compared with T cells. In B cells, an enrichment of genes with differentially methylated probes in genetic at-risk loci was observed, suggesting involvement of both genetic and epigenetic abnormalities in the same genes. Methylation alterations in B cells were more frequent in some specific pathways including Interferon Regulated Genes, mainly among patients who were autoantibody positive. Moreover, genes with differentially methylated probes were over-represented in B cells from patients with active disease. Conclusions This study demonstrated more important deregulation of DNA methylation patterns in B cells compared with T cells, emphasising the importance of B cells in the pathogenesis of the disease. Overlap between genes with differentially methylated probes in B lymphocytes and genetic at-risk loci is a new finding highlighting their importance in pSS. PMID:26183421

  17. Exploring drug combinations in genetic interaction network

    PubMed Central

    2012-01-01

    Background Drug combination that consists of distinctive agents is an attractive strategy to combat complex diseases and has been widely used clinically with improved therapeutic effects. However, the identification of efficacious drug combinations remains a non-trivial and challenging task due to the huge number of possible combinations among the candidate drugs. As an important factor, the molecular context in which drugs exert their functions can provide crucial insights into the mechanism underlying drug combinations. Results In this work, we present a network biology approach to investigate drug combinations and their target proteins in the context of genetic interaction networks and the related human pathways, in order to better understand the underlying rules of effective drug combinations. Our results indicate that combinatorial drugs tend to have a smaller effect radius in the genetic interaction networks, which is an important parameter to describe the therapeutic effect of a drug combination from the network perspective. We also find that drug combinations are more likely to modulate functionally related pathways. Conclusions This study confirms that the molecular networks where drug combinations exert their functions can indeed provide important insights into the underlying rules of effective drug combinations. We hope that our findings can help shortcut the expedition of the future discovery of novel drug combinations. PMID:22595004

  18. Binocular Combination of Second-Order Stimuli

    PubMed Central

    Zhou, Jiawei; Liu, Rong; Zhou, Yifeng; Hess, Robert F.

    2014-01-01

    Phase information is a fundamental aspect of visual stimuli. However, the nature of the binocular combination of stimuli defined by modulations in contrast, so-called second-order stimuli, is presently not clear. To address this issue, we measured binocular combination for first- (luminance modulated) and second-order (contrast modulated) stimuli using a binocular phase combination paradigm in seven normal adults. We found that the binocular perceived phase of second-order gratings depends on the interocular signal ratio as has been previously shown for their first order counterparts; the interocular signal ratios when the two eyes were balanced was close to 1 in both first- and second-order phase combinations. However, second-order combination is more linear than previously found for first-order combination. Furthermore, binocular combination of second-order stimuli was similar regardless of whether the carriers in the two eyes were correlated, anti-correlated, or uncorrelated. This suggests that, in normal adults, the binocular phase combination of second-order stimuli occurs after the monocular extracting of the second-order modulations. The sensory balance associated with this second-order combination can be obtained from binocular phase combination measurements. PMID:24404180

  19. Binocular combination of second-order stimuli.

    PubMed

    Zhou, Jiawei; Liu, Rong; Zhou, Yifeng; Hess, Robert F

    2014-01-01

    Phase information is a fundamental aspect of visual stimuli. However, the nature of the binocular combination of stimuli defined by modulations in contrast, so-called second-order stimuli, is presently not clear. To address this issue, we measured binocular combination for first- (luminance modulated) and second-order (contrast modulated) stimuli using a binocular phase combination paradigm in seven normal adults. We found that the binocular perceived phase of second-order gratings depends on the interocular signal ratio as has been previously shown for their first order counterparts; the interocular signal ratios when the two eyes were balanced was close to 1 in both first- and second-order phase combinations. However, second-order combination is more linear than previously found for first-order combination. Furthermore, binocular combination of second-order stimuli was similar regardless of whether the carriers in the two eyes were correlated, anti-correlated, or uncorrelated. This suggests that, in normal adults, the binocular phase combination of second-order stimuli occurs after the monocular extracting of the second-order modulations. The sensory balance associated with this second-order combination can be obtained from binocular phase combination measurements. PMID:24404180

  20. Strategy application, observability, and the choice combinator.

    SciTech Connect

    Winter, Victor Lono

    2004-03-01

    In many strategic systems, the choice combinator provides a powerful mechanism for controlling the application of rules and strategies to terms. The ability of the choice combinator to exercise control over rewriting is based on the premise that the success and failure of strategy application can be observed. In this paper we present a higher-order strategic framework with the ability to dynamically construct strategies containing the choice combinator. To this framework, a combinator called hide is introduced that prevents the successful application of a strategy from being observed by the choice combinator. We then explore the impact of this new combinator on a real-world problem involving a restricted implementation of the Java Virtual Machine.

  1. IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

    PubMed Central

    Kochan, Jakub; Wawro, Mateusz

    2016-01-01

    ABSTRACT MCPIP1 and IER3 are recently described proteins essential for maintenance of immune homeostasis. IER3 is involved in the regulation of apoptosis and differentiation and has been shown lately to protect activated T cells and macrophages from apoptosis. MCPIP1 is an RNase critical for controlling inflammation-related mRNAs. MCPIP1 interacts with and degrades a set of stem-loop-containing mRNAs (including IL-6). Our results demonstrate the involvement of MCPIP1 in the regulation of IER3 mRNA levels. A dual luciferase assay revealed that over-expression of MCPIP1 resulted in a decrease of luciferase activity in the samples co-transfected with constructs containing luciferase CDS attached to IER3 3′UTR. We identified a stem-loop structure similar to that described to be important for destabilization of the IL-6 mRNA by MCPIP1. Examination of IER3 3′UTR sequence, structure and evolutionary conservation revealed that the identified stem-loop is buried within a bigger element. Deletion of this fragment abolished the regulation of IER3 3′UTR-containing transcript by MCPIP1. Finally, using immunofluorescence-combined single-molecule RNA FISH we have shown that the MCPIP1 protein co-localizes with IER3 mRNA. By this method we also proved that the presence of the wild-type NYN/PIN-like domain of MCPIP1 correlated with the decreased level of IER3 mRNA. RNA immunoprecipitation further confirmed the interaction of MCPIP1 with IER3 transcripts in vivo. PMID:27256408

  2. Combined eye-atmosphere visibility model

    NASA Technical Reports Server (NTRS)

    Kaufman, Y. J.

    1981-01-01

    Existing models of the optical characteristics of the eye are combined with a recent model of optical characteristics of the atmosphere given by its modulation transfer function. This combination results in the combined eye-atmosphere performance given by the product of their modulation transfer functions. An application for the calculation of visibility thresholds in the case of a two-halves field is given.

  3. New combination solution for RS positions

    NASA Astrophysics Data System (ADS)

    Yatskiv, Y. S.; Kur'yanova, A. N.; Lytvyn, S. O.

    2006-10-01

    Main Astronomical Observatory of the NAS of Ukraine is involved in the work of a redetermination of the ICRF, that was initiated by the IVS. We have carried out several combination runs based on individual catalogues provided by 8 IVS Analysis Centers and have selected the final version RSC(GAO UA)05 C 03. In comparison with the ICRF and other combined catalogues, orientation parameters and uncertainty of this new combined catalogue are given.

  4. Current update on combined hepatocellular-cholangiocarcinoma

    PubMed Central

    Maximin, Suresh; Ganeshan, Dhakshina Moorthy; Shanbhogue, Alampady K.; Dighe, Manjiri K.; Yeh, Matthew M.; Kolokythas, Orpheus; Bhargava, Puneet; Lalwani, Neeraj

    2014-01-01

    Combined hepatocellular-cholangiocarcinoma is a rare but unique primary hepatic tumor with characteristic histology and tumor biology. Recent development in genetics and molecular biology support the fact that combined hepatocellular-cholangiocarcinoma is closely linked with cholangiocarcinoma, rather than hepatocellular carcinoma. Combined hepatocellular cholangiocarcinoma tends to present with an more aggressive behavior and a poorer prognosis than either hepatocellular carcinoma or cholangiocarcinoma. An accurate preoperative diagnosis and aggressive treatment planning can play crucial roles in appropriate patient management. PMID:26937426

  5. Combined DSEK and Transconjunctival Pars Plana Vitrectomy

    PubMed Central

    Sane, Mona; Shaikh, Naazli

    2016-01-01

    We report here three patients who underwent combined Descemet's stripping with endothelial keratoplasty and transconjunctival pars plana vitrectomy for bullous keratopathy and posterior segment pathology. A surgical technique and case histories are described. Anatomic and visual outcomes of combined Descemet's stripping with endothelial keratoplasty and vitrectomy were excellent. Our experience provides technical guidelines and limitations. The combined minimally invasive techniques allow for rapid anatomical recovery and return of function and visual acuity in a single sitting. PMID:27413563

  6. Combination Antifungal Therapy for Invasive Aspergillosis Revisited

    PubMed Central

    Panackal, Anil A.

    2016-01-01

    Invasive aspergillosis (IA) causes significant morbidity and mortality among immunocompromised hosts. Combination therapy with mold-active triazoles and echinocandins has been used with the hope of improving outcomes over monotherapy, especially in the setting of refractory disease. Herein, I update our prior systematic review and meta-analysis on combination therapy for salvage IA in the context of the recently published randomized clinical trial of combination therapy for primary IA. Clinicians should consider combination antifungals for IA in refractory disease despite immune reconstitution when there are concerns for resistance or pharmacokinetic variability. PMID:27441304

  7. Grating rhomb diode laser power combiner

    NASA Technical Reports Server (NTRS)

    Minott, Peter O.; Abshire, James B.

    1987-01-01

    A compact device for spectrally combining many laser-diode beams into a single multi-wavelength beam has been developed for use in NASA's intersatellite communications programs. The prototype device combines seven 30 milliwatt beams into a single beam with 70 percent efficiency producing an output of approximately 150 milliwatts. All beams are coaxial and can be collimated with a single transmitter optical system. The combining technique is relatively insensitive to drifts in the laser-diode wavelength and provides both increased power output and laser-diode source redundancy. Combination of more than 100 laser-diodes producing an output greater than 5 watts appears feasible with this technique.

  8. 24 CFR 3285.313 - Combination systems.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 5 2011-04-01 2011-04-01 false Combination systems. 3285.313 Section 3285.313 Housing and Urban Development Regulations Relating to Housing and Urban Development... systems. Support systems that combine both load-bearing capacity and uplift resistance must also be...

  9. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Combination packaging. 6.93 Section 6.93 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and...

  10. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Combination packaging. 6.93 Section 6.93 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and...

  11. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Combination packaging. 6.93 Section 6.93 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and...

  12. COMBINED-SEWER OVERFLOW CONTROL AND TREATMENT

    EPA Science Inventory

    Combined-sewer overflow (CSO), along with sanitary-sewer overflow and stormwater are significant contributors of contamination to surface waters. During a rain event, the flow in a combined sewer system may exceed the capacity of the intercepting sewer leading to the wastewater t...

  13. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Combination packaging. 6..., DEPARTMENT OF THE TREASURY LIQUORS âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and distributing distilled spirits, wine, or malt beverages in...

  14. OPTIMIZATION OF COMBINED SEWER OVERFLOW CONTROL SYSTEMS

    EPA Science Inventory

    The highly variable and intermittent pollutant concentrations and flowrates associated with wet-weather events in combined sewersheds necessitates the use of storage-treatment systems to control pollution.An optimized combined-sewer-overflow (CSO) control system requires a manage...

  15. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Combination packaging. 6..., DEPARTMENT OF THE TREASURY LIQUORS âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and distributing distilled spirits, wine, or malt beverages in...

  16. 24 CFR 3285.313 - Combination systems.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 5 2010-04-01 2010-04-01 false Combination systems. 3285.313 Section 3285.313 Housing and Urban Development Regulations Relating to Housing and Urban Development... systems. Support systems that combine both load-bearing capacity and uplift resistance must also be...

  17. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 1 2013-01-01 2013-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  18. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 1 2012-01-01 2012-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  19. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 1 2014-01-01 2014-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  20. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  1. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 1 2011-01-01 2011-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  2. OPIMIZATION OF COMBINED SEWER OVERFLOW CONTROL SYSTEMS

    EPA Science Inventory

    The highly variable and intermittent pollutant concentrations and flowrates associated with wet-weather events in combined sewersheds necessitates the use of storage-treatment systems to control pollution. A strategy should be adopted to develop an optimized combined sewer overfl...

  3. MANAGEMENT AND CONTROL OF COMBINED SEWER OVERFLOWS

    EPA Science Inventory

    The paper gives a basic overview of the U.S. government's involvements in developing countermeasures for the abatement of combined sewer overflow pollution. batement or prevention of pollution stormwater runoff and combined sewer overflows is one of the most challenging areas in ...

  4. Convergence analysis of combinations of different methods

    SciTech Connect

    Kang, Y.

    1994-12-31

    This paper provides a convergence analysis for combinations of different numerical methods for solving systems of differential equations. The author proves that combinations of two convergent linear multistep methods or Runge-Kutta methods produce a new convergent method of which the order is equal to the smaller order of the two original methods.

  5. 38 CFR 21.124 - Combination course.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... vocational rehabilitation, a course will be considered to be a combination course, if the student spends full... pursue the components of a combination course in the following manner: (1) Concurrent school and on-job... objective which the student attains primarily through school instruction with the on-job portion...

  6. Context and Structure in Conceptual Combination.

    ERIC Educational Resources Information Center

    Medin, Douglas L.; Shoben, Edward J.

    1988-01-01

    Three experiments evaluated modifications of conceptual knowledge associated with judgments of adjective-noun conceptual combinations. The subjects included 109 students at the University of Illinois (Champaign). Results indicate that models that attempt to explain combined categories by adding or changing a single feature are not successful. (TJH)

  7. A linear combination of modified Bessel functions

    NASA Technical Reports Server (NTRS)

    Shitzer, A.; Chato, J. C.

    1971-01-01

    A linear combination of modified Bessel functions is defined, discussed briefly, and tabulated. This combination was found to recur in the analysis of various heat transfer problems and in the analysis of the thermal behavior of living tissue when modeled by cylindrical shells.

  8. The GRAVITY integrated optics beam combination

    NASA Astrophysics Data System (ADS)

    Jocou, L.; Perraut, K.; Nolot, A.; Berger, J. P.; Moulin, T.; Labeye, P.; Lacour, S.; Perrin, G.; Lebouquin, J. B.; Bartko, H.; Thiel, M.; Eisenhauer, F.

    2010-07-01

    Gravity is a 2nd generation interferometric instrument for VLTI. It will combine 4 telescopes in dual feed in the K band to study general relativity effects around the Galactic Center black hole. The concept of Gravity is based on two equivalent beam combiner instruments: the scientific one fed by the science target (Sgr A*) and the fringe tracker fed by a bright reference star (See Gillessen et al.1). Both beam combination instruments are based on silica on silicon integrated optics (IO) component glued to fluoride glass fiber array. The beam combiners are implemented in a cryogenic vessel cooled at 200°K and back-illuminated by a high power laser used for metrology (Bartko et al.2). This paper is dedicated to the description of the development of the integrated beam combiner assembly.

