Parametric modeling of cellular state transitions as measured with flow cytometry

<p>Abstract</p> <p>Background</p> <p>Gradual or sudden transitions among different states as exhibited by cell populations in a biological sample under particular conditions or stimuli can be detected and profiled by flow cytometric time course data. Often such temporal profiles contain features due to transient states that present unique modeling challenges. These could range from asymmetric non-Gaussian distributions to outliers and tail subpopulations, which need to be modeled with precision and rigor.</p> <p>Results</p> <p>To ensure precision and rigor, we propose a parametric modeling framework StateProfiler based on finite mixtures of skew <it>t</it>-Normal distributions that are robust against non-Gaussian features caused by asymmetry and outliers in data. Further, we present in StateProfiler a new greedy EM algorithm for fast and optimal model selection. The parsimonious approach of our greedy algorithm allows us to detect the genuine dynamic variation in the key features as and when they appear in time course data. We also present a procedure to construct a well-fitted profile by merging any redundant model components in a way that minimizes change in entropy of the resulting model. This allows precise profiling of unusually shaped distributions and less well-separated features that may appear due to cellular heterogeneity even within clonal populations.</p> <p>Conclusions</p> <p>By modeling flow cytometric data measured over time course and marker space with StateProfiler, specific parametric characteristics of cellular states can be identified. The parameters are then tested statistically for learning global and local patterns of spatio-temporal change. We applied StateProfiler to identify the temporal features of yeast cell cycle progression based on knockout of S-phase triggering cyclins Clb5 and Clb6, and then compared the S-phase delay phenotypes due to differential regulation of the two cyclins. We also used StateProfiler to construct the temporal profile of clonal divergence underlying lineage selection in mammalian hematopoietic progenitor cells.</p

B -> Xs l_i^+ l_j^+ Decays with R-parity Violation

We derive the upper bounds on certain products of R-parity- and lepton-flavor-violating couplings from B \ra X_s {l_i}^+ {l_j}^- decays. These modes of B-meson decays can constrain the product combinations of the couplings with one or more heavy generation indices which are comparable with or stronger than the present bounds. From the studies of the invariant dilepton mass spectrum and the forward backward asymmetry of the emitted leptons we note the possibility of detecting R-parity-violating signals even when the total decay rate due to R-parity violating couplings is comparable with that in the standard model and discriminating two types of R-parity-violating signals. The general expectation of the enhancement of the forward backward asymmetry of the emitted leptons in the minimal supersymmetric standard model with R-parity may be corrupted by R-parity violation.Comment: 10 pages, Revtex, 1 table and 2 figure

A data mining approach to face detection [J

a b s t r a c t In this paper, we propose a novel face detection method based on the MAFIA algorithm. Our proposed method consists of two phases, namely, training and detection. In the training phase, we first apply Sobel&apos;s edge detection operator, morphological operator, and thresholding to each training image, and transform it into an edge image. Next, we use the MAFIA algorithm to mine the maximal frequent patterns from those edge images and obtain the positive feature pattern. Similarly, we can obtain the negative feature pattern from the complements of edge images. Based on the feature patterns mined, we construct a face detector to prune non-face candidates. In the detection phase, we apply a sliding window to the testing image in different scales. For each sliding window, if the slide window passes the face detector, it is considered as a human face. The proposed method can automatically find the feature patterns that capture most of facial features. By using the feature patterns to construct a face detector, the proposed method is robust to races, illumination, and facial expressions. The experimental results show that the proposed method has outstanding performance in the MIT-CMU dataset and comparable performance in the BioID dataset in terms of false positive and detection rate

The Sloan Digital Sky Survey Reverberation Mapping Project : the MBH–host relations at 0.2 ∼< z ∼< 0.6 from reverberation mapping and Hubble Space Telescope imaging

Funding: Y.S. acknowledges support from an Alfred P. Sloan Research Fellowship and NSF grants AST-1715579, AST-2009947. Support for Program number HST-GO-14109 was provided through a grant from the STScI under NASA contract NAS5-26555. L.C.H. was supported by the National Key R&D Program of China (2016YFA0400702) and the National Science Foundation of China (11721303, 11991052). E.D.B. is supported by Padua University grants DOR1715817/17, DOR1885254/18, and DOR1935272/19 and by MIUR grant PRIN 201720173ML3WW_001. J.V.H.S.and K.H. acknowledge funds from a Science and Technology Facilities Council grant ST/R000824/1.We present the results of a pilot Hubble Space Telescope (HST) imaging study of the host galaxies of ten quasars from the Sloan Digital Sky Survey Reverberation Mapping (SDSS-RM) project. Probing more than an order of magnitude in BH and stellar masses, our sample is the first statistical sample to study the BH-host correlations beyond z>0.3 with reliable BH masses from reverberation mapping rather than from single-epoch spectroscopy. We perform image decomposition in two HST bands (UVIS-F606W and IR-F110W) to measure host colors and estimate stellar masses using empirical relations between broad-band colors and the mass-to-light ratio. The stellar masses of our targets are mostly dominated by a bulge component. The BH masses and stellar masses of our sample broadly follow the same correlations found for local RM AGN and quiescent bulge-dominant galaxies, with no strong evidence of evolution in the MBH-M*bulge relation to z~0.6. We further compare the host light fraction from HST imaging decomposition to that estimated from spectral decomposition. We found a good correlation between the host fractions derived with both methods. However, the host fraction derived from spectral decomposition is systematically smaller than that from imaging decomposition by ~30%, indicating different systematics in both approaches. This study paves the way for upcoming more ambitious host galaxy studies of quasars with direct RM-based BH masses at high redshift.PostprintPeer reviewe

