Bagel

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H Muther - One of the best experts on this subject based on the ideXlab platform.

  • correlations in nuclei self consistent treatment and the Bagel approach
    Physics Letters B, 1993
    Co-Authors: H Muther, L D Skouras
    Abstract:

    Abstract An approach is presented which allows a self-consistent description of the fragmentation of single-particle strength for nucleons in finite nuclei employing the Green function formalism. The self-energy to be considered in the Dyson equation for the single-particle Green function contains all terms of first (Hartree-Fock) and second order in the residual interaction. It is demonstrated that the fragmentation of the single-particle strength originating from the terms of second order can efficiently be described in terms of the so-called Bagel approximation. Employing this approximation the self-energy can be evaluated in a self-consistent way, i.e. the correlations contained in the Green function are taken into account for the evaluation of the self-energy. As an example this scheme is applied to the nucleus 16 O, using a realistic nucleon nucleon interaction. The effects of the correlations on the occupation probabilities and the binding energy are evaluated.

  • effective interaction derived from the Bagel approach
    Nuclear Physics, 1990
    Co-Authors: L D Skouras, H Muther
    Abstract:

    Abstract Matrix inversion techniques are used to derive an effective hamiltonian for shell-model calculations, which accounts for correlations outside the shell-model space. It is demonstrated that the Bagel approach leads to a very powerful tool to account for the effects of large Q -spaces in a reliable way. An energy-dependent formulation yields stable results even for cases which are divergent in the perturbative approach due to the presence of intruder states. A first application employing modern one-boson exchange potentials produces results which are in very satisfactory agreement with empirical data.

L D Skouras - One of the best experts on this subject based on the ideXlab platform.

  • correlations in nuclei self consistent treatment and the Bagel approach
    Physics Letters B, 1993
    Co-Authors: H Muther, L D Skouras
    Abstract:

    Abstract An approach is presented which allows a self-consistent description of the fragmentation of single-particle strength for nucleons in finite nuclei employing the Green function formalism. The self-energy to be considered in the Dyson equation for the single-particle Green function contains all terms of first (Hartree-Fock) and second order in the residual interaction. It is demonstrated that the fragmentation of the single-particle strength originating from the terms of second order can efficiently be described in terms of the so-called Bagel approximation. Employing this approximation the self-energy can be evaluated in a self-consistent way, i.e. the correlations contained in the Green function are taken into account for the evaluation of the self-energy. As an example this scheme is applied to the nucleus 16 O, using a realistic nucleon nucleon interaction. The effects of the correlations on the occupation probabilities and the binding energy are evaluated.

  • effective interaction derived from the Bagel approach
    Nuclear Physics, 1990
    Co-Authors: L D Skouras, H Muther
    Abstract:

    Abstract Matrix inversion techniques are used to derive an effective hamiltonian for shell-model calculations, which accounts for correlations outside the shell-model space. It is demonstrated that the Bagel approach leads to a very powerful tool to account for the effects of large Q -spaces in a reliable way. An energy-dependent formulation yields stable results even for cases which are divergent in the perturbative approach due to the presence of intruder states. A first application employing modern one-boson exchange potentials produces results which are in very satisfactory agreement with empirical data.

M Ugur D Uygunoglu - One of the best experts on this subject based on the ideXlab platform.

  • myelopathy in behcet s disease the Bagel sign
    Annals of Neurology, 2017
    Co-Authors: M Ugur D Uygunoglu, M Burcu D Zeydan, M Yesim D Ozguler, M Serdal D Ugurlu, M Emire D Seyahi, M Naci D Kocer, M Civan D Islak, M Kejal D Kantarci, M Sabahattin D Saip
    Abstract:

    Objective: To describe the clinical and distinctive imaging features of myelopathy associated with Behcet's disease. Methods: We evaluated the records of patients meeting the following criteria: a) fulfillment of the International Study Group criteria for Behcet's disease; b) clinically suggestive of myelopathy; c) simultaneous spinal cord and brain MRIs within 1 month of acute worsening of myelopathy; d) follow-up duration ≥1 year after initial MRI evaluation. Patients not fulfilling all inclusion criteria and having MRIs with poor quality or missing sequences were excluded. Results: In 11 patients (9 men, 2 women), we studied 14 MRIs during distinct myelopathy episodes and 9 follow-up MRIs. Two distinct MRI patterns of spinal cord involvement were described according to T2W axial images: 1) “Bagel Sign” pattern: A central lesion with hypo-intense core and hyper-intense rim with or without contrast enhancement; 2) “Motor Neuron” pattern: A symmetric involvement of the anterior horn cells. “Bagel Sign” was present in 13 of 14 myelopathy episodes whereas “Motor Neuron” pattern was observed in 1 of 14 MRIs. Of the 13 MRIs with “Bagel Sign” long myelopathy (n=9), both long and short myelopathy (n=2), and short myelopathy (n=2) was observed. All patterns cleared with some residual lesions after steroid use and immunomodulation with associated clinical recovery in patients. Interpretation: The signal characteristics of the “Bagel Sign” potentially represent venous engorgement and/or acute blood products within the spinal cord. To our knowledge, “Bagel Sign” has not been observed in other forms of longitudinal myelopathy outside of BD including neuromyelitis optica. This article is protected by copyright. All rights reserved.

Jason Moffat - One of the best experts on this subject based on the ideXlab platform.