  9. Full Band Millimeter-Wave Power-Combining Amplifier Using a Lossy Power-Combining Network

    NASA Astrophysics Data System (ADS)

    Xie, Xiaoqiang; Yang, Guiting; Zhang, Yunhua; Zhao, Xuan; She, Yuchen

    2016-04-01

    This paper presents a millimeter-wave broadband power-combining amplifier using a novel lossy waveguide-based power combiner. The lossy combiner has a performance of broadband low-loss combining symmetrically and has properties of good match and high isolation at and between ports, because lossy planar lines are embedded in the lossy combiner and even-mode excitations are weakened. The measured results show that the lossy combiners has a loss of about 0.14 dB and achieves reflection and isolation of about—15 dB in 26.5-40 GHz. And then, using the lossy combiner, a compact lossy waveguide-based four-way-combining network is fabricated. The lossy network has a measured loss of about 0.25 dB and achieves good improvements of match and isolation in the full Ka-band. The improvements can enhance stability of amplifying units when the lossy combining network used in multi-way power-combining amplifier. Using the lossy combining network, a solid-state power-combining amplifier is developed, and corresponding experimental results show that output power is more than 30 dBm and combining efficiency is more than 80 % in the full Ka-band.

  10. [Combination treatment of hypertension in 2015].

    PubMed

    Špinar, Jindřich; Vítovec, Jiří; Špinarová, Lenka; Bendová, Miroslava

    2015-05-01

    We present an overview of the present views on combination treatment and on fixed combinations in the treatment of hypertension according to guidelines of ESH/ESC and ČSH from 2013. The most frequently recommended dual combinations include a blocker of the renin-angiotensin system (ACEI or sartan) and a calcium channel blocker, and further a blocker of the renin-angiotensin system and a diuretic and a calcium channel blocker and a diuretic. In 2014 a fixed-dose combination of an ACE inhibitor (perindopril), a calcium channel blocker (amlodipine) and an diuretic (indapamide) appeared on the Czech market. Within the PIANIST study including 4 731 insufficiently controlled hypertensives, a fixed-dose triple combination of perindopril, amlodipine and indapamide led to a decrease in blood pressure by 28.3/13.8 mm Hg and to a sufficient control of hypertension in 92 % of patients. The advantage of fixed combinations primarily consists in greater compliance of patients and thereby in a better control of hypertension. About 1/3 of hypertensives need a triple combination for a satisfactory blood pressure control. PMID:26075856

  11. Pharmacological properties of combination therapies for hypertension.

    PubMed

    Abernethy, D R

    1997-03-01

    Single drug therapy for the treatment of hypertension has traditionally been a standard of practice. More recently combination therapy as first-line treatment has gained acceptance both by the medical practice community and the US Food and Drug Administration. The advantages of combinations may be a synergistic or additive antihypertensive effect, metabolic improvement, or both. The combination of a thiazide-type diuretic and a potassium-sparing diuretic has been quite useful in the past to prevent the need for potassium supplementation. The combination of beta-adrenoceptor blockade and a thiazide diuretic results in an additive antihypertensive effect that permits the effective use of very low thiazide doses. The mechanism of antihypertensive effects of each member of the combination are complimentary with increased sympathetic outflow and renin-angiotensin axis activation induced by the diuretic being blunted by beta1-adrenergic blockade. Combinations not used as first-line therapy, such as angiotensin converting enzyme inhibitors or angiotensin receptor blockade and a thiazide diuretic, have complimentary antihypertensive mechanisms and have been useful in treating patient groups who do not respond well to converting enzyme inhibitor monotherapy. The combination of a calcium antagonist with diuretic therapy has an additive hypertensive effect as well; however, the complimentary mechanisms are less obvious. Finally, the combination of angiotensin converting enzyme inhibition and calcium antagonist therapy has been useful in selected patients, but again the complimentary mechanisms are less obvious. As first-line therapy, combinations for diuretics and beta1-receptor blockers have been useful for achieving increased antihypertensive effect with decreased adverse drug effect. PMID:9056702

  12. Whole-genome DNA methylation and hydroxymethylation profiling for HBV-related hepatocellular carcinoma.

    PubMed

    Ye, Chao; Tao, Ran; Cao, Qingyi; Zhu, Danhua; Wang, Yini; Wang, Jie; Lu, Juan; Chen, Ermei; Li, Lanjuan

    2016-08-01

    Hepatocellular carcinoma (HCC) is a common solid tumor worldwide with a poor prognosis. Accumulating evidence has implicated important regulatory roles of epigenetic modifications in the occurrence and progression of HCC. In the present study, we analyzed 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels in the tumor tissues and paired adjacent peritumor tissues (APTs) from four individual HCC patients using a (hydroxy)methylated DNA immunoprecipitation approach combined with deep sequencing [(h)MeDIP-Seq]. Bioinformatics analysis revealed that the 5-mC levels in the promoter regions of 2796 genes and the 5-hmC levels in 507 genes differed significantly between HCC tissues and APTs. These differential genes were grouped into various clusters and pathways and found to be particularly enriched in the 'metabolic pathways' that include 'Glycolysis/gluconeogenesis', 'Oxidative phosphorylation' and 'Citrate cycle (TCA cycle)', implicating a potential role of metabolic alterations in HCC. Furthermore, 144 genes had both 5-mC and 5-hmC changes in HCC patients, and 10 of them (PCNA, MDM2, STAG1, E2F4, FGF4, FGF19, RHOBTB2, UBE2QL1, DCN and HSP90AA1) were enriched and interconnected in five pathways including the 'Cell cycle', 'Pathway in cancer', 'Ubiquitin mediated proteolysis', 'Melanoma' and 'Prostate cancer' pathways. The genome-wide mapping of 5-mC and 5-hmC in HCC tissues and APTs indicated that both 5-mC and 5-hmC epigenetic modifications play important roles in the regulation of HCC, and there may be some interconnections between them. Taken together, in the present study we conducted the first genome-wide mapping of DNA methylation combined with hydroxymethylation in HBV-related HCC and provided a series of potential novel epigenetic biomarkers for HCC. PMID:27221337

  13. Combination Levothyroxine + Liothyronine Treatment in Pregnancy.

    PubMed

    Foeller, Megan E; Silver, Robert M

    2015-09-01

    Hypothyroidism is one of the most common endocrine disorders in young women and affects 3% to 4% of all pregnancies. Inadequately treated maternal hypothyroidism is associated with numerous adverse fetal and maternal outcomes. Because of growing popularity of levothyroxine (L-T4) + liothyronine (L-T3) combination therapy for hypothyroidism in nonpregnant individuals, pregnant women are taking these medications with increasing frequency. This article reviews the theoretical dangers of combination L-T4 + L-T3 treatment during pregnancy by outlining physiological regulation of maternal and fetal thyroid homeostasis, proposed adverse fetal outcomes to combination therapy, and current recommendations on thyroid replacement in pregnancy from professional societies. PMID:26403562

  14. Fat embolism syndrome after combined aesthetic surgery.

    PubMed

    Erba, Paolo; Farhadi, Jian; Schaefer, Dirk Johannes; Pierer, Gerhard

    2011-02-01

    Fat embolism syndrome is a rare complication that develops after extended soft tissue disruption by liposuction, in particular if combined with time consuming, multiple procedures. Early signs are non-specific and often not considered, so that diagnosis and correct management may be delayed. We report a case in which liposuction combined with other aesthetic surgical procedures caused a fat embolism syndrome in a 46-year-old woman, which was followed by multiple organ failure and the development of sepsis with perimammary abscesses. Extended liposuction of the abdomen and thighs, bilateral augmentation mammaplasty, and stripping of both greater saphenous veins were combined. PMID:20158423

  15. Combination solar photovoltaic heat engine energy converter

    NASA Technical Reports Server (NTRS)

    Chubb, Donald L.

    1987-01-01

    A combination solar photovoltaic heat engine converter is proposed. Such a system is suitable for either terrestrial or space power applications. The combination system has a higher efficiency than either the photovoltaic array or the heat engine alone can attain. Advantages in concentrator and radiator area and receiver mass of the photovoltaic heat engine system over a heat-engine-only system are estimated. A mass and area comparison between the proposed space station organic Rankine power system and a combination PV-heat engine system is made. The critical problem for the proposed converter is the necessity for high temperature photovoltaic array operation. Estimates of the required photovoltaic temperature are presented.

  16. Crankshaft position sensing with combined starter alternator

    DOEpatents

    Brandenburg, Larry Raymond; Miller, John Michael

    2000-06-13

    A crankshaft position sensing apparatus for use with an engine (16) having a combined starter/alternator assembly (18). The crankshaft position sensing apparatus includes a tone ring (38) with a sensor (36) and bandpass filter (46), having a cylinder identification input from a camshaft sensor (48), and a gain limiter (54). The sensing apparatus mounts near the rotor (30) of the combined starter/alternator assembly (18). The filtered crankshaft position signal can then be input into a vehicle system controller (58) and an inner loop controller (60). The starter/alternator assembly (18) in combination with an internal combustion engine is particularly useful for a hybrid electric vehicle system.

  17. Crankshaft position sensing with combined starter alternator

    SciTech Connect

    Brandenburg, L.R.; Miller, J.M.

    2000-06-13

    A crankshaft position sensing apparatus is described for use with an engine having a combined starter/alternator assembly. The crankshaft position sensing apparatus includes a tone ring with a sensor and bandpass filter, having a cylinder identification input from a camshaft sensor, and a gain limiter. The sensing apparatus mounts near the rotor of the combined starter/alternator assembly. The filtered crankshaft position signal can then be input into a vehicle system controller and an inner loop controller. The starter/alternator assembly in combination with an internal combustion engine is particularly useful for a hybrid electric vehicle system.

  18. Cost Comparison of Conventional Gray Combined Sewer Overflow Control Infrastructure versus a Green/Gray Combination

    EPA Science Inventory

    This paper outlines a life-cycle cost analysis comparing a green (rain gardens) and gray (tunnels) infrastructure combination to a gray-only option to control combined sewer overflow in the Turkey Creek Combined Sewer Overflow Basin, in Kansas City, MO. The plan area of this Bas...

  19. The solubility of antibiotic and corticosteroid combinations.

    PubMed

    Lee, B L; Matoba, A Y; Osato, M S; Robinson, N M

    1992-08-15

    The use of collagen shields soaked in various combinations of medications has been advocated to enhance drug delivery to the cornea. Recently, severe corneal toxicity associated with aggregate formation in mixtures of gentamicin and methylprednisolone prompted our study of the effect of drug concentration, pH, and temperature on the solubility of several antibiotic and corticosteroid formulations commonly used to treat ocular disease. Selected combinations of cefazolin, vancomycin, tobramycin, gentamicin, methylprednisolone, and dexamethasone were evaluated. Mixtures of tobramycin and vancomycin produced no precipitates, but many spheroid aggregates were seen when methylprednisolone and gentamicin were combined. Although the effects of precipitate formation on drug bioavailability and toxicity have not been fully determined, until such information is available, the use of combinations of drugs that remain in solution during administration is recommended. PMID:1642298

  20. 78 FR 13050 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-26

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Docket Numbers:...

  1. Unrewarded Object Combinations in Captive Parrots

    PubMed Central

    Auersperg, Alice Marie Isabel; Oswald, Natalie; Domanegg, Markus; Gajdon, Gyula Koppany; Bugnyar, Thomas

    2015-01-01

    In primates, complex object combinations during play are often regarded as precursors of functional behavior. Here we investigate combinatory behaviors during unrewarded object manipulation in seven parrot species, including kea, African grey parrots and Goffin cockatoos, three species previously used as model species for technical problem solving. We further examine a habitually tool using species, the black palm cockatoo. Moreover, we incorporate three neotropical species, the yellow- and the black-billed Amazon and the burrowing parakeet. Paralleling previous studies on primates and corvids, free object-object combinations and complex object-substrate combinations such as inserting objects into tubes/holes or stacking rings onto poles prevailed in the species previously linked to advanced physical cognition and tool use. In addition, free object-object combinations were intrinsically structured in Goffin cockatoos and in kea. PMID:25984564

  2. Self-Calibrating Respiratory-Flowmeter Combination

    NASA Technical Reports Server (NTRS)

    Westenskow, Dwayne R.; Orr, Joseph A.

    1990-01-01

    Dual flowmeters ensure accuracy over full range of human respiratory flow rates. System for measurement of respiratory flow employs two flowmeters; one compensates for deficiencies of other. Combination yields easily calibrated system accurate over wide range of gas flow.

  3. [Combined chemotherapy of disseminated skin melanoma].

    PubMed

    Dement'eva, N P; Voznyĭ, E K; Koroleva, L A

    1978-01-01

    The author's experience with nitrosomethylurea+prospidine treatment in 37 patients having disseminated melanoma is described. The mentioned scheme of the combination therapy is proved to be effective. PMID:741699

  4. Genetics Home Reference: combined pituitary hormone deficiency

    MedlinePlus

    ... People with combined pituitary hormone deficiency may have hypothyroidism, which is underactivity of the butterfly-shaped thyroid gland in the lower neck. Hypothyroidism can cause many symptoms, including weight gain and ...

  5. Combination Classes and "Hora de comunicacion."

    ERIC Educational Resources Information Center

    Eldredge, Dee L.

    1989-01-01

    Ways to combine small classes of higher education students studying Spanish at various levels are described, including judicious use of language laboratories, staggering of the different level groups, and rotation of activities geared toward students' individual proficiency levels. (CB)

  6. Novel Combination Treatments in Multiple Myeloma.

    PubMed

    Nooka, Ajay K; Lonial, Sagar

    2016-05-01

    The last decade has witnessed the identification of several novel druggable targets in multiple myeloma, leading to identification of novel therapies with clinically proven efficacy, both in the newly diagnosed and relapsed setting. More importantly, a common theme of good outcomes was observed among prospective randomized studies that have utilized combinations of agents with different mechanisms of action. The correlation between achieving a deeper response and the improvement in progression-free survival and overall survival has never been so clear. In this article, we elucidate the rationale for use of novel drug combinations in patients with myeloma, and review current evidence-based data supporting the use of specific combinations in various settings. We also attempt to craft a framework to guide clinicians in optimizing the use of combination therapies, to enable patients to derive maximal benefit. PMID:27188677

  7. 7 CFR 29.1008 - Combination symbols.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... tobacco. As applied to flue-cured tobacco, the combination symbols are XL—lug side, PO—oxidized primings...-bodied nondescript, LP—lemon (primings side), and FP—orange (primings side), KK-excessively scorched....

  8. REMOVAL OF METALS IN COMBINED TREATMENT SYSTEMS

    EPA Science Inventory

    This project assessed the variables influencing the removal of eight metals through combined industrial-municipal treatment plants. The eight metals investigated were: aluminum, cadmium, chromium, copper, iron, lead, nickel, and zinc. The metals were studied at subtoxic influent ...

