Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics

Background
High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures. 
Results
We developed Yeast Features, an intuitive online tool to help establish the significance of finding a diverse set of shared features among a collection of yeast proteins. A total of 18,786 features from the Saccharomyces Genome Database are considered, including annotation based on the Gene Ontology’s molecular function, biological process and cellular compartment, as well as conserved domains, protein-protein and genetic interactions, complexes, metabolic pathways, phenotypes and publications. The significance of shared features is estimated using a hypergeometric probability, but novel options exist to improve the significance by adding background knowledge of the experimental system. For instance, increased statistical significance is achieved in gene deletion experiments because interactions with essential genes will never be observed. We further demonstrate the utility by suggesting the functional roles of the indirect targets of an aminoglycoside with a known mechanism of action, and also the targets of an herbal extract with a previously unknown mode of action. The identification of shared functional features may also be used to propose novel roles for proteins of unknown function, including a role in protein synthesis for YKL075C.
Conclusions
Yeast Features (YF) is an easy to use web-based application (http://software.dumontierlab.com/yeastfeatures/) which can identify and prioritize features that are shared among a set of yeast proteins. This approach is shown to be valuable in the analysis of complex data sets, in which the extracted associations revealed significant functional relationships among the gene products.
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Outpatient Treatment of SARS-CoV-2 Infection to Prevent COVID-19 Progression

As of March 2021, COVID-19 has caused more than 123 million infections, and almost 3 million deaths worldwide. Dramatic advances have been made in vaccine development and non-pharmaceutical interventions to stop the spread of infection. But treatments to stop the progression of disease are limited. A wide variety of "repurposed" drugs explored for treatment of COVID-19 have had little or no benefit. More recently, intravenous monoclonal antibody (mAb) combinations have been authorized by the US FDA for emergency use (EUA) for outpatients with mild to moderate COVID-19 including some active against emerging SARS-COV-2 variants of concern (VOC). Easier to administer therapeutics including intramuscular and subcutaneous mAbs and oral antivirals are in clinical trials. Reliable, safe, effective COVID-19 treatment for early infection in the outpatient setting is of urgent and critical importance. Availability of such treatment should lead to reduced progression of COVID-19

The Remarkable Be Star HD110432

HD110432 has gained considerable attention because it is a hard, variable X-ray source similar to gamma Cas. From time-serial echelle data obtained over two weeks during 2005 January and February, we find several remarkable characteristics in the star's optical spectrum. The line profiles show rapid variations on some nights which can be most likely be attributed to irregularly occurring and short-lived migrating subfeatures. Such features have only been observed to date in gamma Cas and AB Dor, two stars for which it is believed magnetic fields force circumstellar clouds to corotate over the stellar surface. The star's optical spectrum also exhibits a number of mainly FeII and HeI emission features with profiles typical of an optically thin disk viewed edge-on. Using spectral synthesis techniques, we find that its temperature is 9800K +/-300K, that its projected area is a remarkably large 100 stellar areas, and its emitting volume resides at a distance of 1 AU from the star. We also find that the star's absorption profiles extend to +/-1000 km/s, a fact which we cannot explain. Otherwise, HD110432 and gamma Cas share similarly peculiar X-ray and optical characteristics such as high X-ray temperature, erratic X-ray variability on timescales of a few hours, optical emission lines, and submigrating features in optical line profiles. Because of these similarities, we suggest that this star is a new member of a select class of "gamma Cas analogs."Comment: 31 pages, 9 figures, accepted by ApJ (3/20/06

