75 research outputs found
A Curated Database of miRNA Mediated Feed-Forward Loops Involving MYC as Master Regulator
BACKGROUND: The MYC transcription factors are known to be involved in the biology of many human cancer types. But little is known about the Myc/microRNAs cooperation in the regulation of genes at the transcriptional and post-transcriptional level. METHODOLOGY/PRINCIPAL FINDINGS: Employing independent databases with experimentally validated data, we identified several mixed microRNA/Transcription Factor Feed-Forward Loops regulated by Myc and characterized completely by experimentally supported regulatory interactions, in human. We then studied the statistical and functional properties of these circuits and discussed in more detail a few interesting examples involving E2F1, PTEN, RB1 and VEGF. CONCLUSIONS/SIGNIFICANCE: We have assembled and characterized a catalogue of human mixed Transcription Factor/microRNA Feed-Forward Loops, having Myc as master regulator and completely defined by experimentally verified regulatory interactions
Calcium Dependent CAMTA1 in Adult Stem Cell Commitment to a Myocardial Lineage
The phenotype of somatic cells has recently been found to be reversible. Direct reprogramming of one cell type into another has been achieved with transduction and over expression of exogenous defined transcription factors emphasizing their role in specifying cell fate. To discover early and novel endogenous transcription factors that may have a role in adult-derived stem cell acquisition of a cardiomyocyte phenotype, mesenchymal stem cells from human and mouse bone marrow and rat liver were co-cultured with neonatal cardiomyocytes as an in vitro cardiogenic microenvironment. Cell-cell communications develop between the two cell types as early as 24 hrs in co-culture and are required for elaboration of a myocardial phenotype in the stem cells 8-16 days later. These intercellular communications are associated with novel Ca(2+) oscillations in the stem cells that are synchronous with the Ca(2+) transients in adjacent cardiomyocytes and are detected in the stem cells as early as 24-48 hrs in co-culture. Early and significant up-regulation of Ca(2+)-dependent effectors, CAMTA1 and RCAN1 ensues before a myocardial program is activated. CAMTA1 loss-of-function minimizes the activation of the cardiac gene program in the stem cells. While the expression of RCAN1 suggests involvement of the well-characterized calcineurin-NFAT pathway as a response to a Ca(2+) signal, the CAMTA1 up-regulated expression as a response to such a signal in the stem cells was unknown. Cell-cell communications between the stem cells and adjacent cardiomyocytes induce Ca(2+) signals that activate a myocardial gene program in the stem cells via a novel and early Ca(2+)-dependent intermediate, up-regulation of CAMTA1
One thousand plant transcriptomes and the phylogenomics of green plants
Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life
Tests of General Relativity with GW150914
The LIGO detection of GW150914 provides an unprecedented opportunity to study the two-body motion of a compact-object binary in the large-velocity, highly nonlinear regime, and to witness the final merger of the binary and the excitation of uniquely relativistic modes of the gravitational field. We carry out several investigations to determine whether GW150914 is consistent with a binary black-hole merger in general relativity. We find that the final remnant’s mass and spin, as determined from the low-frequency (inspiral) and high-frequency (postinspiral) phases of the signal, are mutually consistent with the binary black-hole solution in general relativity. Furthermore, the data following the peak of GW150914 are consistent with the least-damped quasinormal mode inferred from the mass and spin of the remnant black hole. By using waveform models that allow for parametrized general-relativity violations during the inspiral and merger phases, we perform quantitative tests on the gravitational-wave phase in the dynamical regime and we determine the first empirical bounds on several high-order post-Newtonian coefficients. We constrain the graviton Compton wavelength, assuming that gravitons are dispersed in vacuum in the same way as particles with mass, obtaining a 90%-confidence lower bound of 1013 km. In conclusion, within our statistical uncertainties, we find no evidence for violations of general relativity in the genuinely strong-field regime of gravity
