7,402 research outputs found

    Antibody-based detection of protein phosphorylation status to track the efficacy of novel therapies using nanogram protein quantities from stem cells and cell lines

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    This protocol describes a highly reproducible antibody-based method that provides protein level and phosphorylation status information from nanogram quantities of protein cell lysate. Nanocapillary isoelectric focusing (cIEF) combines with UV-activated linking chemistry to detect changes in phosphorylation status. As an example application, we describe how to detect changes in response to tyrosine kinase inhibitors (TKIs) in the phosphorylation status of the adaptor protein ​CrkL, a major substrate of the oncogenic tyrosine kinase ​BCR-​ABL in chronic myeloid leukemia (CML), using highly enriched CML stem cells and mature cell populations in vitro. This protocol provides a 2.5 pg/nl limit of protein detection (<0.2% of a stem cell sample containing <104 cells). Additional assays are described for phosphorylated tyrosine 207 (pTyr207)-​CrkL and the protein tyrosine phosphatase ​PTPRC/​CD45; these assays were developed using this protocol and applied to CML patient samples. This method is of high throughput, and it can act as a screen for in vitro cancer stem cell response to drugs and novel agents

    Discriminating Lambda-Terms Using Clocked Boehm Trees

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    As observed by Intrigila, there are hardly techniques available in the lambda-calculus to prove that two lambda-terms are not beta-convertible. Techniques employing the usual Boehm Trees are inadequate when we deal with terms having the same Boehm Tree (BT). This is the case in particular for fixed point combinators, as they all have the same BT. Another interesting equation, whose consideration was suggested by Scott, is BY = BYS, an equation valid in the classical model P-omega of lambda-calculus, and hence valid with respect to BT-equality but nevertheless the terms are beta-inconvertible. To prove such beta-inconvertibilities, we employ `clocked' BT's, with annotations that convey information of the tempo in which the data in the BT are produced. Boehm Trees are thus enriched with an intrinsic clock behaviour, leading to a refined discrimination method for lambda-terms. The corresponding equality is strictly intermediate between beta-convertibility and Boehm Tree equality, the equality in the model P-omega. An analogous approach pertains to Levy-Longo and Berarducci Trees. Our refined Boehm Trees find in particular an application in beta-discriminating fixed point combinators (fpc's). It turns out that Scott's equation BY = BYS is the key to unlocking a plethora of fpc's, generated by a variety of production schemes of which the simplest was found by Boehm, stating that new fpc's are obtained by postfixing the term SI, also known as Smullyan's Owl. We prove that all these newly generated fpc's are indeed new, by considering their clocked BT's. Even so, not all pairs of new fpc's can be discriminated this way. For that purpose we increase the discrimination power by a precision of the clock notion that we call `atomic clock'.Comment: arXiv admin note: substantial text overlap with arXiv:1002.257

    The WFIRST Galaxy Survey Exposure Time Calculator

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    This document describes the exposure time calculator for the Wide-Field Infrared Survey Telescope (WFIRST) high-latitude survey. The calculator works in both imaging and spectroscopic modes. In addition to the standard ETC functions (e.g. background and S/N determination), the calculator integrates over the galaxy population and forecasts the density and redshift distribution of galaxy shapes usable for weak lensing (in imaging mode) and the detected emission lines (in spectroscopic mode). The source code is made available for public use.Comment: 44 pages. The current C source code and version history can be found at http://www.tapir.caltech.edu/~chirata/web/software/space-etc/ ; IPAC maintains a web interface at http://wfirst-web.ipac.caltech.edu/wfDepc/wfDepc.js

    Atmospheric NLTE-Models for the Spectroscopic Analysis of Blue Stars with Winds. II. Line-Blanketed Models

