USNO Analysis Center for Source Structure Report

This report summarizes the activities of the United States Naval Observatory Analysis Center for Source Structure for the 2012 calendar year and the activities planned for the year 2013

The Gaussian Plasma Lens in Astrophysics. Refraction

We consider the geometrical optics for refraction of a distant radio source by an interstellar plasma lens, with application to a lens with a Gaussian electron column density profile. The refractive properties of the lens are specified completely by a dimensionless parameter, alpha, which is a function of the wavelength of observation, the lens' electron column density, the lens-observer distance, and the transverse diameter of the lens. Relative motion of the observer and lens produces modulations in the source's light curve. Plasma lenses are diverging so the light curve displays a minimum, when the lens is on-axis, surrounded by enhancements above the unlensed flux density. Lensing can also produce caustics, multiple imaging, and angular position wander of the background source. If caustics are formed, the separation of the outer caustics can constrain alpha, while the separation of the inner caustics can constrain the size of the lens. We apply our analysis to 0954+654, a source for which we can identify caustics in its light curve, and 1741-038, for which polarization observations were obtained during and after the scattering event. We find general agreement between modelled and observed light curves at 2.25 GHz, but poor agreement at 8.1 GHz. The discrepancies may result from a combination of lens substructure or anisotropic shape, a lens that only grazes the source, or unresolved source substructure. Our analysis places the following constraints on the lenses: Toward 0954+654 (1741-038) the lens was 0.38 AU (0.065 AU) in diameter, with a peak column density of 0.24 pc cm^{-3} (1E-4 pc cm^{-3}) and an electron density of 1E5 cm^{-3} (300 cm^{-3}). The angular wander caused by the lens was 250 mas (0.4 mas) at 2.25 GHz. For 1741-038, we place an upper limit of 100 mG on the lens' magnetic field.Comment: 26 pages, LaTeX2e using AASTeX macro aaspp4, 11 PostScript figures; to be published in Ap

Angular Broadening of Intraday Variable AGN. II. Interstellar and Intergalactic Scattering

We analyze a sample of 58 multi-wavelength, Very Long Baseline Array observations of active galactic nuclei (AGN) to determine their scattering properties. Approximately 75% of the sample consists of AGN that exhibit centimeter-wavelength intraday variability (interstellar scintillation) while the other 25% do not show intraday variability. We find that interstellar scattering is measurable for most of these AGN, and the typical broadening diameter is 2 mas at 1 GHz. We find that the scintillating AGN are typically at lower Galactic latitudes than the non-scintillating AGN, consistent with the scenario that intraday variability is a propagation effect from the Galactic interstellar medium. The magnitude of the inferred interstellar broadening measured toward the scintillating AGN, when scaled to higher frequencies, is comparable to the diameters inferred from analyses of the light curves for the more well-known intraday variable sources. However, we find no difference in the amount of scattering measured toward the scintillating versus non-scintillating AGN. A consistent picture is one in which the scintillation results from localized regions ("clumps") distributed throughout the Galactic disk, but which individually make little contribution to the angular broadening. Of the 58 AGN observed, 37 (64%) have measured redshifts. At best, a marginal trend is found for scintillating (non-scintillating) AGN to have smaller (larger) angular diameters at higher redshifts. We also use our observations to try to constrain the possibility of intergalactic scattering. While broadly consistent with the scenario of a highly turbulent intergalactic medium, our observations do not place significant constraints on its properties.Comment: 13 pages, 4 figures; AASTeX format; ApJ in pres

U.S. Naval Observatory VLBI Analysis Center

This report summarizes the activities of the VLBI Analysis Center at the United States Naval Observatory for the 2012 calendar year. Over the course of the year, Analysis Center personnel continued analysis and timely submission of IVS-R4 databases for distribution to the IVS. During the 2012 calendar year, the USNO VLBI Analysis Center produced two VLBI global solutions designated as usn2012a and usn2012b. Earth orientation parameters (EOP) based on this solution and updated by the latest diurnal (IVS-R1 and IVS-R4) experiments were routinely submitted to the IVS. Sinex files based upon the bi-weekly 24-hour experiments were also submitted to the IVS. During the 2012 calendar year, Analysis Center personnel continued a program to use the Very Long Baseline Array (VLBA) operated by the NRAO for the purpose of measuring UT1-UTC. Routine daily 1-hour duration Intensive observations were initiated using the VLBA antennas at Pie Town, NM and Mauna Kea, HI. High-speed network connections to these two antennas are now routinely used for electronic transfer of VLBI data over the Internet to a USNO point of presence. A total of 270 VLBA Intensive experiments were observed and electronically transferred to and processed at USNO in 2012