An improved analysis of GW150914 using a fully spin-precessing waveform model
This paper presents updated estimates of source parameters for GW150914, a binary black-hole coalescence event detected by the Laser Interferometer Gravitational-wave Observatory (LIGO) on September 14, 2015 [1]. Reference presented parameter estimation [2] of the source using a 13-dimensional, phenomenological precessing-spin model (precessing IMRPhenom) and a 11-dimensional nonprecessing effective-one-body (EOB) model calibrated to numerical-relativity simulations, which forces spin alignment (nonprecessing EOBNR). Here we present new results that include a 15-dimensional precessing-spin waveform model (precessing EOBNR) developed within the EOB formalism. We find good agreement with the parameters estimated previously [2], and we quote updated component masses of and (where errors correspond to 90% symmetric credible intervals). We also present slightly tighter constraints on the dimensionless spin magnitudes of the two black holes, with a primary spin estimate and a secondary spin estimate at 90% probability. Reference [2] estimated the systematic parameter-extraction errors due to waveform-model uncertainty by combining the posterior probability densities of precessing IMRPhenom and nonprecessing EOBNR. Here we find that the two precessing-spin models are in closer agreement, suggesting that these systematic errors are smaller than previously quoted
Properties of the Binary Black Hole Merger GW150914
On September 14, 2015, the Laser Interferometer Gravitational-Wave Observatory (LIGO) detected a gravitational-wave transient (GW150914); we characterize the properties of the source and its parameters. The data around the time of the event were analyzed coherently across the LIGO network using a suite of accurate waveform models that describe gravitational waves from a compact binary system in general relativity. GW150914 was produced by a nearly equal mass binary black hole of masses 36+5−4M⊙ and 29+4−4M⊙; for each parameter we report the median value and the range of the 90% credible interval. The dimensionless spin magnitude of the more massive black hole is bound to be <0.7 (at 90% probability). The luminosity distance to the source is 410+160−180 Mpc, corresponding to a redshift 0.09+0.03−0.04 assuming standard cosmology. The source location is constrained to an annulus section of 610 deg2, primarily in the southern hemisphere. The binary merges into a black hole of mass 62+4−4M⊙ and spin 0.67+0.05−0.07. This black hole is significantly more massive than any other inferred from electromagnetic observations in the stellar-mass regime
Directly comparing GW150914 with numerical solutions of Einstein's equations for binary black hole coalescence
We compare GW150914 directly to simulations of coalescing binary black holes in full general relativity, including
several performed specifically to reproduce this event. Our calculations go beyond existing semianalytic
models, because for all simulations – including sources with two independent, precessing spins – we perform
comparisons which account for all the spin-weighted quadrupolar modes, and separately which account for all
the quadrupolar and octopolar modes. Consistent with the posterior distributions reported in LVC-PE[1] (at
the 90% credible level), we find the data are compatible with a wide range of nonprecessing and precessing
simulations. Followup simulations performed using previously-estimated binary parameters most resemble the
data, even when all quadrupolar and octopolar modes are included. Comparisons including only the quadrupolar
modes constrain the total redshifted mass Mz ∈ [64M� − 82M�], mass ratio 1/q = m2/m1 ∈ [0.6, 1], and
effective aligned spin χeff ∈ [−0.3, 0.2], where χeff = (S1/m1 + S2/m2) · Lˆ /M. Including both quadrupolar
and octopolar modes, we find the mass ratio is even more tightly constrained. Even accounting for precession,
simulations with extreme mass ratios and effective spins are highly inconsistent with the data, at any mass.
Several nonprecessing and precessing simulations with similar mass ratio and χeff are consistent with the data.