  9. Synergistic combination of document security techniques

    NASA Astrophysics Data System (ADS)

    van Renesse, Rudolf L.

    2000-04-01

    The value of security features tends to decrease gradually, partly because of the continuously increasing ability of counterfeiters to counterfeit or imitate these features and partly because of the increasing capability and availability of equipment. As a countermeasure, numerous non-iridescent and iridescent optically variable devices (OVDs) are continuously being developed. The former comprise novel laser engraving techniques, the latter DOVIDs and ISISs. Although these novel techniques appear highly effective, there are indications that they are beginning to fail, not in the least because organized crime appears to have acquired some of those newer techniques. The response is the synergistic combination of those techniques, which combination expectedly remains beyond the capability of criminal organizations. This ongoing development is currently providing new and exciting security potential. Examples are combinations of diffractive and interference phenomena and of laser perforation techniques with OVDs. The latter combination provide strong protection against counterfeiting as well as forgery.

  10. Novel Combination Chemotherapy for Localized Ewing Sarcoma

    Cancer.gov

    In this clinical trial, researchers will test whether the addition of the drug combination vincristine, topotecan, and cyclophosphamide to a standard chemotherapy regimen improves overall survival in patients with extracranial Ewing

  11. 12 CFR 32.5 - Combination rules.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 1 2013-01-01 2013-01-01 false Combination rules. 32.5 Section 32.5 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY LENDING LIMITS § 32.5 Combination rules. (a) General rule. Loans or extensions of credit to one borrower will be attributed to another person and each person will be deemed a borrower—...

  12. 12 CFR 32.5 - Combination rules.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 1 2012-01-01 2012-01-01 false Combination rules. 32.5 Section 32.5 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY LENDING LIMITS § 32.5 Combination rules. (a) General rule. Loans or extensions of credit to one borrower will be attributed to another person and each person will be deemed a borrower—...

  13. A study of RSI under combined stresses

    NASA Technical Reports Server (NTRS)

    Kibler, J. J.; Rosen, B. W.

    1974-01-01

    The behavior of typical rigidized surface insulation material (RSI) under combined loading states was investigated. In particular, the thermal stress states induced during reentry of the space shuttle were of prime concern. A typical RSI tile was analyzed for reentry thermal stresses under computed thermal gradients for a model of the RSI material. The results of the thermal stress analyses were then used to aid in defining typical combined stress states for the failure analysis of RSI.

  14. Simulation of a combined-cycle engine

    NASA Technical Reports Server (NTRS)

    Vangerpen, Jon

    1991-01-01

    A FORTRAN computer program was developed to simulate the performance of combined-cycle engines. These engines combine features of both gas turbines and reciprocating engines. The computer program can simulate both design point and off-design operation. Widely varying engine configurations can be evaluated for their power, performance, and efficiency as well as the influence of altitude and air speed. Although the program was developed to simulate aircraft engines, it can be used with equal success for stationary and automative applications.

  15. Microwave Power Combiner With Switching Diodes

    NASA Technical Reports Server (NTRS)

    Conroy, B. L.; Postal, R. B.; Boreham, J. F.

    1986-01-01

    In multiple-port microwave power combiner, each of outputs of two or more power amplifiers of same frequency and phase passed to common output port separately or together. Each amplifier connected to combiner through switch consisting of resonant structures, radio-frequency chokes, and diode. Switches not only permit flexiblity in selection of amplifiers but isolate unused amplifiers from network, all while operating at relatively low power loss.

  16. Recent Advances in Combined Modality Therapy

    PubMed Central

    Nyati, Mukesh K.; Morgan, Meredith A.; Lawrence, Theodore S.

    2010-01-01

    Combined modality therapy emerged from preclinical data showing that carefully chosen drugs could enhance the sensitivity of tumor cells to radiation while having nonoverlapping toxicities. Recent advances in molecular biology involving the identification of cellular receptors, enzymes, and pathways involved in tumor growth and immortality have resulted in the development of biologically targeted drugs. This review highlights the recent clinical data in support of newer generation cytotoxic chemotherapies and systemic targeted agents in combination with radiation therapy. PMID:20413642

  17. Rifampin Combination Therapy for Nonmycobacterial Infections

    PubMed Central

    Forrest, Graeme N.; Tamura, Kimberly

    2010-01-01

    Summary: The increasing emergence of antimicrobial-resistant organisms, especially methicillin-resistant Staphylococcus aureus (MRSA), has resulted in the increased use of rifampin combination therapy. The data supporting rifampin combination therapy in nonmycobacterial infections are limited by a lack of significantly controlled clinical studies. Therefore, its current use is based upon in vitro or in vivo data or retrospective case series, all with major limitations. A prominent observation from this review is that rifampin combination therapy appears to have improved treatment outcomes in cases in which there is a low organism burden, such as biofilm infections, but is less effective when effective surgery to obtain source control is not performed. The clinical data support rifampin combination therapy for the treatment of prosthetic joint infections due to methicillin-sensitive S. aureus (MSSA) after extensive debridement and for the treatment of prosthetic heart valve infections due to coagulase-negative staphylococci. Importantly, rifampin-vancomycin combination therapy has not shown any benefit over vancomycin monotherapy against MRSA infections either clinically or experimentally. Rifampin combination therapy with daptomycin, fusidic acid, and linezolid needs further exploration for these severe MRSA infections. Lastly, an assessment of the risk-benefits is needed before the addition of rifampin to other antimicrobials is considered to avoid drug interactions or other drug toxicities. PMID:20065324

  18. Tailoring a Combination Preerythrocytic Malaria Vaccine

    PubMed Central

    Bauza, Karolis; Malinauskas, Tomas; Blagborough, Andrew M.; Reyes-Sandoval, Arturo

    2015-01-01

    The leading malaria vaccine candidate, RTS,S, based on the Plasmodium falciparum circumsporozoite protein (CSP), will likely be the first publicly adopted malaria vaccine. However, this and other subunit vaccines, such as virus-vectored thrombospondin-related adhesive protein (TRAP), provide only intermediate to low levels of protection. In this study, the Plasmodium berghei homologues of antigens CSP and TRAP are combined. TRAP is delivered using adenovirus- and vaccinia virus-based vectors in a prime-boost regime. Initially, CSP is also delivered using these viral vectors; however, a reduction of anti-CSP antibodies is seen when combined with virus-vectored TRAP, and the combination is no more protective than either subunit vaccine alone. Using an adenovirus-CSP prime, protein-CSP boost regime, however, increases anti-CSP antibody titers by an order of magnitude, which is maintained when combined with virus-vectored TRAP. This combination regime using protein CSP provided 100% protection in C57BL/6 mice compared to no protection using virus-vectored TRAP alone and 40% protection using adenovirus-CSP prime and protein-CSP boost alone. This suggests that a combination of CSP and TRAP subunit vaccines could enhance protection against malaria. PMID:26667840

  19. VLBI-SLR Combination Solution Using GEODYN

    NASA Astrophysics Data System (ADS)

    MacMillan, D. S.; Lemoine, F. G.; Chinn, D. S.; Pavlis, E. C.; Rowlands, D. D.

    2009-12-01

    The traditional procedure followed by the IERS for generating an ITRF is to perform a combination at the technique level. Each geodetic technique provides a solution that itself is a combination of the solutions produced by the technique analysis centers. Alternatively, we would like to generate a multi-technique solution using the same software and using the same a priori models. We seek to produce such a solution combining all of the geodetic techniques at the normal equation level using GEODYN but here, as a first step, consider only the SLR-VLBI combination. The data from each 24-hour VLBI session is initially processed to generate VLBI observation and solution parametrization files for input to GEODYN. Extensive tests have been performed to ensure that the VLBI theoretical delay as calculated by the VLBI Calc/Solve software is the same (to 1 ps) as that calculated by GEODYN. Initially, we ran test solutions with GEODYN using only VLBI data to verify that VLBI solution results produced with GEODYN agree with results using Calc/Solve. Then we combine the VLBI normal equations in GEODYN with weekly SLR normal equations for the period 2004-2008 Lageos1/2 to estimate station positions and Earth orientation parameters. To connect the techniques, we apply the ground ties used by the IERS. Here we report on the results of the combination.

  20. SPS solid state antenna power combiner

    NASA Technical Reports Server (NTRS)

    Fitzsimmons, G. W.

    1980-01-01

    A concept for a solar power satellite antenna power combiner which utilizes solid state dc-rf converters is described. To avoid the power combining losses associated with circuit hybrids it is proposed that the power from multiple solid state amplifiers be combined by direct coupling of each amplifier's output to the radiating antenna structure. The selected power-combining antenna consists of a printed (metalized) microstrip circuit on a ceramic type dielectric substrate which is backed by a shallow lightweight aluminum cavity which sums the power of four microwave sources. The antenna behaves like two one-half wavelength slot-line antennas coupled together via their common cavity structure. A significant feature of the antenna configuration selected is that the radiated energy is summed to yield a single radiated output phase which represents the average insertion phase of the four power amplifiers. This energy may be sampled and, by comparison with the input signal, one can phase error correct to maintain the insertion phase of all solid state power combining modules at exactly the same value. This insures that the insertion phase of each SPS power combining antenna module is identical. An experiment verification program is described.

  1. Tailoring a Combination Preerythrocytic Malaria Vaccine.

    PubMed

    Bauza, Karolis; Atcheson, Erwan; Malinauskas, Tomas; Blagborough, Andrew M; Reyes-Sandoval, Arturo

    2015-01-01

    The leading malaria vaccine candidate, RTS,S, based on the Plasmodium falciparum circumsporozoite protein (CSP), will likely be the first publicly adopted malaria vaccine. However, this and other subunit vaccines, such as virus-vectored thrombospondin-related adhesive protein (TRAP), provide only intermediate to low levels of protection. In this study, the Plasmodium berghei homologues of antigens CSP and TRAP are combined. TRAP is delivered using adenovirus- and vaccinia virus-based vectors in a prime-boost regime. Initially, CSP is also delivered using these viral vectors; however, a reduction of anti-CSP antibodies is seen when combined with virus-vectored TRAP, and the combination is no more protective than either subunit vaccine alone. Using an adenovirus-CSP prime, protein-CSP boost regime, however, increases anti-CSP antibody titers by an order of magnitude, which is maintained when combined with virus-vectored TRAP. This combination regime using protein CSP provided 100% protection in C57BL/6 mice compared to no protection using virus-vectored TRAP alone and 40% protection using adenovirus-CSP prime and protein-CSP boost alone. This suggests that a combination of CSP and TRAP subunit vaccines could enhance protection against malaria. PMID:26667840

  2. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation.

    PubMed

    Li, Daofeng; Zhang, Bo; Xing, Xiaoyun; Wang, Ting

    2015-01-15

    DNA CpG methylation is a widespread epigenetic mark in high eukaryotes including mammals. DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and control of gene expression. Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to measure DNA methylation in a genome-wide fashion, making it possible to comprehensively investigate the role of DNA methylation. Several methods have been developed, such as Whole Genome Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS), and enrichment-based methods including Methylation Dependent ImmunoPrecipitation followed by sequencing (MeDIP-seq), methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq), methyltransferase-directed Transfer of Activated Groups followed by sequencing (mTAG), and Methylation-sensitive Restriction Enzyme digestion followed by sequencing (MRE-seq). These methods differ by their genomic CpG coverage, resolution, quantitative accuracy, cost, and software for analyzing the data. Among these, WGBS is considered the gold standard. However, it is still a cost-prohibitive technology for a typical laboratory due to the required sequencing depth. We found that by integrating two enrichment-based methods that are complementary in nature (i.e., MeDIP-seq and MRE-seq), we can significantly increase the efficiency of whole DNA methylome profiling. By using two recently developed computational algorithms (i.e., M&M and methylCRF), the combination of MeDIP-seq and MRE-seq produces genome-wide CpG methylation measurement at high coverage and high resolution, and robust predictions of differentially methylated regions. Thus, the combination of the two enrichment-based methods provides a cost-effective alternative to WGBS. In this article we describe both the experimental protocols for performing MeDIP-seq and MRE

  3. A combination approach to treating fungal infections

    PubMed Central

    Shrestha, Sanjib K.; Fosso, Marina Y.; Garneau-Tsodikova, Sylvie

    2015-01-01

    Azoles are antifungal drugs used to treat fungal infections such as candidiasis in humans. Their extensive use has led to the emergence of drug resistance, complicating antifungal therapy for yeast infections in critically ill patients. Combination therapy has become popular in clinical practice as a potential strategy to fight resistant fungal isolates. Recently, amphiphilic tobramycin analogues, C12 and C14, were shown to display antifungal activities. Herein, the antifungal synergy of C12 and C14 with four azoles, fluconazole (FLC), itraconazole (ITC), posaconazole (POS), and voriconazole (VOR), was examined against seven Candida albicans strains. All tested strains were synergistically inhibited by C12 when combined with azoles, with the exception of C. albicans 64124 and MYA-2876 by FLC and VOR. Likewise, when combined with POS and ITC, C14 exhibited synergistic growth inhibition of all C. albicans strains, except C. albicans MYA-2876 by ITC. The combinations of FLC-C14 and VOR-C14 showed synergistic antifungal effect against three C. albicans and four C. albicans strains, respectively. Finally, synergism between C12/C14 and POS were confirmed by time-kill and disk diffusion assays. These results suggest the possibility of combining C12 or C14 with azoles to treat invasive fungal infections at lower administration doses or with a higher efficiency. PMID:26594050

  4. Bayesian active learning for drug combinations.

    PubMed

    Park, Mijung; Nassar, Marcel; Vikalo, Haris

    2013-11-01

    The dynamics of complex diseases are governed by intricate interactions of myriad factors. Drug combinations, formed by mixing several single-drug treatments at various doses, can enhance the effectiveness of the therapy by targeting multiple contributing factors. The main challenge in designing drug combinations is the highly nonlinear interaction of the constituent drugs. Prior work focused on guided space-exploratory heuristics that require discretization of drug doses. While being more efficient than random sampling, these methods are impractical if the drug space is high dimensional or if the drug sensitivity is unknown. Furthermore, the effectiveness of the obtained combinations may decrease if the resolution of the discretization grid is not sufficiently fine. In this paper, we model the biological system response to a continuous combination of drug doses by a Gaussian process (GP). We perform closed-loop experiments that rely on the expected improvement criterion to efficiently guide the exploration process toward drug combinations with the optimal response. When computing the criterion, we marginalize out the GP hyperparameters in a fully Bayesian manner using a particle filter. Finally, we employ a hybrid Monte Carlo algorithm to rapidly explore the high-dimensional continuous search space. We demonstrate the effectiveness of our approach on a fully factorial Drosophila dataset, an antiviral drug dataset for Herpes simplex virus type 1, and simulated human Apoptosis networks. The results show that our approach significantly reduces the number of required trials compared to existing methods. PMID:23846437