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    We present new or improved methods for calculating NLTE, line-blanketed model atmospheres for hot stars with winds (spectral types A to O), with particular emphasis on a fast performance. These methods have been implemented into a previous, more simple version of the model atmosphere code FASTWIND (Santolaya-Rey et al.1997) and allow to spectroscopically analyze rather large samples of massive stars in a reasonable time-scale, using state-of-the-art physics. We describe our (partly approximate) approach to solve the equations of statistical equilibrium for those elements which are primarily responsible for line-blocking and blanketing, as well as an approximate treatment of the line-blocking itself, which is based on a simple statistical approach using suitable means for line opacities and emissivities. Furthermore, we comment on our implementation of a consistent temperature structure. In the second part, we concentrate on a detailed comparison with results from those two codes which have been used in alternative spectroscopical investigations, namely CMFGEN (Hillier & Miller 1998) and WM-Basic (Pauldrach et al. 2001). All three codes predict almost identical temperature structures and fluxes for lambda > 400 A, whereas at lower wavelengths a number of discrepancies are found. Optical H/He lines as synthesized by FASTWIND are compared with results from CMFGEN, obtaining a remarkable coincidence, except for the HeI singlets in the temperature range between 36,000 to 41,000 K for dwarfs and between 31,000 to 35,000 K for supergiants, where CMFGEN predicts much weaker lines. Consequences due to these discrepancies are discussed.Comment: 30 pages incl. 20 figures, accepted by A&

    Metabonomic Profiles Delineate the Effect of Traditional Chinese Medicine Sini Decoction on Myocardial Infarction in Rats

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    Background: In spite of great advances in target-oriented Western medicine for treating myocardial infarction (MI), it is still a leading cause of death in a worldwide epidemic. In contrast to Western medicine, Traditional Chinese medicine (TCM) uses a holistic and synergistic approach to restore the balance of Yin-Yang of body energy so the body’s normal function can be restored. Sini decoction (SND) is a well-known formula of TCM which has been used to treat MI for many years. However, its holistic activity evaluation and mechanistic understanding are still lacking due to its complex components. Methodology/Principal Findings: A urinary metabonomic method based on nuclear magnetic resonance and ultra highperformance liquid chromatography coupled to mass spectrometry was developed to characterize MI-related metabolic profiles and delineate the effect of SND on MI. With Elastic Net for classification and selection of biomarkers, nineteen potential biomarkers in rat urine were screened out, primarily related to myocardial energy metabolism, including the glycolysis, citrate cycle, amino acid metabolism, purine metabolism and pyrimidine metabolism. With the altered metabolism pathways as possible drug targets, we systematically analyze the therapeutic effect of SND, which demonstrated that SND administration could provide satisfactory effect on MI through partially regulating the perturbed myocardial energy metabolism. Conclusions/Significance: Our results showed that metabonomic approach offers a useful tool to identify MI-relate

    SPICES: Spectro-Polarimetric Imaging and Characterization of Exoplanetary Systems

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    SPICES (Spectro-Polarimetric Imaging and Characterization of Exoplanetary Systems) is a five-year M-class mission proposed to ESA Cosmic Vision. Its purpose is to image and characterize long-period extrasolar planets and circumstellar disks in the visible (450 - 900 nm) at a spectral resolution of about 40 using both spectroscopy and polarimetry. By 2020/22, present and near-term instruments will have found several tens of planets that SPICES will be able to observe and study in detail. Equipped with a 1.5 m telescope, SPICES can preferentially access exoplanets located at several AUs (0.5-10 AU) from nearby stars (<<25 pc) with masses ranging from a few Jupiter masses to Super Earths (∼\sim2 Earth radii, ∼\sim10 M⊕_{\oplus}) as well as circumstellar disks as faint as a few times the zodiacal light in the Solar System

    Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending

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    Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA difH, representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in difH defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division

    The finite-temperature Monte Carlo method and its application to superfluid helium clusters

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    We review the use of the path integral Monte Carlo (PIMC) methodology to the study of finite-size quantum clusters, with particular emphasis on recent applications to pure and impurity-doped He clusters. We describe the principles of PIMC, the use of the multilevel Metropolis method for sampling particle permutations, and the methods used to accurately incorporate anisotropic molecule-helium interactions into the path integral scheme. Applications to spectroscopic studies of embedded atoms and molecules are summarized, with discussion of the new concepts of local and nanoscale superfluidity that have been generated by recent PIMC studies of the impurity-doped He clusters.Comment: P. Huang, Y. Kwon, and K. B. Whaley, in "Quantum Fluids in Confinement", Vol. 4 of "Advances in Quantum Many-Body Theories", edited by E. Krotscheck and J. Navarro (World Scientific, Singapore, 2002), in pres
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