  • Bagel a computational framework for identifying essential genes from pooled library screens
    BMC Bioinformatics, 2016
    Co-Authors: Traver Hart, Jason Moffat
    Abstract:

    Background The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed.

  • Bagel: a computational framework for identifying essential genes from pooled library screens
    BMC Bioinformatics, 2016
    Co-Authors: Traver Hart, Jason Moffat
    Abstract:

    The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed. We offer Bagel (Bayesian Analysis of Gene EssentiaLity), a supervised learning method for analyzing gene knockout screens. Coupled with gold-standard reference sets of essential and nonessential genes, Bagel offers significantly greater sensitivity than current methods, while computational optimizations reduce runtime by an order of magnitude. Using Bagel, we identify ~2000 fitness genes in pooled library knockout screens in human cell lines at 5 % FDR, a major advance over competing platforms. Bagel shows high sensitivity and specificity even across screens performed by different labs using different libraries and reagents.

  • Bagel a computational framework for identifying essential genes from pooled library screens
    bioRxiv, 2015
    Co-Authors: Traver Hart, Jason Moffat
    Abstract:

    Background: The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed. Results: We offer Bagel (Bayesian Analysis of Gene EssentiaLity), a supervised learning method for analyzing gene knockout screens. Coupled with gold-standard reference sets of essential and nonessential genes, Bagel offers significantly greater sensitivity than current methods, while computational optimizations reduce runtime by an order of magnitude. Conclusions: Using Bagel, we identify ~2,000 fitness genes in pooled library knockout screens in human cell lines at 5% FDR, a major advance over competing platforms. Bagel shows high sensitivity and specificity even across screens with highly variable reagent quality.

John C Reed - One of the best experts on this subject based on the ideXlab platform.

  • bag1 proteins regulate growth and survival of zr 75 1 human breast cancer cells
    Cancer Research, 2002
    Co-Authors: M Kudoh, Deborah A Knee, Shinichi Takayama, John C Reed
    Abstract:

    Bag1 proteins bind heat shock protein Mr 70,000 (Hsp 70) family molecular chaperonesand regulate diverse pathways involved in cell proliferation, apoptosis, and stress responses. Four isoforms of Bag1 can be produced froma single gene in humans, including a nuclear-targeted long version (Bag1L)and a shorter cytosolic isoform (Bag1). Because overexpression of Bag1and Bag1L has been reported in breast cancers, we explored the effects of Bag1 and Bag1L on the growth of ZR-75-1 human breast cancer cells cultured in vitro and in tumor xenograft models using immunocompromised mice. Cells stably transfected with expression plasmids encoding either Bag1 or Bag1L displayed comparable rates of growth in cultures containing 10% serum, compared with control-transfected ZR-75-1 cells. In contrast, ZR-75-1 cells stably expressing mutants of Bag1 or Bag1L, which lack the COOH-terminal domain (ΔC) required for heat shock protein Mr 70,000 binding, displayed retarded growth rates. When cultured without serum, the viability of control-transfected, as well as Bag1ΔC- and Bag1LΔC-expressing, cells declined with time, whereas Bag1- and Bag1L-overexpressing ZR-75-1 cells survived for over a week in culture. Caspase protease activation induced by serum deprivation was also prevented by stable expression of either Bag1 or Bag1L in ZR-75-1 cells. In addition, sensitivity to anchorage dependence was restored partially in ZR-75-1 cells expressing dominant-negative Bag1ΔC and Bag1LΔC. In tumor xenograft studies involving injection of ZR-75-1 cells into mammary fat pads of female nu/nu mice, ZR-75-1 cells expressing Bag1 or Bag1L formed 1.4–1.6-fold larger tumors compared with control-transfected cells, whereas tumors formed by Bag1ΔC- and Bag1LΔC-expressing cells grew very slowly and reached sizes

  • structure function analysis of bag1 proteins effects on androgen receptor transcriptional activity
    Journal of Biological Chemistry, 2001
    Co-Authors: Deborah A Knee, Barbara A Froesch, Ulrike Nuber, Shinichi Takayama, John C Reed
    Abstract:

    Abstract Bag1 is a regulator of heat shock protein 70 kDa (Hsp70/Hsc70) family proteins that interacts with steroid hormone receptors. Four isoforms of Bag1 have been recognized: Bag1, Bag1S, Bag1M (RAP46/HAP46), and Bag1L. Although Bag1L, Bag1M, and Bag1 can bind the androgen receptor (AR) in vitro, only Bag1L enhanced AR transcriptional activity. Bag1L was determined to be a nuclear protein by immunofluorescence microscopy, whereas Bag1, Bag1S, and Bag1M were predominantly cytoplasmic. Forced nuclear targeting of Bag1M, but not Bag1 or Bag1S, resulted in potent AR coactivation, indicating that Bag1M possesses the necessary structural features provided it is expressed within the nucleus. The ability of Bag1L to enhance AR activity was reduced with the removal of an NH2-terminal domain of Bag1L, which was found to be required for efficient nuclear localization and/or retention. In contrast, deletion of a conserved ubiquitin-like domain from Bag1L did not interfere with its nuclear targeting or AR regulatory activity. Thus, both the unique NH2-terminal domain and the COOH-terminal Hsc70-binding domain of Bag1L are simultaneously required for its function as an AR regulator, whereas the conserved ubiquitin-like domain is expendable.