Taking the Measure of the Universe: Precision Astrometry with SIM PlanetQuest

Precision astrometry at microarcsecond accuracy has application to a wide range of astrophysical problems. This paper is a study of the science questions that can be addressed using an instrument that delivers parallaxes at about 4 microarcsec on targets as faint as V = 20, differential accuracy of 0.6 microarcsec on bright targets, and with flexible scheduling. The science topics are drawn primarily from the Team Key Projects, selected in 2000, for the Space Interferometry Mission PlanetQuest (SIM PlanetQuest). We use the capabilities of this mission to illustrate the importance of the next level of astrometric precision in modern astrophysics. SIM PlanetQuest is currently in the detailed design phase, having completed all of the enabling technologies needed for the flight instrument in 2005. It will be the first space-based long baseline Michelson interferometer designed for precision astrometry. SIM will contribute strongly to many astronomical fields including stellar and galactic astrophysics, planetary systems around nearby stars, and the study of quasar and AGN nuclei. SIM will search for planets with masses as small as an Earth orbiting in the `habitable zone' around the nearest stars using differential astrometry, and could discover many dozen if Earth-like planets are common. It will be the most capable instrument for detecting planets around young stars, thereby providing insights into how planetary systems are born and how they evolve with time. SIM will observe significant numbers of very high- and low-mass stars, providing stellar masses to 1%, the accuracy needed to challenge physical models. Using precision proper motion measurements, SIM will probe the galactic mass distribution and the formation and evolution of the Galactic halo. (abridged)Comment: 54 pages, 28 figures, uses emulateapj. Submitted to PAS

Range expansion and the origin of USA300 north american epidemic methicillin-resistant Staphylococcus aureus

The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity and increases in derived allele frequency with geographic distance from the Pennsylvania region. These signatures account for approximately half of the core nucleotide variation of this clone, occur genome wide, and are robust to heterogeneity in temporal sampling of isolates, human population density, and recombination detection methods. The potential for positive selection of a gyrA fluoroquinolone resistance allele and several intergenic regions, along with a 2.4 times higher recombination rate in a resistant subclade, is noted. These results are the first to show a pattern of genetic variation that is consistent with a range expansion of an epidemic bacterial clone, and they highlight a rarely considered but potentially common mechanism by which genetic drift may profoundly influence bacterial genetic variation. IMPORTANCE The process of geographic spread of an origin population by a series of smaller populations can result in distinctive patterns of genetic variation. We detect these patterns for the first time with an epidemic bacterial clone and use them to uncover the clone’s geographic origin and variants associated with its spread. We study the USA300 clone of methicillin-resistant Staphylococcus aureus, which was first noticed in the early 2000s and subsequently became the leading cause of skin and soft tissue infections in the United States. The eastern United States is the most likely origin of epidemic USA300. Relatively few variants, which include an antibiotic resistance mutation, have persisted during this clone’s spread. Our study suggests that an early chapter in the genetic history of this epidemic bacterial clone was greatly influenced by random subsampling of isolates during the clone’s geographic spread

Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia.

Histone lysine methylation, mediated by mixed-lineage leukemia (MLL) proteins, is now known to be critical in the regulation of gene expression, genomic stability, cell cycle and nuclear architecture. Despite MLL proteins being postulated as essential for normal development, little is known about the specific functions of the different MLL lysine methyltransferases. Here we report heterozygous variants in the gene KMT2B (also known as MLL4) in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance and characteristic brain magnetic resonance imaging findings. Over time, the majority of affected individuals developed prominent cervical, cranial and laryngeal dystonia. Marked clinical benefit, including the restoration of independent ambulation in some cases, was observed following deep brain stimulation (DBS). These findings highlight a clinically recognizable and potentially treatable form of genetic dystonia, demonstrating the crucial role of KMT2B in the physiological control of voluntary movement.Funding for the project was provided by the Wellcome Trust for UK10K (WT091310) and DDD Study. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003] - see www.ddduk.org/access.html for full acknowledgement. This work was supported in part by the Intramural Research Program of the National Human Genome Research Institute and the Common Fund, NIH Office of the Director. This work was supported in part by the German Ministry of Research and Education (grant nos. 01GS08160 and 01GS08167; German Mental Retardation Network) as part of the National Genome Research Network to A.R. and D.W. and by the Deutsche Forschungsgemeinschaft (AB393/2-2) to A.R. Brain expression data was provided by the UK Human Brain Expression Consortium (UKBEC), which comprises John A. Hardy, Mina Ryten, Michael Weale, Daniah Trabzuni, Adaikalavan Ramasamy, Colin Smith and Robert Walker, affiliated with UCL Institute of Neurology (J.H., M.R., D.T.), King’s College London (M.R., M.W., A.R.) and the University of Edinburgh (C.S., R.W.)

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project