The Sloan Digital Sky Survey Reverberation Mapping Project : UV–optical accretion disk measurements with the Hubble Space Telescope

Funding: Y.H., J.R.T., and G.F.A. acknowledge support from NASA grants HST-GO-15650 and 18-2ADAP18-0177 and NSF grant CAREER-1945546. K.H. acknowledges support from STFC grant ST/R000824/1. C.J.G. acknowledges support from NSF grant AST-2009949. Y.S. acknowledges support from NSF grants AST-1715579 and AST-2009947. P.H. acknowledges support from the Natural Sciences and Engineering Research Council of Canada (NSERC), funding reference number 2017-05983. L.C.H. was supported by the National Science Foundation of China (11721303, 11991052) and the National Key R&D Program of China (2016YFA0400702).We present accretion-disk structure measurements from UV–optical reverberation mapping (RM) observations of a sample of eight quasars at 0.24 < z < 0.85. Ultraviolet photometry comes from two cycles of Hubble Space Telescope monitoring, accompanied by multiband optical monitoring by the Las Cumbres Observatory network and Liverpool Telescopes. The targets were selected from the Sloan Digital Sky Survey Reverberation Mapping project sample with reliable black hole mass measurements from Hβ RM results. We measure significant lags between the UV and various optical griz bands using JAVELIN and CREAM methods. We use the significant lag results from both methods to fit the accretion-disk structure using a Markov Chain Monte Carlo approach. We study the accretion disk as a function of disk normalization, temperature scaling, and efficiency. We find direct evidence for diffuse nebular emission from Balmer and Fe ii lines over discrete wavelength ranges. We also find that our best-fit disk color profile is broadly consistent with the Shakura & Sunyaev disk model. We compare our UV–optical lags to the disk sizes inferred from optical–optical lags of the same quasars and find that our results are consistent with these quasars being drawn from a limited high-lag subset of the broader population. Our results are therefore broadly consistent with models that suggest longer disk lags in a subset of quasars, for example, due to a nonzero size of the ionizing corona and/or magnetic heating contributing to the disk response.Publisher PDFPeer reviewe

SCUBA-2 Ultra Deep Imaging EAO Survey (STUDIES). II. Structural Properties and Near-infrared Morphologies of Faint Submillimeter Galaxies

We present structural parameters and morphological properties of faint 450 μm selected submillimeter galaxies (SMGs) from the JCMT Large Program, STUDIES, in the COSMOS-CANDELS region. Their properties are compared to an 850 μm selected and a matched star-forming samples. We investigate stellar structures of 169 faint 450 μm sources (S 450 = 2.8–29.6 mJy; S/N > 4) at z 2 mJy) and more extended than the star-forming galaxies in the same redshift range. For the stellar mass and SFR-matched sample at z sime 1 and z sime 2, the size differences are marginal between faint SMGs and the matched galaxies. Moreover, faint SMGs have similar Sérsic indices and projected axis ratios as star-forming galaxies with the same stellar mass and SFR. Both SMGs and the matched galaxies show high fractions (~70%) of disturbed features at z sime 2, and the fractions depend on the SFRs. These suggest that their star formation activity is related to galaxy merging and the stellar structures of SMGs are similar to those of star-forming galaxies. We show that the depths of submillimeter surveys are approaching the lower luminosity end of star-forming galaxies, allowing us to detect galaxies on the main sequence

The Sloan Digital Sky Survey Reverberation Mapping Project : how broad emission line widths change when luminosity changes

Funding: National Science Foundation of China (11721303, 11890693, 11991052) and the National Key R&D Program of China (2016YFA0400702, 2016YFA0400703). YS acknowledges support from an Alfred P. Sloan Research Fellowship and NSF grant AST-1715579. CJG, WNB, JRT, and DPS acknowledge support from NSF grants AST-1517113 and AST-1516784. KH acknowledges support from STFC grant ST/R000824/1. PBH acknowledges support from NSERC grant 2017-05983. YH acknowledges support from NASA grant HST-GO-15650.Quasar broad emission lines are largely powered by photoionization from the accretion continuum. Increased central luminosity will enhance line emissivity in more distant clouds, leading to increased average distance of the broad-line-emitting clouds and decreased averaged line width, known as the broad-line region (BLR) "breathing". However, different lines breathe differently, and some high-ionization lines, such as C IV, can even show "anti-breathing" where the line broadens when luminosity increases. Using multi-year photometric and spectroscopic monitoring data from the Sloan Digital Sky Survey Reverberation Mapping project, we quantify the breathing effect (Δlog W=αΔlog L) of broad Hα, Hβ, Mg II, C IV,and C III] for statistical quasar samples over z≈0.1−2.5. We found that Hβ displays the most consistent normal breathing expected from the virial relation (α∼−0.25), Mg II and Hα on average show no breathing (α∼0), and C IV (and similarly C III] and Si IV mostly shows anti-breathing (α>0). The anti-breathing of C IV can be well understood by the presence of a non-varying core component in addition to a reverberating broad-base component, consistent with earlier findings. The deviation from canonical breathing introduces extra scatter (aluminosity-dependent bias) in single-epoch virial BH mass estimates due to intrinsic quasar variability, which underlies the long argued caveats of C IV single-epoch masses. Using the line dispersion instead of FWHM leads to less, albeit still substantial, deviations from canonical breathing in most cases. Our results strengthen the need for reverberation mapping to provide reliable quasar BH masses, and quantify the level of variability-induced bias in single-epoch BH masses based on various lines.PostprintPeer reviewe