Bridging the Divide between Manual Gating and Bioinformatics with the Bioconductor Package flowFlowJo

In flow cytometry, different cell types are usually selected or “gated” by a series of 1- or 2-dimensional geometric subsets of the measurements made on each cell. This is easily accomplished in commercial flow cytometry packages but it is difficult to work computationally with the results of this process. The ability to retrieve the results and work with both them and the raw data is critical; our experience points to the importance of bioinformatics tools that will allow us to examine gating robustness, combine manual and automated gating, and perform exploratory data analysis. To provide this capability, we have developed a Bioconductor package called flowFlowJo that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. We present this package and illustrate some of the ways in which it can be used

Highly Polarized Optically-Selected BL Lacertae Objects

Observations of candidate BL Lacertae objects spectroscopically selected from the Sloan Digital Sky Survey (SDSS) reveal a large fraction with high polarization (P > 3%). This result confirms that synchrotron radiation makes an important contribution to the observed optical continuum for most objects in the sample. The SDSS sample can be divided into separate categories, with objects of undetermined redshift generally having the highest optical polarization. Polarization as high as 23% and the lack of spectral features suggests that the synchrotron continuum completely dominates the spectra of these sources. The mean polarization levels observed for objects having measured redshifts is much lower, with the maximum observed polarization for this group being ~10%. The lower polarizations of these objects are reminiscent of the less spectacular polarization levels shown by BL Lac objects discovered in X-ray surveys. We find no SDSS BL Lac candidates at z > 1 with P > 3%, calling their classification as BL Lac objects into question. In addition, the existence of radio-quiet BL Lac objects is not verified since none of 10 potentially radio-weak BL Lac candidates observed are highly polarized. Regardless of whether the high-redshift and radio-weak objects are included in this optical sample, the overall levels of polarization observed are intermediate between those seen for X-ray and radio-selected BL Lac objects.Comment: 9 pages, 3 figures, 2 table

Survey of coherent ∼1 Hz waves in Mercury's inner magnetosphere from MESSENGER observations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95559/1/jgra22073.pd

MMS, Van Allen Probes, GOES 13, and Groundâ Based Magnetometer Observations of EMIC Wave Events Before, During, and After a Modest Interplanetary Shock

The stimulation of electromagnetic ion cyclotron (EMIC) waves by a magnetospheric compression is perhaps the closest thing to a controlled experiment that is currently possible in magnetospheric physics, in that one prominent factor that can increase wave growth acts at a wellâ defined time. We present a detailed analysis of EMIC waves observed in the outer dayside magnetosphere by the four Magnetosphere Multiscale (MMS) spacecraft, Van Allen Probe A, and GOES 13 and by four very high latitude ground magnetometer stations in the western hemisphere before, during, and after a modest interplanetary shock on 14 December 2015. Analysis shows several features consistent with current theory, as well as some unexpected features. During the most intense MMS wave burst, which began ~ 1 min after the end of a brief magnetosheath incursion, independent transverse EMIC waves with orthogonal linear polarizations appeared simultaneously at all four spacecraft. He++ band EMIC waves were observed by MMS inside the magnetosphere, whereas almost all previous studies of He++ band EMIC waves observed them only in the magnetosheath and magnetopause boundary layers. Transverse EMIC waves also appeared at Van Allen Probe A and GOES 13 very near the times when the magnetic field compression reached their locations, indicating that the compression lowered the instability threshold to allow for EMIC wave generation throughout the outer dayside magnetosphere. The timing of the EMIC waves at both MMS and Van Allen Probe A was consistent with theoretical expectations for EMIC instabilities based on characteristics of the proton distributions observed by instruments on these spacecraft.Key PointsMMS observed a burst of independent transverse EMIC waves with orthogonal linear polarizations following the shockWave onsets at both MMS and Van Allen Probe A were consistent with theoretical expectations based on particle observationsA rarely observed minimum in wave power at the gyrofrequency of He++ ions was present both before and after the shockPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146614/1/jgra54570_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146614/2/jgra54570.pd

Validity of Recall of Tobacco Use in Two Prospective Cohorts

This project studied the convergent validity of current recall of tobacco-related health behaviors, compared with prospective self-report collected earlier at two sites. Cohorts were from the Oregon Research Institute at Eugene (N = 346, collected 19.5 years earlier) and the University of Pittsburgh, Pennsylvania (N = 294, collected 3.9 years earlier). Current recall was examined through computer-assisted interviews with the Lifetime Tobacco Use Questionnaire from 2005 through 2008. Convergent validity estimates demonstrated variability. Validity estimates of some tobacco use measures were significant for Oregon subjects (age at first cigarette, number of cigarettes/day, quit attempts yes/no and number of attempts, and abstinence symptoms at quitting; all P < 0.03). Validity estimates of Pittsburgh subjects’ self-reports of tobacco use and abstinence symptoms were significant (P < 0.001) for all tobacco use and abstinence symptoms and for responses to initial use of tobacco. These findings support the utility of collecting recalled self-report information for reconstructing salient lifetime health behaviors and underscore the need for careful interpretation

Poxvirus Protein N1L Targets the I-κB Kinase Complex, Inhibits Signaling to NF-κB by the Tumor Necrosis Factor Superfamily of Receptors, and Inhibits NF-κB and IRF3 Signaling by Toll-like Receptors

