On the relationship between dissipation and the rate of spontaneous entropy production from linear irreversible thermodynamics

When systems are far from equilibrium, the temperature, the entropy and the thermodynamic entropy production are not defined and the Gibbs entropy does not provide useful information about the physical properties of a system. Furthermore, far from equilibrium, or if the dissipative field changes in time, the spontaneous entropy production of linear irreversible thermodynamics becomes irrelevant. In 2000 we introduced a definition for the dissipation function and showed that for systems of arbitrary size, arbitrarily near or far from equilibrium, the time integral of the ensemble average of this quantity can never decrease. In the low-field limit, its ensemble average becomes equal to the spontaneous entropy production of linear irreversible thermodynamics. We discuss how these quantities are related and why one should use dissipation rather than entropy or entropy production for non-equilibrium systems

Gene expression profiling of whole blood: Comparison of target preparation methods for accurate and reproducible microarray analysis

<p>Abstract</p> <p>Background</p> <p>Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is complicated by the need to minimize artifacts associated with highly abundant globin RNA transcripts. The impact of globin RNA transcripts on expression profiling data can potentially be reduced by using RNA preparation and labeling methods that remove or block globin RNA during the microarray assay. We compared four different methods for preparing microarray hybridization targets from human whole blood collected in PAXGene tubes. Three of the methods utilized the Affymetrix one-cycle cDNA synthesis/in vitro transcription protocol but varied treatment of input RNA as follows: i. no treatment; ii. treatment with GLOBINclear; or iii. treatment with globin PNA oligos. In the fourth method cDNA targets were prepared with the Ovation amplification and labeling system.</p> <p>Results</p> <p>We find that microarray targets generated with labeling methods that reduce globin mRNA levels or minimize the impact of globin transcripts during hybridization detect more transcripts in the microarray assay compared with the standard Affymetrix method. Comparison of microarray results with quantitative PCR analysis of a panel of genes from the NF-kappa B pathway shows good correlation of transcript measurements produced with all four target preparation methods, although method-specific differences in overall correlation were observed. The impact of freezing blood collected in PAXGene tubes on data reproducibility was also examined. Expression profiles show little or no difference when RNA is extracted from either fresh or frozen blood samples.</p> <p>Conclusion</p> <p>RNA preparation and labeling methods designed to reduce the impact of globin mRNA transcripts can significantly improve the sensitivity of the DNA microarray expression profiling assay for whole blood samples. While blockage of globin transcripts during first strand cDNA synthesis with globin PNAs resulted in the best overall performance in this study, we conclude that selection of a protocol for expression profiling studies in blood should depend on several factors, including implementation requirements of the method and study design. RNA isolated from either freshly collected or frozen blood samples stored in PAXGene tubes can be used without altering gene expression profiles.</p

The new galaxy evolution paradigm revealed by the Herschel surveys

The Herschel Space Observatory has revealed a very different galaxyscape from that shown by optical surveys, which presents a challenge for galaxy-evolution models. The Herschel surveys reveal (1) that there was rapid galaxy evolution in the very recent past and (2) that galaxies lie on a a single Galaxy Sequence (GS) rather than a star-forming ‘main sequence’ and a separate region of ‘passive’ or ‘red-and-dead’ galaxies. The form of the GS is now clearer because far-infrared surveys such as the Herschel ATLAS pick up a population of optically-red star-forming galaxies that would have been classified as passive using most optical criteria. The space-density of this population is at least as high as the traditional star-forming population. By stacking spectra of H-ATLAS galaxies over the redshift range 0.001 < z < 0.4, we show that the galaxies responsible for the rapid low-redshift evolution have high stellar masses, high star-formation rates but, even several billion years in the past, old stellar populations— they are thus likely to be relatively recent ancestors of early-type galaxies in the Universe today. The form of the GS is inconsistent with rapid quenching models and neither the analytic bathtub model nor the hydrodynamical EAGLE simulation can reproduce the rapid cosmic evolution. We propose a new gentler model of galaxy evolution that can explain the new Herschel results and other key properties of the galaxy population

The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: cosmological analysis of the DR12 galaxy sample