  5. Analysis of drug combinations: current methodological landscape

    PubMed Central

    Foucquier, Julie; Guedj, Mickael

    2015-01-01

    Combination therapies exploit the chances for better efficacy, decreased toxicity, and reduced development of drug resistance and owing to these advantages, have become a standard for the treatment of several diseases and continue to represent a promising approach in indications of unmet medical need. In this context, studying the effects of a combination of drugs in order to provide evidence of a significant superiority compared to the single agents is of particular interest. Research in this field has resulted in a large number of papers and revealed several issues. Here, we propose an overview of the current methodological landscape concerning the study of combination effects. First, we aim to provide the minimal set of mathematical and pharmacological concepts necessary to understand the most commonly used approaches, divided into effect-based approaches and dose–effect-based approaches, and introduced in light of their respective practical advantages and limitations. Then, we discuss six main common methodological issues that scientists have to face at each step of the development of new combination therapies. In particular, in the absence of a reference methodology suitable for all biomedical situations, the analysis of drug combinations should benefit from a collective, appropriate, and rigorous application of the concepts and methods reviewed here. PMID:26171228

  6. Combined therapy in the treatment of dyslipidemia.

    PubMed

    Reiner, Zeljko

    2010-02-01

    This systematic review analyses the efficacy, tolerability and safety of combinations of different medicines used to treat dyslipidemias in clinical practice. A PubMed search up to January 2009, was conducted to identify relevant studies. Criteria used to identify studies included (1) English language, (2) published studies with original data or meta-analyses in peer-reviewed journals. Although statin treatment is a mainstay of dyslipidemia management today, complementary effects of other lipid-lowering and/or HDL-cholesterol-raising therapies might substantially increase the clinical benefits not only in the small minority of patients with severe dyslipidemias but in others as well. These therapies include combinations with bile acid sequestrants (cholestyramine, colestipol, colesevelam), ezetimibe, niacin, plant sterols, fibrates (fenofibrate, bezafibrate, gemfibrozil), and prescription omega-3 fatty acids. Therapeutic approaches which incorporate the use of multiple drugs combinations for dyslipidemia treatment should be more widely adopted since combination therapy might offer a means to increase the number of patients able to meet their lipoprotein goals according to the guidelines. However, it has to be stated that for most of these combination therapies data on cardiovascular outcomes are still lacking. PMID:19682080

  7. Geometry-free linear combinations for Galileo

    NASA Astrophysics Data System (ADS)

    Henkel, Patrick

    2009-11-01

    Global navigation satellites of the European Galileo system transmit code signals on four carriers in the L1, E5a, E5b and E6 band. New geometry-free linear combinations are presented that eliminate the geometry terms (user to satellite ranges and orbital errors), the clock errors of the user and satellites and the tropospheric delay. The remaining parameters of these carrier phase combinations include integer ambiguities, ionospheric delays, carrier phase multipath and phase noise. The weighting coefficients are designed such that the integer nature of ambiguities is maintained. The use of four frequency combinations is highly recommended due to a noise reduction of up to 14.4 dB and an ionospheric reduction of up to 25.6 dB compared to two frequency geometry-free combinations. Moreover, a modified Least-squares Ambiguity Decorrelation Adjustment (LAMBDA) algorithm is suggested, which differs in two points from the traditional approach: the baseline is replaced by the ionospheric delay and the correlation is caused by linear combinations instead of double differences. For correct ambiguity resolution, the ionospheric delay can be determined with millimeter accuracy. This is quite beneficial as the ionosphere represents the largest source of error for absolute positioning.

  8. A combined cycle engine test facility

    NASA Astrophysics Data System (ADS)

    Engers, R.; Cresci, D.; Tsai, C.

    Rocket-Based Combined-Cycle (RBCC) engines intended for missiles and/or space launch applications incorporate features of rocket propulsion systems operating in concert with airbreathing engine cycles. Performance evaluation of these types of engines, which are intended to operate from static sea level take-off to supersonic cruise or accerlerate to orbit, requires ground test capabilities which integrate rocket component testing with airbreathing engine testing. A combined cycle engine test facility has been constructed in the General Applied Science Laboratories, Inc. (GASL) Aeropropulsion Test Laboratory to meet this requirement. The facility was designed to support the development of an innovative combined cycle engine concept which features a rocket based ramjet combustor. The test requirements included the ability to conduct tests in which the propulsive force was generated by rocket only, the ramjet only and simultaneous rocket and ramjet power (combined cycle) to evaluate combustor operation over the entire engine cycle. The test facility provides simulation over the flight Mach number range of 0 to 8 and at various trajectories. The capabilities of the combined cycle engine test facility are presented.

  9. A combination approach to treating fungal infections.

    PubMed

    Shrestha, Sanjib K; Fosso, Marina Y; Garneau-Tsodikova, Sylvie

    2015-01-01

    Azoles are antifungal drugs used to treat fungal infections such as candidiasis in humans. Their extensive use has led to the emergence of drug resistance, complicating antifungal therapy for yeast infections in critically ill patients. Combination therapy has become popular in clinical practice as a potential strategy to fight resistant fungal isolates. Recently, amphiphilic tobramycin analogues, C12 and C14, were shown to display antifungal activities. Herein, the antifungal synergy of C12 and C14 with four azoles, fluconazole (FLC), itraconazole (ITC), posaconazole (POS), and voriconazole (VOR), was examined against seven Candida albicans strains. All tested strains were synergistically inhibited by C12 when combined with azoles, with the exception of C. albicans 64124 and MYA-2876 by FLC and VOR. Likewise, when combined with POS and ITC, C14 exhibited synergistic growth inhibition of all C. albicans strains, except C. albicans MYA-2876 by ITC. The combinations of FLC-C14 and VOR-C14 showed synergistic antifungal effect against three C. albicans and four C. albicans strains, respectively. Finally, synergism between C12/C14 and POS were confirmed by time-kill and disk diffusion assays. These results suggest the possibility of combining C12 or C14 with azoles to treat invasive fungal infections at lower administration doses or with a higher efficiency. PMID:26594050

  10. Canadian Forum on Combined Organ Transplantation.

    PubMed

    Cantarovich, Marcelo; Blydt-Hansen, Tom D; Gill, John; Tinckam, Kathryn; Schiff, Jeffrey; Alwayn, Ian; Bain, Vince; Dipchand, Anne I; Isaac, Debra; Kim, S Joseph; Lien, Dale; Zaltzman, Jeffrey; Young, Kimberly; Nickerson, Peter

    2016-06-01

    The Canadian Society of Transplantation and Canadian Blood Services conducted a consensus forum on combined renal/nonrenal transplants, as they are not part of Canadian organ-specific allocation models at present. The purpose of this initiative was to make recommendations, develop eligibility criteria, and a decision-making model on listing and allocation. Forty-two participants with expertise in combined transplantation participated in the consensus forum. The United States and Canadian data were reviewed. The consensus forum made recommendations regarding the following: (1) investigation of etiology, severity, duration, and level of renal dysfunction; (2) documentation of degree of nonreversible kidney injury; (3) eligibility for combined (either simultaneous or staged) transplantation; (4) research. Key recommendations were: (1) patients with end-stage nonrenal disease with estimated glomerular filtration rate less than 30 mL/min per 1.73 m for longer than 1 month or on dialysis less than 3 months, who fulfill criteria for nonreversibility of renal dysfunction (by level and duration of renal dysfunction, imaging, and pathology findings), would be eligible for combined renal/nonrenal transplantation; (2) patients on dialysis longer than 3 months would be eligible for combined renal/nonrenal transplantation; (3) staged renal after nonrenal transplantation with subsequent prioritized allocation of renal transplant was endorsed in selected cases. The validation and impact of these recommendations on allocation will require further studies. PMID:26588007

  11. A combined cycle engine test facility

    SciTech Connect

    Engers, R.; Cresci, D.; Tsai, C.

    1995-09-01

    Rocket-Based Combined-Cycle (RBCC) engines intended for missiles and/or space launch applications incorporate features of rocket propulsion systems operating in concert with airbreathing engine cycles. Performance evaluation of these types of engines, which are intended to operate from static sea level take-off to supersonic cruise or accerlerate to orbit, requires ground test capabilities which integrate rocket component testing with airbreathing engine testing. A combined cycle engine test facility has been constructed in the General Applied Science Laboratories, Inc. (GASL) Aeropropulsion Test Laboratory to meet this requirement. The facility was designed to support the development of an innovative combined cycle engine concept which features a rocket based ramjet combustor. The test requirements included the ability to conduct tests in which the propulsive force was generated by rocket only, the ramjet only and simultaneous rocket and ramjet power (combined cycle) to evaluate combustor operation over the entire engine cycle. The test facility provides simulation over the flight Mach number range of 0 to 8 and at various trajectories. The capabilities of the combined cycle engine test facility are presented.

  12. Combination of Face Regions in Forensic Scenarios.

    PubMed

    Tome, Pedro; Fierrez, Julian; Vera-Rodriguez, Ruben; Ortega-Garcia, Javier

    2015-07-01

    This article presents an experimental analysis of the combination of different regions of the human face on various forensic scenarios to generate scientific knowledge useful for the forensic experts. Three scenarios of interest at different distances are considered comparing mugshot and CCTV face images using MORPH and SC face databases. One of the main findings is that inner facial regions combine better in mugshot and close CCTV scenarios and outer facial regions combine better in far CCTV scenarios. This means, that depending of the acquisition distance, the discriminative power of the facial regions change, having in some cases better performance than the full face. This effect can be exploited by considering the fusion of facial regions which results in a very significant improvement of the discriminative performance compared to just using the full face. PMID:26189995

  13. Spinal hemangioblastoma combined with pilocytic astrocytoma.

    PubMed

    Li, Wei-Qing; Wang, Xiang; Zhong, Nan-Zhe; Li, Yi-Ming

    2015-07-01

    The combination of vascular anomalies with gliomas is rarely seen in the CNS, and is defined as "angioglioma". However, the definition, category, and histopathogenesis of angiogliomas remain controversial. Here, we present an unusual case of spinal hemangioblastoma (HB) combined with pilocytic astrocytoma (PA). Spinal MRI revealed lesions extending from T9 to T12 segments, in a "sandwich-like" fashion. After resection of the tumor, histopathologic study confirmed the diagnosis of HB as well as PA. A comprehensive review of the literature was further conducted. We describe a case of spinal HB combined with PA, in addition we discuss the clinicopathological relationship between HB and PA under these conditions, which may facilitate the understanding of the histogenesis of an angioglioma and guide its diagnosis and treatment. PMID:26166599

  14. [Combined spinal and epidural analgesia in urology].

    PubMed

    Bovianska, N

    1995-01-01

    Combined spinal and epidural analgesia is a new concept in the field of regional anesthesia. It combines the positive qualities of spinal and epidural analgesia, and is performed by the "needle-in-needle" technique, described in the paper. This type of analgesia is practically implemented in the Clinical Center of Urology over the past few months, and shows encouraging results. This is a report on clinical experience had with 10 combined analgesia procedures, running a course free of any complications against the background of stable hemodynamics and respiration of the patients. The block induced is with 4-hour duration, and lends itself to prolongation through an epidural catheter. This renders the method variable and suited for postoperative analgesia too. The Espokan set technical devices used make puncture of the spinal-epidural space readily practicable. PMID:8648963

  15. On the combination procedure of correlated errors

    NASA Astrophysics Data System (ADS)

    Erler, Jens

    2015-09-01

    When averages of different experimental determinations of the same quantity are computed, each with statistical and systematic error components, then frequently the statistical and systematic components of the combined error are quoted explicitly. These are important pieces of information since statistical errors scale differently and often more favorably with the sample size than most systematical or theoretical errors. In this communication we describe a transparent procedure by which the statistical and systematic error components of the combination uncertainty can be obtained. We develop a general method and derive a general formula for the case of Gaussian errors with or without correlations. The method can easily be applied to other error distributions, as well. For the case of two measurements, we also define disparity and misalignment angles, and discuss their relation to the combination weight factors.

  16. Statin combination therapy and cardiovascular risk reduction.

    PubMed

    Toth, Peter P; Farnier, Michel; Tomassini, Joanne E; Foody, JoAnne M; Tershakovec, Andrew M

    2016-05-01

    In numerous clinical trials, lowering LDL-C with statin therapy has been demonstrated to reduce the risk of cardiovascular disease (CVD) in primary and secondary prevention settings. Guidelines recommend statins for first-line therapy in cholesterol-lowering management of patients with CVD risk. Despite increased statin monotherapy use over the last decade, a number of patients with high CVD risk do not achieve optimal LDL-C lowering. Guidelines recommend consideration of statin combination therapy with nonstatin agents for these patients. However, combination therapy approaches have been hampered by neutral findings. Recently, ezetimibe added to simvastatin therapy reduced cardiovascular events in acute coronary syndrome patients, more than simvastatin alone. This article provides an overview of various agents in combination with statin therapy on cardiovascular outcomes. Other lipid-lowering agents in development, including PCSK9 and CETP inhibitors in development, are also described. PMID:27079178

  17. Combination therapy for metastatic renal cell carcinoma

    PubMed Central

    Buonerba, Carlo; Di Lorenzo, Giuseppe

    2016-01-01

    Current therapy for metastatic clear cell renal cell carcinoma (RCC) consists of the serial administration of single agents. Combinations of VEGF and mTOR inhibitors have been disappointing in previous randomized trials. However, the combination of lenvatinib, a multitargeted agent that inhibits VEGF as well as FGF receptors, and everolimus demonstrated promising results in a randomized phase II trial. Moreover, the emergence of programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) inhibitors has spawned the investigation of combinations of these agents with VEGF inhibitors and cytotoxic T-lymphocyte antigen 4 (CTLA-4) inhibitors. These ongoing phase III trials in conjunction with the development of predictive biomarkers and agents inhibiting novel therapeutic targets may provide much needed advances in this still largely incurable disease. PMID:27047959

  18. Combined bending-torsion fatigue reliability. III

    NASA Technical Reports Server (NTRS)

    Kececioglu, D.; Chester, L. B.; Nolf, C. F., Jr.

    1975-01-01

    Results generated by three, unique fatigue reliability research machines which can apply reversed bending loads combined with steady torque are presented. AISI 4340 steel, grooved specimens with a stress concentration factor of 1.42 and 2.34, and Rockwell C hardness of 35/40 were subjected to various combinations of these loads and cycled to failure. The generated cycles-to-failure and stress-to-failure data are statistically analyzed to develop distributional S-N and Goodman diagrams. Various failure theories are investigated to determine which one represents the data best. The effects of the groove, and of the various combined bending-torsion loads, on the S-N and Goodman diagrams are determined. Two design applications are presented which illustrate the direct useability and value of the distributional failure governing strength and cycles-to-failure data in designing for specified levels of reliability and in predicting the reliability of given designs.

  19. Combined Confocal and Magnetic Resonance Microscopy

    SciTech Connect

    Wind, Robert A.; Majors, Paul D.; Minard, Kevin R.; Ackerman, Eric J.; Daly, Don S.; Holtom, Gary R.; Thrall, Brian D.; Weber, Thomas J.

