269 research outputs found
Redox-Based Probes for Protein Tyrosine Phosphatases
No AbstractPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/83769/1/4423_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/83769/2/anie_201007871_sm_miscellaneous_information.pd
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.
The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine
Automated data processing architecture for the Gemini Planet Imager Exoplanet Survey
The Gemini Planet Imager Exoplanet Survey (GPIES) is a multi-year direct
imaging survey of 600 stars to discover and characterize young Jovian
exoplanets and their environments. We have developed an automated data
architecture to process and index all data related to the survey uniformly. An
automated and flexible data processing framework, which we term the Data
Cruncher, combines multiple data reduction pipelines together to process all
spectroscopic, polarimetric, and calibration data taken with GPIES. With no
human intervention, fully reduced and calibrated data products are available
less than an hour after the data are taken to expedite follow-up on potential
objects of interest. The Data Cruncher can run on a supercomputer to reprocess
all GPIES data in a single day as improvements are made to our data reduction
pipelines. A backend MySQL database indexes all files, which are synced to the
cloud, and a front-end web server allows for easy browsing of all files
associated with GPIES. To help observers, quicklook displays show reduced data
as they are processed in real-time, and chatbots on Slack post observing
information as well as reduced data products. Together, the GPIES automated
data processing architecture reduces our workload, provides real-time data
reduction, optimizes our observing strategy, and maintains a homogeneously
reduced dataset to study planet occurrence and instrument performance.Comment: 21 pages, 3 figures, accepted in JATI
Improving and Assessing Planet Sensitivity of the GPI Exoplanet Survey with a Forward Model Matched Filter
We present a new matched filter algorithm for direct detection of point
sources in the immediate vicinity of bright stars. The stellar Point Spread
Function (PSF) is first subtracted using a Karhunen-Lo\'eve Image Processing
(KLIP) algorithm with Angular and Spectral Differential Imaging (ADI and SDI).
The KLIP-induced distortion of the astrophysical signal is included in the
matched filter template by computing a forward model of the PSF at every
position in the image. To optimize the performance of the algorithm, we conduct
extensive planet injection and recovery tests and tune the exoplanet spectra
template and KLIP reduction aggressiveness to maximize the Signal-to-Noise
Ratio (SNR) of the recovered planets. We show that only two spectral templates
are necessary to recover any young Jovian exoplanets with minimal SNR loss. We
also developed a complete pipeline for the automated detection of point source
candidates, the calculation of Receiver Operating Characteristics (ROC), false
positives based contrast curves, and completeness contours. We process in a
uniform manner more than 330 datasets from the Gemini Planet Imager Exoplanet
Survey (GPIES) and assess GPI typical sensitivity as a function of the star and
the hypothetical companion spectral type. This work allows for the first time a
comparison of different detection algorithms at a survey scale accounting for
both planet completeness and false positive rate. We show that the new forward
model matched filter allows the detection of fainter objects than a
conventional cross-correlation technique with a Gaussian PSF template for the
same false positive rate.Comment: ApJ accepte
Performance of the Gemini Planet Imager Non-Redundant Mask and spectroscopy of two close-separation binaries HR 2690 and HD 142527
The Gemini Planet Imager (GPI) contains a 10-hole non-redundant mask (NRM),
enabling interferometric resolution in complement to its coronagraphic
capabilities. The NRM operates both in spectroscopic (integral field
spectrograph, henceforth IFS) and polarimetric configurations. NRM observations
were taken between 2013 and 2016 to characterize its performance. Most
observations were taken in spectroscopic mode with the goal of obtaining
precise astrometry and spectroscopy of faint companions to bright stars. We
find a clear correlation between residual wavefront error measured by the AO
system and the contrast sensitivity by comparing phase errors in observations
of the same source, taken on different dates. We find a typical 5-
contrast sensitivity of at . We explore the
accuracy of spectral extraction of secondary components of binary systems by
recovering the signal from a simulated source injected into several datasets.
We outline data reduction procedures unique to GPI's IFS and describe a newly
public data pipeline used for the presented analyses. We demonstrate recovery
of astrometry and spectroscopy of two known companions to HR 2690 and HD
142527. NRM+polarimetry observations achieve differential visibility precision
of in the best case. We discuss its limitations on
Gemini-S/GPI for resolving inner regions of protoplanetary disks and prospects
for future upgrades. We summarize lessons learned in observing with NRM in
spectroscopic and polarimetric modes.Comment: Accepted to AJ, 22 pages, 14 figure
GPI spectra of HR 8799 c, d, and e from 1.5 to 2.4m with KLIP Forward Modeling
We explore KLIP forward modeling spectral extraction on Gemini Planet Imager
coronagraphic data of HR 8799, using PyKLIP and show algorithm stability with
varying KLIP parameters. We report new and re-reduced spectrophotometry of HR
8799 c, d, and e in H & K bands. We discuss a strategy for choosing optimal
KLIP PSF subtraction parameters by injecting simulated sources and recovering
them over a range of parameters. The K1/K2 spectra for HR 8799 c and d are
similar to previously published results from the same dataset. We also present
a K band spectrum of HR 8799 e for the first time and show that our H-band
spectra agree well with previously published spectra from the VLT/SPHERE
instrument. We show that HR 8799 c and d show significant differences in their
H & K spectra, but do not find any conclusive differences between d and e or c
and e, likely due to large error bars in the recovered spectrum of e. Compared
to M, L, and T-type field brown dwarfs, all three planets are most consistent
with mid and late L spectral types. All objects are consistent with low gravity
but a lack of standard spectra for low gravity limit the ability to fit the
best spectral type. We discuss how dedicated modeling efforts can better fit HR
8799 planets' near-IR flux and discuss how differences between the properties
of these planets can be further explored.Comment: Accepted to AJ, 25 pages, 16 Figure
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