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
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
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
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
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
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
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 (2 Earth radii, 10 M) 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
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
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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