    2002-05-12

    Confocal and magnetic resonance microscopy are both used to study live cells in a minimally invasive way. Both techniques provide complementary information. Therefore, by examining cells simultaneously with both methodologies, more detailed information is obtained than is possible with each of the microscopes individually. In this paper two configurations of a combined confocal and magnetic resonance microscope described. In both cases the sample compartment is part of a temperature regulated perfusion system. The first configuration is capable of studying large single cells or three-dimensional cell agglomerates, whereas with the second configuration monolayers of mammalian cells can be investigated . Combined images are shown of Xenopus laevis frog oocytes, model JB6 tumor spheroids, and a single layer of Chinese hamster ovary cells. Finally, potential applications of the combined microscope are discussed.

  20. Spinal hemangioblastoma combined with pilocytic astrocytoma

    PubMed Central

    Li, Wei-Qing; Wang, Xiang; Zhong, Nan-Zhe; Yi-Li, Ming

    2015-01-01

    The combination of vascular anomalies with gliomas is rarely seen in the CNS, and is defined as ‘angioglioma’. However, the definition, category, and histopathogenesis of angiogliomas remain controversial. Here, we present an unusual case of spinal hemangioblastoma (HB) combined with pilocytic astrocytoma (PA). Spinal MRI revealed lesions extending from T9 to T12 segments, in a “sandwich-like” fashion. After resection of the tumor, histopathologic study confirmed the diagnosis of HB as well as PA. A comprehensive review of the literature was further conducted. We describe a case of spinal HB combined with PA, in addition we discuss the clinicopathological relationship between HB and PA under these conditions, which may facilitate the understanding of the histogenesis of an angioglioma and guide its diagnosis and treatment. PMID:26166599

  1. Radial/axial power divider/combiner

    NASA Technical Reports Server (NTRS)

    Vaddiparty, Yerriah P. (Inventor)

    1987-01-01

    An electromagnetic power divider/combiner comprises N radial outputs (31) having equal powers and preferably equal phases, and a single axial output (20). A divider structure (1) and a preferably identical combiner structure (2) are broadside coupled across a dielectric substrate (30) containing on one side the network of N radial outputs (31) and on its other side a set of N equispaced stubs (42) which are capacitively coupled through the dielectric substrate (30) to the N radial outputs (31). The divider structure (1) and the combiner structure (2) each comprise a dielectric disk (12, 22, respectively) on which is mounted a set of N radial impedance transformers (14, 24, respectively). Gross axial coupling is determined by the thickness of the dielectric layer (30). Rotating the disks (12, 22) with respect to each other effectuates fine adjustment in the degree of axial coupling.

  2. Antibiotic combinations: should they be tested?

    PubMed Central

    Eliopoulos, G M; Eliopoulos, C T

    1988-01-01

    When antibiotic combinations are used to provide a broader spectrum of antimicrobial activity or in an attempt to prevent the emergence of resistant organisms, it is rarely necessary or practical to perform tests of drug interactions in vitro. In vitro testing of combinations may be useful when combinations are used in an attempt to attain synergistic interactions. In some cases, screening methods can be used as substitutes for formal synergy testing. This paper examines the mechanisms of antibiotic interaction leading to synergism or antagonism, surveys attempts to correlate in vitro observations with efficacy in animal models, and reviews clinical data providing evidence for or against a useful role of synergistic antibiotic interactions in the treatment of human infections. PMID:3069193

  3. Combined mechanical loading of composite tubes

    NASA Technical Reports Server (NTRS)

    Derstine, Mark S.; Pindera, Marek-Jerzy; Bowles, David E.

    1988-01-01

    An analytical/experimental investigation was performed to study the effect of material nonlinearities on the response of composite tubes subjected to combined axial and torsional loading. The effect of residual stresses on subsequent mechanical response was included in the investigation. Experiments were performed on P75/934 graphite-epoxy tubes with a stacking sequence of (15/0/ + or - 10/0/ -15), using pure torsion and combined axial/torsional loading. In the presence of residual stresses, the analytical model predicted a reduction in the initial shear modulus. Experimentally, coupling between axial loading and shear strain was observed in laminated tubes under combined loading. The phenomenon was predicted by the nonlinear analytical model. The experimentally observed linear limit of the global shear response was found to correspond to the analytically predicted first ply failure. Further, the failure of the tubes was found to be path dependent above a critical load level.

  4. [Fixed-drug combinations for hypertension].

    PubMed

    Sato, Nobuyuki; Hasebe, Naoyuki

    2014-08-01

    The recent guidelines for the treatment of hypertension recommend a fixed-dose combination (polypill) therapy to achieve optimal blood pressure (BP) control. Among them, angiotensin receptor blockers (ARBs) with calcium channel blockers (CCBs) or diuretics are the representative recommended combination since each drug has evidence of reducing cardiovascular events. Recent studies using ambulatory blood pressure monitoring have also suggested that the fixed-dose ARB-based combination therapies with either CCBs or diuretics are well tolerated and effectively lower the BP throughout a 24-hour interval by their long-acting half-lives, nighttime BP lowering effect and improving adherence. It will become more important to use these fixed-dose antihypertensive drugs adequately for controlling the 24-hour blood pressure. PMID:25167756

  5. Eigenvalue Detonation of Combined Effects Aluminized Explosives

    NASA Astrophysics Data System (ADS)

    Capellos, Christos; Baker, Ernest; Balas, Wendy; Nicolich, Steven; Stiel, Leonard

    2007-06-01

    This paper reports on the development of theory and performance for recently developed combined effects aluminized explosives. Traditional high energy explosives used for metal pushing incorporate high loading percentages of HMX or RDX, whereas blast explosives incorporate some percentage of aluminum. However, the high blast explosives produce increased blast energies, with reduced metal pushing capability due to late time aluminum reaction. Metal pushing capability refers to the early volume expansion work produced during the first few volume expansions associated with cylinder wall velocities and Gurney energies. Our Recently developed combined effects aluminized explosives (PAX-29C, PAX-30, PAX-42) are capable of achieving excellent metal pushing and high blast energies. Traditional Chapman-Jouguet detonation theory does not explain the observed detonation states achieved by these combined effects explosives. This work demonstrates, with the use of cylinder expansion data and thermochemical code calculations (JAGUAR and CHEETAH), that eigenvalue detonation theory explains the observed behavior.

  6. Combined use of ECT with aripiprazole.

    PubMed

    Lopez-Garcia, Pilar; Chiclana, Carlos; Gonzalez, Rafael

    2009-01-01

    This case report is on the combined use of electroconvulsive treatment (ECT) with a partial dopamine agonist, aripiprazole, in the treatment of a 30-year-old man with chronic and refractory paranoid schizophrenia. The patient had been under high doses of typical and atypical antipsychotics with a lack of control of the symptoms, characterized by agitation, suspiciousness, and obsessive fears. ECT therapy was started while receiving antipsychotic treatment and aripiprazole was added to the pharmacological treatment after six sessions of ECT. The convulsive threshold and the seizure duration did not significantly change after the treatment with aripiprazole was initiated. There was a clinical improvement after the combined treatment with ECT and aripiprazole and the combination was well tolerated. PMID:17853257

  7. Mixture dynamics: Combination therapy in oncology.

    PubMed

    Gabrielsson, Johan; Gibbons, Francis D; Peletier, Lambertus A

    2016-06-10

    In recent years combination therapies have become increasingly popular in most therapeutic areas. We present a qualitative and quantitative approach and elucidate some of the challenges and solutions to a more optimal therapy. For tumor growth this involves the study of semi-mechanistic cell-growth/kill models with multiple sites of action. We introduce such models and analyze their dynamic properties using simulations and mathematical analysis. This is done for two specific case studies, one involving a single compound and one a combination of two compounds. We generalize the notion of Tumor Static Concentration to cases when two compounds are involved and develop a graphical method for determining the optimal combination of the two compounds, using ideas akin to those used in studies employing isobolograms. In studying the dynamics of the second case study we focus, not only on the different concentrations, but also on the different dosing regimens and pharmacokinetics of the two compounds. PMID:27050307

  8. Coherent combination of ultrafast fiber amplifiers

    NASA Astrophysics Data System (ADS)

    Hanna, Marc; Guichard, Florent; Zaouter, Yoann; Papadopoulos, Dimitris N.; Druon, Frédéric; Georges, Patrick

    2016-03-01

    We review recent progress in coherent combining of femtosecond pulses amplified in optical fibers as a way to scale the peak and average power of ultrafast sources. Different methods of achieving coherent pulse addition in space (beam combining) and time (divided pulse amplification) domains are described. These architectures can be widely classified into active methods, where the relative phases between pulses are subject to a servomechanism, and passive methods, where phase matching is inherent to the geometry. Other experiments that combine pulses with different spectral contents, pulses that have been nonlinearly broadened or successive pulses from a mode-locked laser oscillator, are then presented. All these techniques allow access to unprecedented parameter range for fiber ultrafast sources.

  9. Optimizing neurotrophic factor combinations for neurite outgrowth

    NASA Astrophysics Data System (ADS)

    Deister, C.; Schmidt, C. E.

    2006-06-01

    Most neurotrophic factors are members of one of three families: the neurotrophins, the glial cell-line derived neurotrophic factor family ligands (GFLs) and the neuropoietic cytokines. Each family activates distinct but overlapping cellular pathways. Several studies have shown additive or synergistic interactions between neurotrophic factors from different families, though generally only a single combination has been studied. Because of possible interactions between the neurotrophic factors, the optimum concentration of a factor in a mixture may differ from the optimum when applied individually. Additionally, the effect of combinations of neurotrophic factors from each of the three families on neurite extension is unclear. This study examines the effects of several combinations of the neurotrophin nerve growth factor (NGF), the GFL glial cell-line derived neurotrophic factor (GDNF) and the neuropoietic cytokine ciliary neurotrophic factor (CNTF) on neurite outgrowth from young rat dorsal root ganglion (DRG) explants. The combination of 50 ng ml-1 NGF and 10 ng ml-1 of each GDNF and CNTF induced the highest level of neurite outgrowth at a 752 ± 53% increase over untreated DRGs and increased the longest neurite length to 2031 ± 97 µm compared to 916 ± 64 µm for untreated DRGs. The optimum concentrations of the three factors applied in combination corresponded to the optimum concentration of each factor when applied individually. These results indicate that the efficacy of future therapies for nerve repair would be enhanced by the controlled release of a combination of neurotrophins, GFLs and neuropoietic cytokines at higher concentrations than used in previous conduit designs.

  10. Combining antipsychotics; is this strategy useful?

    PubMed

    Christy, Jill; Burnside, David; Agius, Mark

    2014-11-01

    Antipsychotic drugs are commonly combined in psychiatric practice in an attempt to treat schizophrenia. Such practice is widespread, despite the lack of explicit endorsement by many of the main regulatory bodies. There are varying rationales behind combining these potent drugs-either to augment the effect of a drug whose action alone is inadequate for patients with treatment resistant schizophrenia (TRS), or to improve the side effects seen due to treatment. Augmentations are most frequently observed with clozapine, a drug reserved for use when other antipsychotic medications have failed. Several drugs have been chosen as adjuvants, including aripiprazole, sulpiride, amisulpiride and risperidone. A small number of RCTs (randomized controlled trials) have been performed but, despite this data and numerous case reports showing positive changes in symptomatology, Cochrane reviews of available studies have been unable to definitively confirm the efficacy of these combinations, frequently citing the need for larger, longer term, prospective studies.Evidence for benefits of combination therapy on side effects is also inadequate. Some RCTs and case series have shown they can positively alter side effects due to drugs such as clozapine, e.g. metabolic side effects. However, despite many of the combinations being relatively well tolerated, there is some evidence they can cause adverse effects of their own. More evidence is essential as, on the current data alone, it is not possible to make a firm recommendation on the efficacy and safety of antipsychotic combinations. In addition it is vital that the importance of a fair trial of monotherapy at adequate dosages is reinforced to clinicians, so that patients are not put onto these relatively unknown treatment strategies unnecessarily. PMID:25413558

  11. Potential Outcome Factors in Subacute Combined Degeneration

    PubMed Central

    Vasconcelos, Olavo M; Poehm, Erika H; McCarter, Robert J; Campbell, William W; Quezado, Zenaide M N

    2006-01-01

    BACKGROUND Subacute combined degeneration is an acquired myelopathy caused by vitamin B12 deficiency. Therapy with B12 leads to improvement in most but to complete recovery in only a few patients. Prognostic indicators in subacute combined degeneration are unknown; therefore, predicting complete recovery of neurologic deficits is challenging. PURPOSE To identify potential correlates of outcome and to generate hypotheses concerning predictors of complete resolution of neurologic deficits in subacute combined degeneration. DATA SOURCE We searched EMBASE (1974 to October 2005), MEDLINE (1968 to October 2005), and references from identified reports. REPORTS SELECTION Reports of patients with subacute combined degeneration containing results of magnetic resonance imaging (MRI) and description of outcome and 1 patient treated by the authors. DATA EXTRACTION, SYNTHESIS We extracted data from 45 reports and 57 patients (36 males, 21 females; age range: 10 to 81) with a diagnosis of subacute combined degeneration, and estimated the strength of association between clinical, laboratory, and radiological factors and complete resolution of signs and symptoms. RESULTS Eight patients (14%) achieved clinical resolution and 49 (86%) improved with B12 therapy. The absence of sensory dermatomal deficit, Romberg, and Babinski signs were associated with a higher complete resolution rate. Patients with MRI lesions in ≤7 segments and age less than 50 also appear to have higher rates of complete resolution. CONCLUSIONS B12 therapy is reported to stop progression and improve neurologic deficits in most patients with subacute combined degeneration. However, complete resolution only occurs in a small percentage of patients and appears to be associated with factors suggestive of less severe disease at the time of diagnosis. PMID:16970556

  12. Choosing a combined oral contraceptive pill

    PubMed Central

    Stewart, Mary; Black, Kirsten

    2015-01-01

    Summary The combined oral contraceptive pill is an effective contraceptive method which can also offer other benefits. However, other contraceptive options should be discussed. If the pill is the chosen method, prescribe a pill with the lowest effective dose of oestrogen and progestogen. Pills containing levonorgestrel or norethisterone in combination with ethinyloestradiol 35 microgram or less are considered first-line. They are effective if taken correctly, have a relatively low risk of venous thromboembolism, and are listed on the Pharmaceutical Benefits Scheme. The pill is usually taken in a monthly cycle. Some women may prefer an extended pill regimen with fewer or no inactive pills. PMID:26648603

  13. [Combined action of caffeine and sydnocarb].

