2,507 research outputs found
An on-line velocity flow profiling system using electrical resistance tomography
A system to display velocity profiles of flows through the CPUT FPRC pipe test loop on-line has been developed. An electrical resistance tomography instrument developed at the University of Cape Town is used to generate conductivity profiles through cross sections of the flow in a 057mm pipe at two points, separated by either 50 or 100mm. The two concentration profiles are cross correlated on a pixel-wise basis to produce a velocity profile. The software was developed using C++ and employs a highly modular structure that allows different image reconstruction and cross correlation algorithms to be implemented without substantial changes to the rest of the application. Results showing the speed performance of the system are presented as well as typical velocity profiles from a sliding bed flow regime
SPIDR: Small-Molecule Peptide-Influenced Drug Repurposing
Background: Conventional de novo drug design is costly and time consuming, making it accessible to only the best resourced research organizations. An emergent approach to new drug development is drug repurposing, in which compounds that have already gone through some level of clinical testing are examined for efficacy against diseases divergent than their original application. Repurposing of existing drugs circumvents the time and considerable cost of early stages of drug development, and can be accelerated by using software to screen existing chemical databases to identify suitable drug candidates.
Results: Small-molecule Peptide-Influenced Drug Repurposing (SPIDR) was developed to identify small molecule drugs that target a specific receptor by exploring the conformational binding space of peptide ligands. SPIDR was tested using the potent and selective 16-amino acid peptide α-conotoxin MII ligand and the α3β2-nicotinic acetylcholine receptor (nAChR) isoform. SPIDR incorporates a genetic algorithm-based, heuristic search procedure, which was used to explore the ligand binding domain of the α3β2-nAChR isoform using a library consisting of 640,000 α-conotoxin MII peptide analogs. The peptides that exhibited the highest affinity for α3β2-nAChR were used as models for a small-molecule structure similarity search of the PubChem Compound database. SPIDR incorporates the SimSearcher utility, which generates shape distribution signatures of molecules and employs multi-level K-means clustering to insure fast database queries. SPIDR identified non-peptide drugs with estimated binding affinities nearly double that of the native α-conotoxin MII peptide.
Conclusions: SPIDR has been generalized and integrated into DockoMatic v 2.1. This software contains an intuitive graphical interface for peptide mutant screening workflow and facilitates mapping, clustering, and searching of local molecular databases, making DockoMatic a valuable tool for researchers in drug design and repurposing
Accurate Assignments of Excited-State Resonance Raman Spectra: A Benchmark Study Combining Experiment and Theory
This is an unofficial translation of an article that appeared in an ACS publication. ACS has not endorsed the content of this translation or the context of its use.Femtosecond stimulated Raman scattering (FSRS) probes the structural dynamics of molecules in electronically excited states by following the evolution of the vibrational spectrum. Interpreting the dynamics requires accurate assignments to connect the vibrational bands with specific nuclear motions of an excited molecule. However, the assignment of FSRS signals is often complicated by mode-specific resonance enhancement effects that are difficult to calculate for molecules in electronically excited states. We present benchmark results for a series of eight aryl-substituted thiophene derivatives to show that calculated off-resonance Raman spectra can be used to assign experimental bands on the basis of a comparison of structurally similar compounds and careful consideration of the resonance condition. Importantly, we show that direct comparison with the off-resonant calculations can lead to incorrect assignments of the experimental spectrum if the resonance condition is neglected. These results highlight the importance of resonance enhancement effects in assigning FSRS spectra
The Sloan Digital Sky Survey Quasar Catalog I. Early Data Release
We present the first edition of the Sloan Digital Sky Survey (SDSS) Quasar
Catalog. The catalog consists of the 3814 objects (3000 discovered by the SDSS)
in the initial SDSS public data release that have at least one emission line
with a full width at half maximum larger than 1000 km/s, luminosities brighter
than M_i^* = -23, and highly reliable redshifts. The area covered by the
catalog is 494 square degrees; the majority of the objects were found in SDSS
commissioning data using a multicolor selection technique. The quasar redshifts
range from 0.15 to 5.03. For each object the catalog presents positions
accurate to better than 0.2" rms per coordinate, five band (ugriz) CCD-based
photometry with typical accuracy of 0.05 mag, radio and X-ray emission
properties, and information on the morphology and selection method. Calibrated
spectra of all objects in the catalog, covering the wavelength region 3800 to
9200 Angstroms at a spectral resolution of 1800-2100, are also available. Since
the quasars were selected during the commissioning period, a time when the
quasar selection algorithm was undergoing frequent revisions, the sample is not
homogeneous and is not intended for statistical analysis.Comment: 27 pages, 4 figures, 4 tables, accepted by A
The Multi-Object, Fiber-Fed Spectrographs for SDSS and the Baryon Oscillation Spectroscopic Survey
We present the design and performance of the multi-object fiber spectrographs
for the Sloan Digital Sky Survey (SDSS) and their upgrade for the Baryon
Oscillation Spectroscopic Survey (BOSS). Originally commissioned in Fall 1999
on the 2.5-m aperture Sloan Telescope at Apache Point Observatory, the
spectrographs produced more than 1.5 million spectra for the SDSS and SDSS-II
surveys, enabling a wide variety of Galactic and extra-galactic science
including the first observation of baryon acoustic oscillations in 2005. The
spectrographs were upgraded in 2009 and are currently in use for BOSS, the
flagship survey of the third-generation SDSS-III project. BOSS will measure
redshifts of 1.35 million massive galaxies to redshift 0.7 and Lyman-alpha
absorption of 160,000 high redshift quasars over 10,000 square degrees of sky,
making percent level measurements of the absolute cosmic distance scale of the
Universe and placing tight constraints on the equation of state of dark energy.