Though correlated, the components’ spins (both in magnitude and directions) are not significantly constrained
by the data: the data is consistent with simulations with component spin magnitudes a1,2 up to at least 0.8, with
random orientations. Further detailed followup calculations are needed to determine if the data contain a weak
imprint from transverse (precessing) spins. For nonprecessing binaries, interpolating between simulations, we
reconstruct a posterior distribution consistent with previous results. The final black hole’s redshifted mass is
consistent with Mf,z
in the range 64.0M� − 73.5M� and the final black hole’s dimensionless spin parameter is
consistent with af = 0.62 − 0.73. As our approach invokes no intermediate approximations to general relativity
and can strongly reject binaries whose radiation is inconsistent with the data, our analysis provides a valuable
complement to LVC-PE[1]
Effects of waveform model systematics on the interpretation of GW150914
PAPER Effects of waveform model systematics on the interpretation of GW150914 B P Abbott1, R Abbott1, T D Abbott2, M R Abernathy3, F Acernese4,5, K Ackley6, C Adams7, T Adams8, P Addesso9,144, R X Adhikari1, V B Adya10, C Affeldt10, M Agathos11, K Agatsuma11, N Aggarwal12, O D Aguiar13, L Aiello14,15, A Ain16, P Ajith17, B Allen10,18,19, A Allocca20,21, P A Altin22, A Ananyeva1, S B Anderson1, W G Anderson18, S Appert1, K Arai1, M C Araya1, J S Areeda23, N Arnaud24, K G Arun25, S Ascenzi15,26, G Ashton10, M Ast27, S M Aston7, P Astone28, P Aufmuth19, C Aulbert10, A Avila-Alvarez23, S Babak29, P Bacon30, M K M Bader11, P T Baker31, F Baldaccini32,33, G Ballardin34, S W Ballmer35, J C Barayoga1, S E Barclay36, B C Barish1, D Barker37, F Barone4,5, B Barr36, L Barsotti12, M Barsuglia30, D Barta38, J Bartlett37, I Bartos39, R Bassiri40, A Basti20,21, J C Batch37, C Baune10, V Bavigadda34, M Bazzan41,42, C Beer10, M Bejger43, I Belahcene24, M Belgin44, A S Bell36, B K Berger1, G Bergmann10, 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Wei54, M Weinert10, A J Weinstein1, R Weiss12, L Wen52, P Weßels10, T Westphal10, K Wette10, J T Whelan107, B F Whiting6, C Whittle120, D Williams36, R D Williams1, A R Williamson94, J L Willis142, B Willke10,19, M H Wimmer10,19, W Winkler10, C C Wipf1, H Wittel10,19, G Woan36, J Woehler10, J Worden37, J L Wright36, D S Wu10, G Wu7, W Yam12, H Yamamoto1, C C Yancey64, M J Yap22, Hang Yu12, Haocun Yu12, M Yvert8, A Zadrożny118, L Zangrando42, M Zanolin103, J-P Zendri42, M Zevin85, L Zhang1, M Zhang129, T Zhang36, Y Zhang107, C Zhao52, M Zhou85, Z Zhou85, S J Zhu10,29, X J Zhu52, M E Zucker1,12, J Zweizig1 (LIGO Scientific Collaboration, Virgo Collaboration), M Boyle143, T Chu97, D Hemberger51, I Hinder29, L E Kidder143, S Ossokine29, M Scheel51, B Szilagyi51, S Teukolsky143 and A Vano Vinuales94 Hide full author list Published 12 April 2017 • © 2017 IOP Publishing Ltd Classical and Quantum Gravity, Volume 34, Number 10 Focus Issue: Gravitational Waves Article PDF Figures References Citations PDF 258 Total downloads Cited by 1 articles Article has an altmetric score of 3 Turn on MathJax Get permission to re-use this article Share this article Article information Abstract Parameter estimates of GW150914 were obtained using Bayesian inference, based on three semi-analytic waveform models for binary black hole coalescences. These waveform models differ from each other in their treatment of black hole spins, and all three models make some simplifying assumptions, notably to neglect sub-dominant waveform harmonic modes and orbital eccentricity. Furthermore, while the models are calibrated to agree with waveforms obtained by full numerical solutions of Einstein's equations, any such calibration is accurate only to some non-zero tolerance and is limited by the accuracy of the underlying phenomenology, availability, quality, and parameter-space coverage of numerical simulations. This paper complements the original analyses of GW150914 with an investigation of the effects of possible systematic errors in the waveform models on estimates of its source parameters. To test for systematic errors we repeat the original Bayesian analysis on mock signals from numerical simulations of a series of binary configurations with parameters similar to those found for GW150914. Overall, we find no evidence for a systematic bias relative to the statistical error of the original parameter recovery of GW150914 due to modeling approximations or modeling inaccuracies. However, parameter biases are found to occur for some configurations disfavored by the data of GW150914: for binaries inclined edge-on to the detector over a small range of choices of polarization angles, and also for eccentricities greater than ~0.05. For signals with higher signal-to-noise ratio than GW150914, or in other regions of the binary parameter space (lower masses, larger mass ratios, or higher spins), we expect that systematic errors in current waveform models may impact gravitational-wave measurements, making more accurate models desirable for future observations
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