    PubMed

    Zakusov, V V; Tozhanova, N M

    1983-08-01

    Combined application of two stimulants caffeine and sydnocarb (a sydnonimine derivative) was studied in rabbits, rats and mice using the method of summation of impulses in the central nervous system, the method of conditioned avoidance response, forced swimming and hexobarbital sleep in order to find out the changes in their main and side effects. It was established that the main stimulant effect of the drug combination given in optimal doses appeared to be additive, while side effects on the ECG and blood pressure remained unchanged. PMID:6136303

  14. EARS, MARS combined radio observations - 2014

    NASA Astrophysics Data System (ADS)

    Tomezzoli, Giancarlo

    2014-02-01

    The Lyrid meteor shower was generated on 21-22 April 2014 by the passage of the Earth through the path of the debris of the comet C/1861 G1 (Thatcher). The Camelopardalids meteor shower was generated on 23-24 May 2014 by the passage of the Earth through the path of the debris of the comet 209P/Linear. The EurAstro Radio Station (EARS) and the Malta Astro Radio Station (MARS) were operated in parallel for two combined radio observation campaigns. The campaigns revealed that further combined radio observation campaigns are necessary to solve the problem of estimating the number of lost radio meteor echoes.

  15. Next ICRF: Single global solution versus combination

    NASA Astrophysics Data System (ADS)

    Yatskiv, Yaroslav; Malkin, Zinovy

    2007-09-01

    Two approaches to generate the ICRF-2 are compared. The first approach, which has been used for the creation of the current ICRF realization, implies computation of the radio source positions in a single analysis center making use of the most advanced models, software and analysis strategy. However, the latter cannot guarantee that the reference frame is free of systematic errors. The second approach is based on combination of several CRF realizations after investigation and accounting for their stochastic and systematic errors. This procedure is intended to mitigate the systematic errors and improve the precision of the final combined solution. In this presentation, the advantages and shortcomings of both the approaches are discussed.

  16. Tendon Transfers for Combined Peripheral Nerve Injuries.

    PubMed

    Makarewich, Christopher A; Hutchinson, Douglas T

    2016-08-01

    Combined peripheral nerve injuries present a unique set of challenges to the hand surgeon when considering tendon transfers. They are often associated with severe soft tissue trauma, including lacerations to remaining innervated muscles and tendons, significant scar formation, and substantial sensory loss. In the case of combined nerve injuries, there are typically fewer options for tendon transfers due to fewer tendons of shared function that are expendable as well as associated injuries to tendon or muscle bellies. As such, careful preoperative planning must be performed to make the most of remaining muscle tendon units. PMID:27387081

  17. Raman beam combining for laser brightness enhancement

    SciTech Connect

    Dawson, Jay W.; Allen, Graham S.; Pax, Paul H.; Heebner, John E.; Sridharan, Arun K.; Rubenchik, Alexander M.; Barty, Chrisopher B. J.

    2015-10-27

    An optical source capable of enhanced scaling of pulse energy and brightness utilizes an ensemble of single-aperture fiber lasers as pump sources, with each such fiber laser operating at acceptable pulse energy levels. Beam combining involves stimulated Raman scattering using a Stokes' shifted seed beam, the latter of which is optimized in terms of its temporal and spectral properties. Beams from fiber lasers can thus be combined to attain pulses with peak energies in excess of the fiber laser self-focusing limit of 4 MW while retaining the advantages of a fiber laser system of high average power with good beam quality.

  18. Combination neutron-gamma ray detector

    DOEpatents

    Stuart, Travis P.; Tipton, Wilbur J.

    1976-10-26

    A radiation detection system capable of detecting neutron and gamma events and distinguishing therebetween. The system includes a detector for a photomultiplier which utilizes a combination of two phosphor materials, the first of which is in the form of small glass beads which scintillate primarily in response to neutrons and the second of which is a plastic matrix which scintillates in response to gammas. A combination of pulse shape and pulse height discrimination techniques is utilized to provide an essentially complete separation of the neutron and gamma events.

  19. [When to propose a combined surgery].

    PubMed

    Lachkar, Y

    2009-03-01

    Combined cataract and glaucoma surgery is underused, generallly due to a fear of per- et postsurgical complications. It is a more difficult surgery than simple phacoemulsification, but its benefit on intraocular pressure is established and is maintained over the time (at the difference of phacoemulsification), and permit to preserve the visual field. Optimal surgical technique and adequate follow-up are able to limit postoperative complications. Guidelines published by the European Glaucoma Society (EGS) clearly defined the combined surgery indications: cataract, in a patient with glaucoma uncontrolled by medical treatment or treated with a burdensome multitherapy. PMID:19515339

  20. Sulfur capture in combination bark boilers

    SciTech Connect

    Someshwar, A.V.; Jain, A.K. )

    1993-07-01

    A review of sulfur dioxide emission data for eight combination bark boilers in conjunction with the sulfur contents of the fuels reveals significant sulfur capture ranging from 10% to over 80% within the solid ash phase. Wood ash characteristics similar to activated carbon as well as the significant wood ash alkali oxide and carbonate fractions are believed responsible for the sulfur capture. Sulfur emissions from combination bark-fossil fuel firing are correlated to the sulfur input per ton of bark or wood residue fired.

  1. Eigenvalue Detonation of Combined Effects Aluminized Explosives

    NASA Astrophysics Data System (ADS)

    Capellos, C.; Baker, E. L.; Nicolich, S.; Balas, W.; Pincay, J.; Stiel, L. I.

    2007-12-01

    Theory and performance for recently developed combined—effects aluminized explosives are presented. Our recently developed combined-effects aluminized explosives (PAX-29C, PAX-30, PAX-42) are capable of achieving excellent metal pushing, as well as high blast energies. Metal pushing capability refers to the early volume expansion work produced during the first few volume expansions associated with cylinder and wall velocities and Gurney energies. Eigenvalue detonation explains the observed detonation states achieved by these combined effects explosives. Cylinder expansion data and thermochemical calculations (JAGUAR and CHEETAH) verify the eigenvalue detonation behavior.

  2. Combined cycle comes to the Philippines

    SciTech Connect

    1995-03-01

    The first combined cycle power station in the Philippines has gone into operation at National Power Corporation`s (NPC) Limay Bataan site, some 40 km west of Manila. The plant comprises two 300 MW blocks in 3+3+1 configuration, based on ABB Type GT11N gas turbines. It was built by a consortium of ABB, with their Japanese licensee Kawasaki Heavy Industries, and Marubeni Corporation. This paper discusses Philippine power production, design and operation of the Limay Bataan plant, and conversion of an existing turbine of the nuclear plant project that was abandoned earlier, into a combined cycle operation. 6 figs.

  3. Combined air and water pollution control system

    NASA Technical Reports Server (NTRS)

    Wolverton, Billy C. (Inventor); Jarrell, Lamont (Inventor)

    1990-01-01

    A bioaquatic air pollution control system for controlling both water and atmospheric pollution is disclosed. The pollution control system includes an exhaust for directing polluted gases out of a furnace and a fluid circulating system which circulates fluid, such as waste water, from a source, past the furnace where the fluid flow entrains the pollutants from the furnace. The combined fluid and pollutants are then directed through a rock/plant/microbial filtering system. A suction pump pumps the treated waste water from the filter system past the exhaust to again entrain more pollutants from the furnace where they are combined with the fluid (waste water) and directed to the filter system.

  4. Widespread differences in cortex DNA methylation of the "language gene" CNTNAP2 between humans and chimpanzees.

    PubMed

    Schneider, Eberhard; El Hajj, Nady; Richter, Steven; Roche-Santiago, Justin; Nanda, Indrajit; Schempp, Werner; Riederer, Peter; Navarro, Bianca; Bontrop, Ronald E; Kondova, Ivanela; Scholz, Claus Jürgen; Haaf, Thomas

    2014-04-01

    CNTNAP2, one of the largest genes in the human genome, has been linked to human-specific language abilities and neurodevelopmental disorders. Our hypothesis is that epigenetic rather than genetic changes have accelerated the evolution of the human brain. To compare the cortex DNA methylation patterns of human and chimpanzee CNTNAP2 at ultra-high resolution, we combined methylated DNA immunoprecipitation (MeDIP) with NimbleGen tiling arrays for the orthologous gene and flanking sequences. Approximately 1.59 Mb of the 2.51 Mb target region could be aligned and analyzed with a customized algorithm in both species. More than one fifth (0.34 Mb) of the analyzed sequence throughout the entire gene displayed significant methylation differences between six human and five chimpanzee cortices. One of the most striking interspecies differences with 28% methylation in human and 59% in chimpanzee cortex (by bisulfite pyrosequencing) lies in a region 300 bp upstream of human SNP rs7794745 which has been associated with autism and parent-of-origin effects. Quantitative real-time RT PCR revealed that the protein-coding splice variant CNTNAP2-201 is 1.6-fold upregulated in human cortex, compared with the chimpanzee. Transcripts CNTNAP2-001, -002, and -003 did not show skewed allelic expression, which argues against CNTNAP2 imprinting, at least in adult human brain. Collectively, our results suggest widespread cortex DNA methylation changes in CNTNAP2 since the human-chimpanzee split, supporting a role for CNTNAP2 fine-regulation in human-specific language and communication traits. PMID:24434791

  5. Widespread differences in cortex DNA methylation of the “language gene” CNTNAP2 between humans and chimpanzees

    PubMed Central

    Schneider, Eberhard; El Hajj, Nady; Richter, Steven; Roche-Santiago, Justin; Nanda, Indrajit; Schempp, Werner; Riederer, Peter; Navarro, Bianca; Bontrop, Ronald E; Kondova, Ivanela; Scholz, Claus Jürgen; Haaf, Thomas

    2014-01-01

    CNTNAP2, one of the largest genes in the human genome, has been linked to human-specific language abilities and neurodevelopmental disorders. Our hypothesis is that epigenetic rather than genetic changes have accelerated the evolution of the human brain. To compare the cortex DNA methylation patterns of human and chimpanzee CNTNAP2 at ultra-high resolution, we combined methylated DNA immunoprecipitation (MeDIP) with NimbleGen tiling arrays for the orthologous gene and flanking sequences. Approximately 1.59 Mb of the 2.51 Mb target region could be aligned and analyzed with a customized algorithm in both species. More than one fifth (0.34 Mb) of the analyzed sequence throughout the entire gene displayed significant methylation differences between six human and five chimpanzee cortices. One of the most striking interspecies differences with 28% methylation in human and 59% in chimpanzee cortex (by bisulfite pyrosequencing) lies in a region 300 bp upstream of human SNP rs7794745 which has been associated with autism and parent-of-origin effects. Quantitative real-time RT PCR revealed that the protein-coding splice variant CNTNAP2-201 is 1.6-fold upregulated in human cortex, compared with the chimpanzee. Transcripts CNTNAP2-001, -002, and -003 did not show skewed allelic expression, which argues against CNTNAP2 imprinting, at least in adult human brain. Collectively, our results suggest widespread cortex DNA methylation changes in CNTNAP2 since the human-chimpanzee split, supporting a role for CNTNAP2 fine-regulation in human-specific language and communication traits. PMID:24434791

  6. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

    PubMed Central

    Stevens, Michael; Cheng, Jeffrey B.; Li, Daofeng; Xie, Mingchao; Hong, Chibo; Maire, Cécile L.; Ligon, Keith L.; Hirst, Martin; Marra, Marco A.; Costello, Joseph F.; Wang, Ting

    2013-01-01

    Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to map complete DNA methylomes. These include whole-genome bisulfite sequencing (WGBS, MethylC-seq, or BS-seq), reduced-representation bisulfite sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. These methods yield largely comparable results but differ significantly in extent of genomic CpG coverage, resolution, quantitative accuracy, and cost, at least while using current algorithms to interrogate the data. None of these existing methods provides single-CpG resolution, comprehensive genome-wide coverage, and cost feasibility for a typical laboratory. We introduce methylCRF, a novel conditional random fields–based algorithm that integrates methylated DNA immunoprecipitation (MeDIP-seq) and methylation-sensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single-CpG resolution. Our method is a combined computational and experimental strategy to produce DNA methylomes of all 28 million CpGs in the human genome for a fraction (<10%) of the cost of whole-genome bisulfite sequencing methods. methylCRF was benchmarked for accuracy against Infinium arrays, RRBS, WGBS sequencing, and locus-specific bisulfite sequencing performed on the same human embryonic stem cell line. methylCRF transformation of MeDIP-seq/MRE-seq was equivalent to a biological replicate of WGBS in quantification, coverage, and resolution. We used conventional bisulfite conversion, PCR, cloning, and sequencing to validate loci where our predictions do not agree with whole-genome bisulfite data, and in 11 out of 12 cases, methylCRF predictions of methylation level agree better with validated results than does whole-genome bisulfite sequencing. Therefore, methylCRF transformation of MeDIP-seq/MRE-seq data provides an accurate, inexpensive, and widely accessible strategy to create full DNA methylomes. PMID:23804401

  7. Genome-Wide Mapping of 5mC and 5hmC Identified Differentially Modified Genomic Regions in Late-Onset Severe Preeclampsia: A Pilot Study

    PubMed Central

    Zhu, Lisha; Lv, Ruitu; Kong, Lingchun; Cheng, Haidong; Lan, Fei; Li, Xiaotian

    2015-01-01

    Preeclampsia (PE) is a leading cause of perinatal morbidity and mortality. However, as a common form of PE, the etiology of late-onset PE is elusive. We analyzed 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels in the placentas of late-onset severe PE patients (n = 4) and normal controls (n = 4) using a (hydroxy)methylated DNA immunoprecipitation approach combined with deep sequencing ([h]MeDIP-seq), and the results were verified by (h)MeDIP-qPCR. The most significant differentially methylated regions (DMRs) were verified by MassARRAY EppiTYPER in an enlarged sample size (n = 20). Bioinformatics analysis identified 714 peaks of 5mC that were associated with 403 genes and 119 peaks of 5hmC that were associated with 61 genes, thus showing significant differences between the PE patients and the controls (>2-fold, p<0.05). Further, only one gene, PTPRN2, had both 5mC and 5hmC changes in patients. The ErbB signaling pathway was enriched in those 403 genes that had significantly different5mC level between the groups. This genome-wide mapping of 5mC and 5hmC in late-onset severe PE and normal controls demonstrates that both 5mC and 5hmC play epigenetic roles in the regulation of the disease, but work independently. We reveal the genome-wide mapping of DNA methylation and DNA hydroxymethylation in late-onset PE placentas for the first time, and the identified ErbB signaling pathway and the gene PTPRN2 may be relevant to the epigenetic pathogenesis of late-onset PE. PMID:26214307

  8. Genome-Wide Mapping of 5mC and 5hmC Identified Differentially Modified Genomic Regions in Late-Onset Severe Preeclampsia: A Pilot Study.