The twin multi-object fiber spectrographs utilize a simple optical layout
with reflective collimators, gratings, all-refractive cameras, and
state-of-the-art CCD detectors to produce hundreds of spectra simultaneously in
two channels over a bandpass covering the near ultraviolet to the near
infrared, with a resolving power R = \lambda/FWHM ~ 2000. Building on proven
heritage, the spectrographs were upgraded for BOSS with volume-phase
holographic gratings and modern CCD detectors, improving the peak throughput by
nearly a factor of two, extending the bandpass to cover 360 < \lambda < 1000
nm, and increasing the number of fibers from 640 to 1000 per exposure. In this
paper we describe the original SDSS spectrograph design and the upgrades
implemented for BOSS, and document the predicted and measured performances.Comment: 43 pages, 42 figures, revised according to referee report and
accepted by AJ. Provides background for the instrument responsible for SDSS
and BOSS spectra. 4th in a series of survey technical papers released in
Summer 2012, including arXiv:1207.7137 (DR9), arXiv:1207.7326 (Spectral
Classification), and arXiv:1208.0022 (BOSS Overview
Tuberculosis diagnostics and biomarkers: needs, challenges, recent advances, and opportunities
Tuberculosis is unique among the major infectious diseases in that it lacks accurate rapid point-of-care diagnostic tests. Failure to control the spread of tuberculosis is largely due to our inability to detect and treat all infectious cases of pulmonary tuberculosis in a timely fashion, allowing continued Mycobacterium tuberculosis transmission within communities. Currently recommended gold-standard diagnostic tests for tuberculosis are laboratory based, and multiple investigations may be necessary over a period of weeks or months before a diagnosis is made. Several new diagnostic tests have recently become available for detecting active tuberculosis disease, screening for latent M. tuberculosis infection, and identifying drug-resistant strains of M. tuberculosis. However, progress toward a robust point-of-care test has been limited, and novel biomarker discovery remains challenging. In the absence of effective prevention strategies, high rates of early case detection and subsequent cure are required for global tuberculosis control. Early case detection is dependent on test accuracy, accessibility, cost, and complexity, but also depends on the political will and funder investment to deliver optimal, sustainable care to those worst affected by the tuberculosis and human immunodeficiency virus epidemics. This review highlights unanswered questions, challenges, recent advances, unresolved operational and technical issues, needs, and opportunities related to tuberculosis diagnostics
The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment
The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in
operation since July 2014. This paper describes the second data release from
this phase, and the fourteenth from SDSS overall (making this, Data Release
Fourteen or DR14). This release makes public data taken by SDSS-IV in its first
two years of operation (July 2014-2016). Like all previous SDSS releases, DR14
is cumulative, including the most recent reductions and calibrations of all
data taken by SDSS since the first phase began operations in 2000. New in DR14
is the first public release of data from the extended Baryon Oscillation
Spectroscopic Survey (eBOSS); the first data from the second phase of the
Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2),
including stellar parameter estimates from an innovative data driven machine
learning algorithm known as "The Cannon"; and almost twice as many data cubes
from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous
release (N = 2812 in total). This paper describes the location and format of
the publicly available data from SDSS-IV surveys. We provide references to the
important technical papers describing how these data have been taken (both
targeting and observation details) and processed for scientific use. The SDSS
website (www.sdss.org) has been updated for this release, and provides links to
data downloads, as well as tutorials and examples of data use. SDSS-IV is
planning to continue to collect astronomical data until 2020, and will be
followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14
happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov
2017 (this is the "post-print" and "post-proofs" version; minor corrections
only from v1, and most of errors found in proofs corrected
The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey
The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic
data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data
release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median
z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar
spectra, along with the data presented in previous data releases. These spectra
were obtained with the new BOSS spectrograph and were taken between 2009
December and 2011 July. In addition, the stellar parameters pipeline, which
determines radial velocities, surface temperatures, surface gravities, and
metallicities of stars, has been updated and refined with improvements in
temperature estimates for stars with T_eff<5000 K and in metallicity estimates
for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars
presented in DR8, including stars from SDSS-I and II, as well as those observed
as part of the SDSS-III Sloan Extension for Galactic Understanding and
Exploration-2 (SEGUE-2).
The astrometry error introduced in the DR8 imaging catalogs has been
corrected in the DR9 data products. The next data release for SDSS-III will be
in Summer 2013, which will present the first data from the Apache Point
Observatory Galactic Evolution Experiment (APOGEE) along with another year of
data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at
http://www.sdss3.org/dr
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