Poxviruses encode proteins that suppress host immune responses, including secreted decoy receptors for pro-inflammatory cytokines such as interleukin-1 (IL-1) and the vaccinia virus proteins A46R and A52R that inhibit intracellular signaling by members of the IL-1 receptor (IL-1R) and Toll-like receptor (TLR) family. In vivo, the TLRs mediate the innate immune response by serving as pathogen recognition receptors, whose oligomerized intracellular Toll/IL-1 receptor (TIR) domains can initiate innate immune signaling. A family of TIR domain-containing adapter molecules transduces signals from engaged receptors that ultimately activate NF-kappaB and/or interferon regulatory factor 3 (IRF3) to induce pro-inflammatory cytokines. Data base searches detected a significant similarity between the N1L protein of vaccinia virus and A52R, a poxvirus inhibitor of TIR signaling. Compared with other poxvirus virulence factors, the poxvirus N1L protein strongly affects virulence in vivo; however, the precise target of N1L was previously unknown. Here we show that N1L suppresses NF-kappaB activation following engagement of Toll/IL-1 receptors, tumor necrosis factor receptors, and lymphotoxin receptors. N1L inhibited receptor-, adapter-, TRAF-, and IKK-alpha and IKK-beta-dependent signaling to NF-kappaB. N1L associated with several components of the multisubunit I-kappaB kinase complex, most strongly associating with the kinase, TANK-binding kinase 1 (TBK1). Together these findings are consistent with the hypothesis that N1L disrupts signaling to NF-kappaB by Toll/IL-1Rs and TNF superfamily receptors by targeting the IKK complex for inhibition. Furthermore, N1L inhibited IRF3 signaling, which is also regulated by TBK1. These studies define a role for N1L as an immunomodulator of innate immunity by targeting components of NF-kappaB and IRF3 signaling pathways

Detection of a Single Identical Cytomegalovirus (CMV) Strain in Recently Seroconverted Young Women

Infection with multiple CMV strains is common in immunocompromised hosts, but its occurrence in normal hosts has not been well-studied.We analyzed CMV strains longitudinally in women who acquired CMV while enrolled in a CMV glycoprotein B (gB) vaccine trial. Sequencing of four variable genes was performed in samples collected from seroconversion and up to 34 months thereafter.199 cultured isolates from 53 women and 65 original fluids from a subset of 19 women were sequenced. 51 women were infected with one strain each without evidence for genetic drift; only two women shed multiple strains. Genetic variability among strains increased with the number of sequenced genetic loci. Nevertheless, 13 of 53 women proved to be infected with an identical CMV strain based on sequencing at all four variable genes. CMV vaccine did not alter the degree of genetic diversity amongst strains.Primary CMV infection in healthy women nearly always involves shedding of one strain that remains stable over time. Immunization with CMVgB-1 vaccine strain is not selective against specific strains. Although 75% of women harbored their unique strain, or a strain shared with only one other woman, 25% shared a single common strain, suggesting that this predominant strain with a particular combination of genetic loci is advantageous in this large urban area

Ezrin Ubiquitylation by the E3 Ubiquitin Ligase, WWP1, and Consequent Regulation of Hepatocyte Growth Factor Receptor Activity

The membrane cytoskeleton linker ezrin participates in several functions downstream of the receptor Met in response to Hepatocyte Growth Factor (HGF) stimulation. Here we report a novel interaction of ezrin with a HECT E3 ubiquitin ligase, WWP1/Aip5/Tiul1, a potential oncogene that undergoes genomic amplification and overexpression in human breast and prostate cancers. We show that ezrin binds to the WW domains of WWP1 via the consensus motif PPVY477 present in ezrin’s C-terminus. This association results in the ubiquitylation of ezrin, a process that requires an intact PPVY477 motif. Interestingly ezrin ubiquitylation does not target the protein for degradation by the proteasome. We find that ezrin ubiquitylation by WWP1 in epithelial cells leads to the upregulation of Met level in absence of HGF stimulation and increases the response of Met to HGF stimulation as measured by the ability of the cells to heal a wound. Interestingly this effect requires ubiquitylated ezrin since it can be rescued, after depletion of endogenous ezrin, by wild type ezrin but not by a mutant of ezrin that cannot be ubiquitylated. Taken together our data reveal a new role for ezrin in Met receptor stability and activity through its association with the E3 ubiquitin ligase WWP1. Given the role of Met in cell proliferation and tumorigenesis, our results may provide a mechanistic basis for understanding the role of ezrin in tumor progression

Efficient precision quantization in AdS/CFT

Understanding finite-size effects is one of the key open questions in solving planar AdS/CFT. In this paper we discuss these effects in the AdS_5xS^5 string theory at one-loop in the world-sheet coupling. First we provide a very general, efficient way to compute the fluctuation frequencies, which allows to determine the energy shift for very general multi-cut solutions. Then we apply this to two-cut solutions, in particular the giant magnon and determine the finite-size corrections at subleading order. The latter are then compared to the finite-size corrections from Luscher-Klassen-Melzer formulas and found to be in perfect agreement.Comment: 32 pages, 5 figures; v2: typos corrected, refs adde