    PubMed

    Zhu, Lisha; Lv, Ruitu; Kong, Lingchun; Cheng, Haidong; Lan, Fei; Li, Xiaotian

    2015-01-01

    Preeclampsia (PE) is a leading cause of perinatal morbidity and mortality. However, as a common form of PE, the etiology of late-onset PE is elusive. We analyzed 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels in the placentas of late-onset severe PE patients (n = 4) and normal controls (n = 4) using a (hydroxy)methylated DNA immunoprecipitation approach combined with deep sequencing ([h]MeDIP-seq), and the results were verified by (h)MeDIP-qPCR. The most significant differentially methylated regions (DMRs) were verified by MassARRAY EppiTYPER in an enlarged sample size (n = 20). Bioinformatics analysis identified 714 peaks of 5mC that were associated with 403 genes and 119 peaks of 5hmC that were associated with 61 genes, thus showing significant differences between the PE patients and the controls (>2-fold, p<0.05). Further, only one gene, PTPRN2, had both 5mC and 5hmC changes in patients. The ErbB signaling pathway was enriched in those 403 genes that had significantly different 5mC level between the groups. This genome-wide mapping of 5mC and 5hmC in late-onset severe PE and normal controls demonstrates that both 5mC and 5hmC play epigenetic roles in the regulation of the disease, but work independently. We reveal the genome-wide mapping of DNA methylation and DNA hydroxymethylation in late-onset PE placentas for the first time, and the identified ErbB signaling pathway and the gene PTPRN2 may be relevant to the epigenetic pathogenesis of late-onset PE. PMID:26214307

  9. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.

    PubMed

    Stevens, Michael; Cheng, Jeffrey B; Li, Daofeng; Xie, Mingchao; Hong, Chibo; Maire, Cécile L; Ligon, Keith L; Hirst, Martin; Marra, Marco A; Costello, Joseph F; Wang, Ting

    2013-09-01

    Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to map complete DNA methylomes. These include whole-genome bisulfite sequencing (WGBS, MethylC-seq, or BS-seq), reduced-representation bisulfite sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. These methods yield largely comparable results but differ significantly in extent of genomic CpG coverage, resolution, quantitative accuracy, and cost, at least while using current algorithms to interrogate the data. None of these existing methods provides single-CpG resolution, comprehensive genome-wide coverage, and cost feasibility for a typical laboratory. We introduce methylCRF, a novel conditional random fields-based algorithm that integrates methylated DNA immunoprecipitation (MeDIP-seq) and methylation-sensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single-CpG resolution. Our method is a combined computational and experimental strategy to produce DNA methylomes of all 28 million CpGs in the human genome for a fraction (<10%) of the cost of whole-genome bisulfite sequencing methods. methylCRF was benchmarked for accuracy against Infinium arrays, RRBS, WGBS sequencing, and locus-specific bisulfite sequencing performed on the same human embryonic stem cell line. methylCRF transformation of MeDIP-seq/MRE-seq was equivalent to a biological replicate of WGBS in quantification, coverage, and resolution. We used conventional bisulfite conversion, PCR, cloning, and sequencing to validate loci where our predictions do not agree with whole-genome bisulfite data, and in 11 out of 12 cases, methylCRF predictions of methylation level agree better with validated results than does whole-genome bisulfite sequencing. Therefore, methylCRF transformation of MeDIP-seq/MRE-seq data provides an accurate, inexpensive, and widely accessible strategy to create full DNA methylomes. PMID:23804401

  10. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.

    PubMed

    Zhang, Bo; Zhou, Yan; Lin, Nan; Lowdon, Rebecca F; Hong, Chibo; Nagarajan, Raman P; Cheng, Jeffrey B; Li, Daofeng; Stevens, Michael; Lee, Hyung Joo; Xing, Xiaoyun; Zhou, Jia; Sundaram, Vasavi; Elliott, Ginell; Gu, Junchen; Shi, Taoping; Gascard, Philippe; Sigaroudinia, Mahvash; Tlsty, Thea D; Kadlecek, Theresa; Weiss, Arthur; O'Geen, Henriette; Farnham, Peggy J; Maire, Cécile L; Ligon, Keith L; Madden, Pamela A F; Tam, Angela; Moore, Richard; Hirst, Martin; Marra, Marco A; Zhang, Baoxue; Costello, Joseph F; Wang, Ting

    2013-09-01

    DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and tissue-specific gene expression. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA methylomes. This includes one of the most widely applied technologies for measuring DNA methylation: methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq), coupled with a complementary method, methylation-sensitive restriction enzyme sequencing (MRE-seq). A computational approach that integrates data from these two different but complementary assays and predicts methylation differences between samples has been unavailable. Here, we present a novel integrative statistical framework M&M (for integration of MeDIP-seq and MRE-seq) that dynamically scales, normalizes, and combines MeDIP-seq and MRE-seq data to detect differentially methylated regions. Using sample-matched whole-genome bisulfite sequencing (WGBS) as a gold standard, we demonstrate superior accuracy and reproducibility of M&M compared to existing analytical methods for MeDIP-seq data alone. M&M leverages the complementary nature of MeDIP-seq and MRE-seq data to allow rapid comparative analysis between whole methylomes at a fraction of the cost of WGBS. Comprehensive analysis of nineteen human DNA methylomes with M&M reveals distinct DNA methylation patterns among different tissue types, cell types, and individuals, potentially underscoring divergent epigenetic regulation at different scales of phenotypic diversity. We find that differential DNA methylation at enhancer elements, with concurrent changes in histone modifications and transcription factor binding, is common at the cell, tissue, and individual levels, whereas promoter methylation is more prominent in reinforcing fundamental tissue identities. PMID:23804400

  11. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

    PubMed Central

    Zhang, Bo; Zhou, Yan; Lin, Nan; Lowdon, Rebecca F.; Hong, Chibo; Nagarajan, Raman P.; Cheng, Jeffrey B.; Li, Daofeng; Stevens, Michael; Lee, Hyung Joo; Xing, Xiaoyun; Zhou, Jia; Sundaram, Vasavi; Elliott, GiNell; Gu, Junchen; Shi, Taoping; Gascard, Philippe; Sigaroudinia, Mahvash; Tlsty, Thea D.; Kadlecek, Theresa; Weiss, Arthur; O’Geen, Henriette; Farnham, Peggy J.; Maire, Cécile L.; Ligon, Keith L.; Madden, Pamela A.F.; Tam, Angela; Moore, Richard; Hirst, Martin; Marra, Marco A.; Zhang, Baoxue; Costello, Joseph F.; Wang, Ting

    2013-01-01

    DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and tissue-specific gene expression. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA methylomes. This includes one of the most widely applied technologies for measuring DNA methylation: methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq), coupled with a complementary method, methylation-sensitive restriction enzyme sequencing (MRE-seq). A computational approach that integrates data from these two different but complementary assays and predicts methylation differences between samples has been unavailable. Here, we present a novel integrative statistical framework M&M (for integration of MeDIP-seq and MRE-seq) that dynamically scales, normalizes, and combines MeDIP-seq and MRE-seq data to detect differentially methylated regions. Using sample-matched whole-genome bisulfite sequencing (WGBS) as a gold standard, we demonstrate superior accuracy and reproducibility of M&M compared to existing analytical methods for MeDIP-seq data alone. M&M leverages the complementary nature of MeDIP-seq and MRE-seq data to allow rapid comparative analysis between whole methylomes at a fraction of the cost of WGBS. Comprehensive analysis of nineteen human DNA methylomes with M&M reveals distinct DNA methylation patterns among different tissue types, cell types, and individuals, potentially underscoring divergent epigenetic regulation at different scales of phenotypic diversity. We find that differential DNA methylation at enhancer elements, with concurrent changes in histone modifications and transcription factor binding, is common at the cell, tissue, and individual levels, whereas promoter methylation is more prominent in reinforcing fundamental tissue identities. PMID:23804400

  12. 77 FR 56197 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-12

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF AMERICA Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP11-2473-000. Applicants:...

  13. 78 FR 54883 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP13-1272-000....

  14. 75 FR 10239 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings March 1, 2010. Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Docket Numbers: RP10-394-000 Applicants: Quest Pipelines...

  15. 78 FR 79432 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP14-293-000....

  16. Vertebral osteomyelitis combined streptococcal viridans endocarditis.

    PubMed

    Lee, Kuo-Chen; Tsai, Yi-Ting; Lin, Chih-Yuan; Tsai, Chien-Sung

    2003-01-01

    Endocarditis may be difficult to diagnose in patients with osteomyelitis in an early stage because they usually are treated for fever, bone pain and stiffness in the outpatient department. Herein we report an uncommon patient who developed severe lower back pain sustained for 2 months, and streptococcal viridans infected vertebral osteomyelitis combined endocarditis were diagnosed and cured. PMID:12493523

  17. 38 CFR 21.5231 - Combination.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Combination. 21.5231 Section 21.5231 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-Vietnam Era Veterans' Educational Assistance Under 38...

  18. Hybrid Laser Would Combine Power With Efficiency

    NASA Technical Reports Server (NTRS)

    Sipes, Donald L., Jr

    1986-01-01

    Efficient laser system constructed by using two semiconductor lasers to pump neodymium yttrium aluminum garnet (Nd:YAG) device. Hybrid concept allows digital transmission at data rates of several megabits per second with reasonably sized optical aperture of 20 cm. Beams from two GaAs lasers efficiently coupled for pumping Nd:YAG crystal. Combination of lasers exploits best features of each.

  19. 220-kV combined optical transformer

    NASA Astrophysics Data System (ADS)

    Cui, Ying; Ye, Miaoyuan; Zhu, Yong; Xu, Yan; Luo, Sunan

    2000-10-01

    The magneto-optic current and electro-optic voltage sensing technologies were combined into a single phase unit which provides a new solution for combined current and voltage sensing and relaying applications. It senses voltage and current by making utilities of Pockels electro-optic effect of a BGO(Bi4Ge3O12) crystal and Faraday magneto-optic effect of a close-loop flint. The 220 kV high voltage is directly applied on the BGO crystal without capacitive dividers. This design permits true optical voltage measurement to be performed for the highest possible accuracy and stability. In the current sensor, a light beam circles around the current carrying conductor. The effect of the location movement of the conductor and external magnetic field are reduced. It has superior advantages of compact size, light- weight and better performance compared with conventional current and voltage transformers. Composite bushing consisting of a fiberglass tube support and silicone rubber that is filled with SF6 gas is employed for HV insulation. Connections between the Combined Optical Transformers in the substation and the metering and protecting unit in the control house are via optical fiber cable. The fundamental principal, system design and test result of this new 220 kV Combined Optical Transformer will be introduced in this paper.

  20. 78 FR 70298 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-25

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed...

  1. 78 FR 26636 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-07

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has... Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is...

  2. 77 FR 77071 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-31

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to...

  3. 77 FR 58984 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-25

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is...

  4. 75 FR 1767 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-13

    ... Energy Regulatory Commission Combined Notice of Filings December 28, 2009. Take notice that the... . To facilitate electronic service, persons with Internet access who will eFile a document and/or be listed as a contact for an intervenor must create and validate an eRegistration account using the...

  5. 75 FR 65469 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-25

    ... receive e-mail notification when a document is added to a subscribed docket(s). For assistance with any... Energy Regulatory Commission Combined Notice of Filings October 14, 2010. Take notice that the Commission... will eFile a document and/or be listed as a contact for an intervenor must create and validate an...

  6. 78 FR 42515 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-16

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the.... Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More...

  7. 77 FR 71408 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is...

  8. 77 FR 14772 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-13

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling...

  9. 78 FR 56685 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-13

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... in the Commission's eLibrary system by clicking on the links or querying the docket number....

  10. 77 FR 74654 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...'s eLibrary system by clicking on the links or querying the docket number. eFiling is...

  11. 78 FR 24403 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-25

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... comment date. ] The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to...

  12. 77 FR 69448 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-19

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed...

  13. 78 FR 25260 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings April 23, 2013. Take notice that the Commission... accessible in the Commission's eLibrary system by clicking on the links or querying the docket number....

  14. 77 FR 67355 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-09

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the.... The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing...

  15. 78 FR 39723 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-02

    ... Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has... on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed...

  16. 77 FR 41397 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-13

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling...

  17. 77 FR 74655 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to...

  18. 76 FR 61352 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-04

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the....m. Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  19. 78 FR 20905 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-08

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has... accessible in the Commission's eLibrary system by clicking on the links or querying the docket number....

  20. 78 FR 10616 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-14

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing requirements,...

  1. 78 FR 716 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-04

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission received the... are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing requirements,...

  2. 78 FR 70034 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...'s eLibrary system by clicking on the links or querying the docket number. eFiling is...

  3. 75 FR 17136 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-05

    ... Energy Regulatory Commission Combined Notice of Filings March 24, 2010. Take notice that the Commission... . To facilitate electronic service, persons with Internet access who will eFile a document and/or be listed as a contact for an intervenor must create and validate an eRegistration account using the...

  4. 77 FR 71409 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-30

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...:00 p.m. Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  5. 77 FR 33205 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-05

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... proceeding. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to...

  6. 75 FR 1768 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-13

    ... receive e-mail notification when a document is added to a subscribed docket(s). For assistance with any... Energy Regulatory Commission Combined Notice of Filings December 22, 2009. Take notice that the... will eFile a document and/or be listed as a contact for an intervenor must create and validate an...

  7. 78 FR 30914 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-23

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... accessible in the Commission's eLibrary system by clicking on the links or querying the docket number....

  8. 78 FR 70033 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-22

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing requirements,...

  9. 78 FR 23244 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-18

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... necessary to become a party to the proceeding. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More...

  10. 78 FR 38022 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-25

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... date. ] The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to...

  11. 78 FR 25071 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-29

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing requirements,...

  12. 78 FR 39722 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-02

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...: 20130614-5149. Comments Due: 5 p.m. ET 6/26/13. The filings are accessible in the Commission's eLibrary.... Protests may be considered, but intervention is necessary to become a party to the proceeding. eFiling...

  13. 77 FR 33205 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-05

    ... Energy Regulatory Commission Combined Notice of Filings May 30, 2012. Take notice that the Commission has...:00 p.m. Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  14. 75 FR 17138 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-05

    ... document is added to a subscribed docket(s). For assistance with any FERC Online service, please e-mail... Energy Regulatory Commission Combined Notice of Filings March 26, 2010. Take notice that the Commission... electronic service, persons with Internet access who will eFile a document and/or be listed as a contact...

  15. 77 FR 77071 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-31

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed...

  16. 78 FR 76291 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-17

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... eTariff Metadata to be effective 11/1/ 2013. Filed Date: 12/9/13. Accession Number: 20131209-5222.... Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary...

  17. 78 FR 41049 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-09

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the.... The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing...

  18. 75 FR 53285 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-31

    ... subscribers to receive e-mail notification when a document is added to a subscribed dockets(s). For assistance... Energy Regulatory Commission Combined Notice of Filings August 19, 2010. Take notice that the Commission... will eFile a document and/or be listed as a contact for an intervenor must create and validate an...

  19. 78 FR 41049 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-09

    ... Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has... the Commission's eLibrary system by clicking on the links or querying the docket number. Any person... party to the proceeding. eFiling is encouraged. More detailed information relating to...

  20. 78 FR 38023 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-25

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...: 20130614-5149. Comments Due: 5 p.m. ET 6/26/13. The filings are accessible in the Commission's eLibrary.... Protests may be considered, but intervention is necessary to become a party to the proceeding. eFiling...

  1. 78 FR 26635 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-07

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... party to the proceeding. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating...

  2. 78 FR 10616 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-14

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...:00 p.m. Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  3. 77 FR 42299 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... accessible in the Commission's eLibrary system by clicking on the links or querying the docket number....