A Study of Wavelength Calibration of NEWSIPS High-Dispersion Spectra

In this study we cross-correlate many IUE echellograms of a variety of stars to evaluate systematic error sources in the wavelength zeropoint of all three cameras. We first evaluated differences between the final archived ("NEWSIPS") and the originally processed ("IUESIPS") spectra. These show a clear time dependence in zeropoint for the SWP camera due to revisions in the IUESIPS wavelength scale. Small IUESIPS - NEWSIPS differences are also found for the LWR camera. We also examined wavelength zeropoint disparities between data obtained both through the small and large entrance apertures and for observations made by different target acquisition modes for faint and bright stars. We found that velocities resulting from these alternative observing modes are nil. For large-aperture observations the dominant error source is the target position placement in the aperture. We searched for spurious trends with time, and found only a suggestion of time trends for faint stars observed with the SWP camera. We also discovered 1-day, +/-3 km/s sinusoidsal patterns in intensive monitoring data which are ascribable to changes in telescope focus resulting from thermal drifts. In the second part of the paper, we measured mean zeropoint errors of NEWSIPS echellogram data against laboratory results by using the GHRS spectral atlas of the 10 Lac. We find that the derived apparent velocity difference for this star is -1 +/-3.5 km/s. Several less precise comparisons lead to similar results. The zeropoints of the NEWSIPS-processed LWP/LWR cameras are evaluated and are also found to be nearly zero (+/-5 km/s) relative to HST atlases of Arcturus and Procyon atlas. These results do not support result by Gonzalez-Riestra et al. that corrections should be introduced to the wavelength scales of various NEWSIPS high-dispersion data products.Comment: 16 pages, Latex with 12 figures, Accepted by Pub. Astron. Soc. Pacific for July 1, 2001. Files available from ftp://nobel.stsci.edu/pub/iuerv

Remnant Fermi surface in the presence of an underlying instability in layered 1T-TaS_2

We report high resolution angle-scanned photoemission and Fermi surface (FS) mapping experiments on the layered transition-metal dichalcogenide 1T-TaS_2 in the quasi commensurate (QC) and the commensurate (C) charge-density-wave (CDW) phase. Instead of a nesting induced partially removed FS in the CDW phase we find a pseudogap over large portions of the FS. This remnant FS exhibits the symmetry of the one-particle normal state FS even when passing from the QC-phase to the C-phase. Possibly, this Mott localization induced transition represents the underlying instability responsible for the pseudogapped FS

Revised Stellar Properties of Kepler Targets for the Quarter 1-16 Transit Detection Run

We present revised properties for 196,468 stars observed by the NASA Kepler Mission and used in the analysis of Quarter 1-16 (Q1-Q16) data to detect and characterize transiting exoplanets. The catalog is based on a compilation of literature values for atmospheric properties (temperature, surface gravity, and metallicity) derived from different observational techniques (photometry, spectroscopy, asteroseismology, and exoplanet transits), which were then homogeneously fitted to a grid of Dartmouth stellar isochrones. We use broadband photometry and asteroseismology to characterize 11,532 Kepler targets which were previously unclassified in the Kepler Input Catalog (KIC). We report the detection of oscillations in 2,762 of these targets, classifying them as giant stars and increasing the number of known oscillating giant stars observed by Kepler by ~20% to a total of ~15,500 stars. Typical uncertainties in derived radii and masses are ~40% and ~20%, respectively, for stars with photometric constraints only, and 5-15% and ~10% for stars based on spectroscopy and/or asteroseismology, although these uncertainties vary strongly with spectral type and luminosity class. A comparison with the Q1-Q12 catalog shows a systematic decrease in radii for M dwarfs, while radii for K dwarfs decrease or increase depending on the Q1-Q12 provenance (KIC or Yonsei-Yale isochrones). Radii of F-G dwarfs are on average unchanged, with the exception of newly identified giants. The Q1-Q16 star properties catalog is a first step towards an improved characterization of all Kepler targets to support planet occurrence studies.Comment: 20 pages, 14 figures, 5 tables; accepted for publication in ApJS; electronic versions of Tables 4 and 5 are available as ancillary files (see sidebar on the right), and an interactive version of Table 5 is available at the NASA Exoplanet Archive (http://exoplanetarchive.ipac.caltech.edu/