27 research outputs found
Towards Reliable Automatic Protein Structure Alignment
A variety of methods have been proposed for structure similarity calculation,
which are called structure alignment or superposition. One major shortcoming in
current structure alignment algorithms is in their inherent design, which is
based on local structure similarity. In this work, we propose a method to
incorporate global information in obtaining optimal alignments and
superpositions. Our method, when applied to optimizing the TM-score and the GDT
score, produces significantly better results than current state-of-the-art
protein structure alignment tools. Specifically, if the highest TM-score found
by TMalign is lower than (0.6) and the highest TM-score found by one of the
tested methods is higher than (0.5), there is a probability of (42%) that
TMalign failed to find TM-scores higher than (0.5), while the same probability
is reduced to (2%) if our method is used. This could significantly improve the
accuracy of fold detection if the cutoff TM-score of (0.5) is used.
In addition, existing structure alignment algorithms focus on structure
similarity alone and simply ignore other important similarities, such as
sequence similarity. Our approach has the capacity to incorporate multiple
similarities into the scoring function. Results show that sequence similarity
aids in finding high quality protein structure alignments that are more
consistent with eye-examined alignments in HOMSTRAD. Even when structure
similarity itself fails to find alignments with any consistency with
eye-examined alignments, our method remains capable of finding alignments
highly similar to, or even identical to, eye-examined alignments.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
A Likelihood Method for Measuring the Ultrahigh Energy Cosmic Ray Composition
Air fluorescence detectors traditionally determine the dominant chemical
composit ion of the ultrahigh energy cosmic ray flux by comparing the averaged
slant depth of the shower maximum, , as a function of energy to the
slant depths expect ed for various hypothesized primaries. In this paper, we
present a method to make a direct measurement of the expected mean number of
protons and iron by comparing the shap es of the expected
distributions to the distribution for data. The advantages of this method
includes the use of information of the full distribution and its ability to
calculate a flux for various cosmic ray compositi ons. The same method can be
expanded to marginalize uncertainties due to choice of spectra, hadronic models
and atmospheric parameters. We demonstrate the technique with independent
simulated data samples from a parent sample of protons and iron. We accurately
predict the number of protons and iron in the parent sample and show that the
uncertainties are meaningful.Comment: 11 figures, 22 pages, accepted by Astroparticle Physic
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Gaia Early Data Release 3: The celestial reference frame (Gaia-CRF3)
Context. Gaia-CRF3 is the celestial reference frame for positions and proper motions in the third release of data from the Gaia mission, Gaia DR3 (and for the early third release, Gaia EDR3, which contains identical astrometric results). The reference frame is defined by the positions and proper motions at epoch 2016.0 for a specific set of extragalactic sources in the (E)DR3 catalogue. Aims. We describe the construction of Gaia-CRF3 and its properties in terms of the distributions in magnitude, colour, and astrometric quality. Methods. Compact extragalactic sources in Gaia DR3 were identified by positional cross-matching with 17 external catalogues of quasi-stellar objects (QSO) and active galactic nuclei (AGN), followed by astrometric filtering designed to remove stellar contaminants. Selecting a clean sample was favoured over including a higher number of extragalactic sources. For the final sample, the random and systematic errors in the proper motions are analysed, as well as the radio-optical offsets in position for sources in the third realisation of the International Celestial Reference Frame (ICRF3). Results. Gaia-CRF3 comprises about 1.6 million QSO-like sources, of which 1.2 million have five-parameter astrometric solutions in Gaia DR3 and 0.4 million have six-parameter solutions. The sources span the magnitude range G = 13-21 with a peak density at 20.6 mag, at which the typical positional uncertainty is about 1 mas. The proper motions show systematic errors on the level of 12 ÎŒas yr-1 on angular scales greater than 15 deg. For the 3142 optical counterparts of ICRF3 sources in the S/X frequency bands, the median offset from the radio positions is about 0.5 mas, but it exceeds 4 mas in either coordinate for 127 sources. We outline the future of Gaia-CRF in the next Gaia data releases. Appendices give further details on the external catalogues used, how to extract information about the Gaia-CRF3 sources, potential (Galactic) confusion sources, and the estimation of the spin and orientation of an astrometric solution
Scholarly publishing depends on peer reviewers
The peer-review crisis is posing a risk to the scholarly peer-reviewed journal system. Journals have to ask many potential peer reviewers to obtain a minimum acceptable number of peers accepting reviewing a manuscript. Several solutions have been suggested to overcome this shortage. From reimbursing for the job, to eliminating pre-publication reviews, one cannot predict which is more dangerous for the future of scholarly publishing. And, why not acknowledging their contribution to the final version of the article published? PubMed created two categories of contributors: authors [AU] and collaborators [IR]. Why not a third category for the peer-reviewer?Scopu
Geriatric education in schools of pharmacy: Students' and educators' perspectives in Qatar and Canada
Introduction: Older adults constitute the largest population admitted to hospitals due to chronic diseases, which requires appropriate prescribing of medications and comprehensive pharmaceutical care. The views and perspectives of students and educators can inform curriculum review in geriatric education in pharmacy schools. Methods: A cross sectional online survey containing 34 questions covering the areas of curriculum content and perceived needs for geriatric education was administered to students, faculty members, and preceptors. Data analysis included descriptive and inferential statistics. Results: The majority of participants indicated that their pharmacy school offered geriatric education. Pharmacokinetic/Pharmacodynamic Considerations in the Elderly was the topic most frequently reported to be covered in the geriatric curricula. Significantly more use of small groups discussions for delivering the geriatric curriculum was reported by respondents in Qatar than in Canada. Experiential geriatric education was available in both countries, although duration of rotations were reported to be longer in Canada than in Qatar. The majority of respondents perceived that students were moderately prepared for providing geriatric care. Discussion: This is the first study conducted to explore the current state of geriatric education in a pharmacy school in the Middle East in comparison with a well-established Canadian pharmacy curricula. Conclusion: Both pharmacy schools studied offer a compulsory course on special populations that includes a similar geriatric curriculum. Future surveys should investigate how geriatric content in the pharmacy curricula is being evaluated.This research was made possible thanks to Qatar University's Undergraduate Student Grant # QUST-CPH-SPR-15/16-18