  4. 77 FR 66826 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-07

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed...

  5. 76 FR 61353 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-04

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing requirements,...

  6. 78 FR 68050 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-13

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to...

  7. 78 FR 39723 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-02

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed...

  8. 75 FR 28797 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-24

    ... Energy Regulatory Commission Combined Notice of Filings May 13, 2010. Take notice that the Commission has... . To facilitate electronic service, persons with Internet access who will eFile a document and/or be listed as a contact for an intervenor must create and validate an eRegistration account using the...

  9. 78 FR 45520 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-29

    ... Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has...:00 p.m. Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  10. 78 FR 29750 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-21

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... accessible in the Commission's eLibrary system by clicking on the links or querying the docket number....

  11. 78 FR 50053 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-16

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...:00 p.m. Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  12. 78 FR 50053 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-16

    ... Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has.... Description: ACA Compliance Filing--eTariff Viewer Correction to be effective 10/1/2013. Filed Date: 8/5/13... in the Commission's eLibrary system by clicking on the links or querying the docket number....

  13. 78 FR 17650 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...'s eLibrary system by clicking on the links or querying the docket number. eFiling is...

  14. 77 FR 70426 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-26

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...:00 p.m. Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  15. 78 FR 39725 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-02

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... in the Commission's eLibrary system by clicking on the links or querying the docket number....

  16. 78 FR 45921 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-30

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... the Commission's eLibrary system by clicking on the links or querying the docket number. Any person... party to the proceeding. eFiling is encouraged. More detailed information relating to...

  17. 78 FR 45520 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-29

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the.... e.t. 7/30/13. Docket Numbers: RP13-1086-000. Applicants: Maritimes & Northeast Pipeline, L.L.C... Number: 20130718-5107. Comments Due: 5 p.m. e.t. 7/30/13. Docket Numbers: RP13-1087-000....

  18. 75 FR 61730 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-06

    ... Energy Regulatory Commission Combined Notice of Filings September 21, 2010. Take notice that the... filing per 154.203: Cotton Valley--Baseline eTariff Filing to be effective 9/21/2010. Filed Date: 09/21... . To facilitate electronic service, persons with Internet access who will eFile a document and/or...

  19. 77 FR 14358 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-09

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... the specified comment date. ] The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed...

  20. 75 FR 65468 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-25

    ... receive e-mail notification when a document is added to a subscribed docket(s). For assistance with any... Energy Regulatory Commission Combined Notice of Filings October 18, 2010. Take notice that the Commission... Baseline eTariff Filing to be effective 8/13/2010. Filed Date: 10/18/2010. Accession Number:...

  1. 78 FR 76291 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-17

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...: 5 p.m. ET 12/16/13. The filings are accessible in the Commission's eLibrary system by clicking on.... Protests may be considered, but intervention is necessary to become a party to the proceeding. eFiling...

  2. 76 FR 46788 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-03

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... . To facilitate electronic service, persons with Internet access who will eFile a document and/or be listed as a contact for an intervenor must create and validate an eRegistration account using the...

  3. 78 FR 59664 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-27

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing requirements,...

  4. 78 FR 39723 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-02

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...: 20130624-5084. Comments Due: 5 p.m. ET 7/8/13. The filings are accessible in the Commission's eLibrary.... Protests may be considered, but intervention is necessary to become a party to the proceeding. eFiling...

  5. 78 FR 13050 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-26

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the....m. Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  6. 76 FR 67719 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-02

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the.... Eastern time on the specified comment date. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More...

  7. 77 FR 10489 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged....

  8. 78 FR 42515 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-16

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the.... The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to filing...

  9. 78 FR 20901 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-08

    ... Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... proceeding. The filings are accessible in the Commission's eLibrary system by clicking on the links or querying the docket number. eFiling is encouraged. More detailed information relating to...

  10. 78 FR 18969 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-28

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...'s eLibrary system by clicking on the links or querying the docket number. eFiling is...

  11. 75 FR 17139 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-05

    ... link on the Web site that enables subscribers to receive e-mail notification when a document is added... Energy Regulatory Commission Combined Notice of Filings March 18, 2010. Take notice that the Commission... service, persons with Internet access who will eFile a document and/or be listed as a contact for...

  12. A Framework for Remediating Number Combination Deficits

    ERIC Educational Resources Information Center

    Fuchs, Lynn S.; Powell, Sarah R.; Seethaler, Pamela M.; Fuchs, Douglas; Hamlett, Carol L.; Cirino, Paul T.; Fletcher, Jack M.

    2010-01-01

    This article introduces a framework for the remediation of number combination (NC) deficits. Research on the remediation of NC deficits is summarized, and research program studies are used to illustrate the 3 approaches to remediation. The Framework comprises a 2-stage system of remediation. The less intensive stage implementing 1 of 3…

  13. Combining Biomarkers to Optimize Patient Treatment Recommendations

    PubMed Central

    Kang, Chaeryon; Janes, Holly; Huang, Ying

    2014-01-01

    Summary Markers that predict treatment effect have the potential to improve patient outcomes. For example, the Oncotype DX ® Recurrence Score® has some ability to predict the benefit of adjuvant chemotherapy over and above hormone therapy for the treatment of estrogen-receptor-positive breast cancer, facilitating the provision of chemotherapy to women most likely to benefit from it. Given that the score was originally developed for predicting outcome given hormone therapy alone, it is of interest to develop alternative combinations of the genes comprising the score that are optimized for treatment selection. However most methodology for combining markers is useful when predicting outcome under a single treatment. We propose a method for combining markers for treatment selection which requires modeling the treatment effect as a function of markers. Multiple models of treatment effect are fit iteratively by upweighting or “boosting” subjects potentially misclassified according to treatment benefit at the previous stage. The boosting approach is compared to existing methods in a simulation study based on the change in expected outcome under marker-based treatment. The approach improves upon methods in some settings and has comparable performance in others. Our simulation study also provides insights as to the relative merits of the existing methods. Application of the boosting approach to the breast cancer data, using scaled versions of the original markers, produces marker combinations that may have improved performance for treatment selection. PMID:24889663

  14. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  15. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  16. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  17. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  18. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  19. 78 FR 9686 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-11

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP13-492-000....

  20. 78 FR 9684 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-11

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP13-498-000....

  1. Multimodel Combination of Extreme Precipitation Projections

    NASA Astrophysics Data System (ADS)

    Schwartz Madsen, Bo; Ditlevsen, Peter; Feng, Tao

    2015-04-01

    This study seeks to combine projections of extreme precipitation from several RCMs into one single projection. Ensembles of models are increasingly used in climate science. Combining information from several models is a non-trivial task. Most often the models are averaged with equal weights, i.e. "one model, one vote". We seek a combination of models that exploits the strengths of each model. Here we fit a bayesian spatial model (BSM) to the extremes in Denmark, both with data from observations and from RCMs. The parameters of the different BSMs are compared to evaluate the RCMs ability to represent extreme precipitation in Denmark. A BSM is also fitted to future RCM projections in the time periods 2021-2050 and 2071-2100. The parameters of the BSM from each RCM are weighted with respect to that RCM's internal variability, consensus with other RCMs, the variability of the real climate and the collective deviation of all RCMs from reality. With this weighting the combined BSM projects the future extremes on the basis of all the models.

  2. UV-T-RH combined environmental testing

    NASA Technical Reports Server (NTRS)

    Gonzalez, C. C.

    1986-01-01

    A combined environmental aging chamber was developed at the Jet Propulsion Laboratory (JPL). The chamber has an ultraviolet (UV) light source that can be varied between 1 to 2 suns, temperature control from -40 to +175 C, and adjustable humidity. Results from two initial aging experiments (Tedlar and amorphous silicon colar cells) were presented.

  3. 77 FR 31346 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-25

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP12-732-000. Applicants:...

  4. Combined dispersant fluid loss control additives

    SciTech Connect

    Villa, J. L.; Zeiner, R. N.

    1985-12-31

    Water soluble polymer compositions containing polyacrylic acid and copolymer of itaconic acid and acrylamide are useful as combined dispersant and fluid loss control additives for aqueous drilling fluids, particularly fresh water, gypsum and seawater muds. An example is a polymer composition containing about 80% by weight polyacrylic acid and about 20% by weight copolymer of itaconic acid and acrylamide in its ammonium salt form.

  5. 78 FR 8507 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: CP13-57-000 Applicants:...

  6. Fixed-combination and emerging glaucoma therapies.

    PubMed

    Woodward, David F; Chen, June

    2007-05-01

    Ocular hypotensive agents are the only approved pharmacotherapy for glaucoma. Despite significant advances during the past two decades, a large proportion of glaucoma patients require more than one drug. The most recent additions to the armamentarium of antiglaucoma drugs are fixed-combination products for the glaucoma patient who is insufficiently responsive to monotherapy. Fixed-combination products have the combined efficacy of two ocular hypotensive drugs, and the convenience of a two-drug treatment regimen in a single container, which may aid patient adherence to treatment. Available fixed-combination products consist of timolol 0.5% as an invariant with brimonidine 0.2%, dorzolamide 2%, travoprost 0.004%, latanoprost 0.005% or bimatoprost 0.03%. Research on more advanced antiglaucoma medications continues. Promising new directions appear to be the Rho-kinase inhibitors, microtubule-disrupting agents, serotonergics and cannabimimetics. Efforts continue to improve existing antiglaucoma drugs in an attempt to design second-generation cholinomimetics, adrenergics, prostaglandins and prostamides. PMID:17604504

  7. 7 CFR 29.1008 - Combination symbols.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Combination symbols. 29.1008 Section 29.1008 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE COMMODITY STANDARDS AND STANDARD CONTAINER REGULATIONS TOBACCO INSPECTION Standards...

  8. American Holidays: Culture and Language Learning Combined.

    ERIC Educational Resources Information Center

    Wylie, Grace Scott

    Suggestions for combining cultural exposure and language instruction through class activities geared to American holidays are outlined. General information about gathering holiday-related realia and instructional materials from local newspapers and magazines is provided, and four specific holidays are highlighted. For each holiday, sources of…

  9. Combined infrared and freeze-drying.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The drying of the combined infrared (IR) and freeze-drying of food materials has been shown to be very rapid compared to regular freeze drying (FD). The resulting tissue structure of products processed with sequential infrared and freeze drying (SIRFD) tends to have higher crispness than those proce...

  10. Prevalence of Combined Reading and Arithmetic Disabilities

    ERIC Educational Resources Information Center

    Dirks, Evelien; Spyer, Ginny; van Lieshout, Ernest C. D. M.; de Sonneville, Leo

    2008-01-01

    This study assesses the prevalence of combined reading and arithmetic disabilities in 799 Dutch schoolchildren using standardized school achievement tests. Scores of arithmetic, word recognition, reading comprehension, and spelling of children in fourth and fifth grade were used. The main interest involved the co-occurrence of word recognition and…

  11. Combined cycle power plant incorporating coal gasification

    DOEpatents

    Liljedahl, Gregory N.; Moffat, Bruce K.

    1981-01-01

    A combined cycle power plant incorporating a coal gasifier as the energy source. The gases leaving the coal gasifier pass through a liquid couplant heat exchanger before being used to drive a gas turbine. The exhaust gases of the gas turbine are used to generate both high pressure and low pressure steam for driving a steam turbine, before being exhausted to the atmosphere.

  12. 76 FR 17409 - Combined Notice of Filings #

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission received the following electric corporate filings: Docket Numbers: EC11-53-000 Applicants: Caisse de depot et placement du Quebec T, Enbridge Inc., ] IPL...

  13. Articulated Multimedia Physics, Lesson 7, Combining Forces.

    ERIC Educational Resources Information Center

    New York Inst. of Tech., Old Westbury.

    As the seventh lesson of the Articulated Multimedia Physics Course, instructional materials are presented in this study guide with relation to the force combination. The topics are concerned with the definition and units of forces, sliding forces on inclined planes, and the equilibrant of two or more forces. The content is arranged in scrambled…

  14. [Combination treatment in pulmonary arterial hypertension].

    PubMed

    Kramer, Mordechai R

    2011-04-01

    In recent years, there has been a marked improvement in the treatment of pulmonary arterial hypertension (PAH) due to the development of targeted therapies. There are now several treatment options available--oral, inhaled, and those delivered by subcutaneous or intravenous methods. These treatments have greatly improved patient survival, which in the past was 2.5 years on average. Efficient treatment choice generally proceeds from oral therapies--PDE-5 inhibitors (sildenafil) and endothelin receptor antagonists (bosentan or ambrisentan)--to inhaled prostanoids (iloprost) or subcutaneous (treprostinil). Intravenous prostacyclins are used in treating the more severe cases. The different pathways of action of each class of drugs allow a synergistic effect of combination therapy similar to malignancy or patients in congestive heart failure. The updated treatment algorithm includes combinations of therapies that target different pathways. This article will review the literature regarding combination therapy for the treatment of PAH. Combining PAH therapies that target different pathways is now a well-established treatment option, based on numerous international clinical trials, and offers new hope to patients suffering from this severe disease. PMID:22164922

  15. Urban Runoff and Combined Sewer Overflow.

    ERIC Educational Resources Information Center

    Field, Richard; Gardner, Bradford B.

    1978-01-01

    Presents a literature review of wastewater treatment, covering publications of 1976-77. This review includes areas such as: (1) urban runoff quality and quantity; (2) urban hydrology; (3) management practices; and (4) combined sewer overflows. A list of 140 references is also presented. (HM)

  16. Influence of characteristics on combined sewer performance.

    PubMed

    Möderl, M; Kleidorfer, M; Rauch, W

    2012-01-01

    Elements of combined sewer systems are among others sub-catchments, junctions, conduits and weirs with or without storage units. The spatial distribution and attributes of all these elements influence both system characteristics and sewer performance. Until today, little work has been done to analyse the influence of such characteristics in a case unspecific approach. In this study, 250 virtual combined sewer systems are analysed by defining groups of systems, which are representative for their different characteristics. The set was created with a further development of the case study generator (CSG), a tool for automatic generation of branched sewer systems. Combined sewer overflow and flooding is evaluated using performance indicators based on hydrodynamic simulations. The analysis of system characteristics, like those presented in this paper, helps researchers to understand coherences and aids practitioners in designing combined sewers. For instance, it was found that characteristics that have a positive influence on emission reduction frequently have a negative influence on flooding avoidance and vice versa. PMID:22797234

  17. 76 FR 30333 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-25

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Docket Numbers: RP11-2051-000. Applicants: Black Marlin Pipeline...

  18. 78 FR 75554 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP14-226-000....

  19. 78 FR 75554 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP14-241-000....

  20. Combination solar hothouse and silkworm breeding house

    SciTech Connect

    Vardiashvili, A.B.; Muradov, M.; Kim, V.D.

    1980-01-01

    The basic arrangement is shown for a combination silkworm breeding house and solar hothouse with subsoil irrigation and accumulation of heat; it employs a semicylindrical film covering. The process of accumulation of solar heat in the subsoil pebble stores, in water-heater banks, and in the soil is described.