We present cosmological results from the final galaxy clustering data set of the Baryon Oscillation Spectroscopic Survey, part of the Sloan Digital Sky Survey III. Our combined galaxy sample comprises 1.2 million massive galaxies over an effective area of 9329 $deg^2$ and volume of 18.7 $Gpc^3$, divided into three partially overlapping redshift slices centred at effective redshifts 0.38, 0.51, and 0.61. We measure the angular diameter distance DM and Hubble parameter H from the baryon acoustic oscillation (BAO) method after applying reconstruction to reduce non-linear effects on the BAO feature. Using the anisotropic clustering of the pre-reconstruction density field, we measure the product DM*H from the Alcock-Paczynski (AP) effect and the growth of structure, quantified by $f{\sigma}8(z)$, from redshift-space distortions (RSD). We combine measurements presented in seven companion papers into a set of consensus values and likelihoods, obtaining constraints that are tighter and more robust than those from any one method. Combined with Planck 2015 cosmic microwave background measurements, our distance scale measurements simultaneously imply curvature ${\Omega}_K =0.0003+/-0.0026$ and a dark energy equation of state parameter w = -1.01+/-0.06, in strong affirmation of the spatially flat cold dark matter model with a cosmological constant (${\Lambda}$CDM). Our RSD measurements of $f{\sigma}_8$, at 6 per cent precision, are similarly consistent with this model. When combined with supernova Ia data, we find H0 = 67.3+/-1.0 km/s/Mpc even for our most general dark energy model, in tension with some direct measurements. Adding extra relativistic species as a degree of freedom loosens the constraint only slightly, to H0 = 67.8+/-1.2 km/s/Mpc. Assuming flat ${\Lambda}$CDM we find ${\Omega}_m = 0.310+/-0.005$ and H0 = 67.6+/-0.5 km/s/Mpc, and we find a 95% upper limit of $0.16 eV/c^2$ on the neutrino mass sum

Prediction of cis-regulatory elements controlling genes differentially expressed by retinal and choroidal vascular endothelial cells

Cultured endothelial cells of the human retina and choroid demonstrate distinct patterns of gene expression. We hypothesized that differential gene expression reflected differences in the interactions of transcription factors and respective cis-regulatory motifs(s) in these two endothelial cell subpopulations, recognizing that motifs often exist as modules. We tested this hypothesis in silico by using TRANSFAC Professional and CisModule to identify cis-regulatory motifs and modules in genes that were differentially expressed by human retinal versus choroidal endothelial cells, as identified by analysis of a microarray data set. Motifs corresponding to eight transcription factors were significantly (p < 0.05) differentially abundant in genes that were relatively highly expressed in retinal (i.e., glucocorticoid receptor, high mobility group AT-hook 1, heat shock transcription factor 1, p53, vitamin D receptor) or choroidal (i.e., transcription factor E2F, Yin Yang 1, zinc finger 5) endothelial cells. Predicted cis-regulatory modules were quite different for these two groups of genes. Our findings raise the possibility of exploiting specific cis-regulatory motifs to target therapy at the ocular endothelial cells subtypes responsible for neovascular age-related macular degeneration or proliferative diabetic retinopathy

Testing the magnetar scenario for superluminous supernovae with circular polarimetry

Superluminous supernovae (SLSNe) are at least ∼5 times more luminous than common supernovae (SNe). Especially hydrogen-poor SLSN-I are difficult to explain with conventional powering mechanisms. One possible scenario that might explain such luminosities is that SLSNe-I are powered by an internal engine, such as a magnetar or an accreting black hole. Strong magnetic fields or collimated jets can circularly polarize light. In this work, we measured circular polarization of two SLSNe-I with the FOcal Reducer and low dispersion Spectrograph (FORS2) mounted at the ESO’s Very Large Telescope (VLT). PS17bek, a fast evolving SLSN-I, was observed around peak, while OGLE16dmu, a slowly evolving SLSN-I, was observed 100 days after maximum. Neither SLSN shows evidence of circularly polarized light, however, these non-detections do not rule out the magnetar scenario as the powering engine for SLSNe-I. We calculate the strength of the magnetic field and the expected circular polarization as a function of distance from the magnetar, which decreases very fast. Additionally, we observed no significant linear polarization for PS17bek at four epochs, suggesting that the photosphere near peak is close to spherical symmetry

GAMA/G10-COSMOS/3D-HST: The 0<z<5 cosmic star-formation history, stellar- and dust-mass densities

We use the energy-balance code MAGPHYS to determine stellar and dust masses, and dust corrected star-formation rates for over 200,000 GAMA galaxies, 170,000 G10-COSMOS galaxies and 200,000 3D-HST galaxies. Our values agree well with previously reported measurements and constitute a representative and homogeneous dataset spanning a broad range in stellar mass (10^8---10^12 Msol), dust mass (10^6---10^9 Msol), and star-formation rates (0.01---100 Msol per yr), and over a broad redshift range (0.0 < z < 5.0). We combine these data to measure the cosmic star-formation history (CSFH), the stellar-mass density (SMD), and the dust-mass density (DMD) over a 12 Gyr timeline. The data mostly agree with previous estimates, where they exist, and provide a quasi-homogeneous dataset using consistent mass and star-formation estimators with consistent underlying assumptions over the full time range. As a consequence our formal errors are significantly reduced when compared to the historic literature. Integrating our cosmic star-formation history we precisely reproduce the stellar-mass density with an ISM replenishment factor of 0.50 +/- 0.07, consistent with our choice of Chabrier IMF plus some modest amount of stripped stellar mass. Exploring the cosmic dust density evolution, we find a gradual increase in dust density with lookback time. We build a simple phenomenological model from the CSFH to account for the dust mass evolution, and infer two key conclusions: (1) For every unit of stellar mass which is formed 0.0065---0.004 units of dust mass is also formed; (2) Over the history of the Universe approximately 90 to 95 per cent of all dust formed has been destroyed and/or ejected