A revised multi-tissue, multi-platform epigenetic clock model for methylation array data

Epigenetic changes have long been investigated in association with the process of aging in humans. DNA methylation has been extensively used as a surrogate measure of biological age and correlations between "DNA methylation age" and chronological age have been established. A wide variety of epigenetic clocks has been designed to predict age in different tissues and on data obtained from different methylation platforms. We aimed to extend the scope of one of the most used epigenetic age predictors, the Horvath pan-tissue epigenetic clock, to improve its accuracy on data acquired from the latest Illumina methylation platform (BeadChip EPIC). We present three models trained on close to 6,000 samples of various source tissues and platforms and demonstrate their superior performance (Pearson correlation (r) = 0.917-0.921 and median absolute error (MAE) = 3.60-3.85 years) compared to the original model (r= 0.880 and MAE =5.13 years) on a test set of more than 4,000 samples. The gain in accuracy was especially pronounced on EPIC array data (r= 0.89, MAE = 3.54 years vs. r= 0.83, MAE = 6.09 years), which was not available at the time when the original model was created. Our updated epigenetic clocks predict chronological age with great precision in an independent test cohort of samples on multiple tissue types and data platforms. Two of the three presented models exclusively use the covariates of the original epigenetic clock, albeit with different coefficients, allowing for straightforward adaptation for prefiltered datasets previously processed with the original predictor

Quantum Criticality at the Origin of Life

Why life persists at the edge of chaos is a question at the very heart of evolution. Here we show that molecules taking part in biochemical processes from small molecules to proteins are critical quantum mechanically. Electronic Hamiltonians of biomolecules are tuned exactly to the critical point of the metal-insulator transition separating the Anderson localized insulator phase from the conducting disordered metal phase. Using tools from Random Matrix Theory we confirm that the energy level statistics of these biomolecules show the universal transitional distribution of the metal-insulator critical point and the wave functions are multifractals in accordance with the theory of Anderson transitions. The findings point to the existence of a universal mechanism of charge transport in living matter. The revealed bio-conductor material is neither a metal nor an insulator but a new quantum critical material which can exist only in highly evolved systems and has unique material properties.Comment: 10 pages, 4 figure

Optimal multihump filter for photometric redshifts

We propose a novel type filter for multicolor imaging to improve on the photometric redshift estimation of galaxies. An extra filter - specific to a certain photometric system - may be utilized with high efficiency. We present a case study of the Hubble Space Telescope's Advanced Camera for Surveys and show that one extra exposure could cut down the mean square error on photometric redshifts by 34% over the z<1.3 redshift range.Comment: 9 pages, 3 figures, LaTeX AASTeX, accepted to A

Objective Identification of Informative Wavelength Regions in Galaxy Spectra

Understanding the diversity in spectra is the key to determining the physical parameters of galaxies. The optical spectra of galaxies are highly convoluted with continuum and lines which are potentially sensitive to different physical parameters. Defining the wavelength regions of interest is therefore an important question. In this work, we identify informative wavelength regions in a single-burst stellar populations model by using the CUR Matrix Decomposition. Simulating the Lick/IDS spectrograph configuration, we recover the widely used Dn(4000), Hbeta, and HdeltaA to be most informative. Simulating the SDSS spectrograph configuration with a wavelength range 3450-8350 Angstrom and a model-limited spectral resolution of 3 Angstrom, the most informative regions are: first region-the 4000 Angstrom break and the Hdelta line; second region-the Fe-like indices; third region-the Hbeta line; fourth region-the G band and the Hgamma line. A Principal Component Analysis on the first region shows that the first eigenspectrum tells primarily the stellar age, the second eigenspectrum is related to the age-metallicity degeneracy, and the third eigenspectrum shows an anti-correlation between the strengths of the Balmer and the Ca K and H absorptions. The regions can be used to determine the stellar age and metallicity in early-type galaxies which have solar abundance ratios, no dust, and a single-burst star formation history. The region identification method can be applied to any set of spectra of the user's interest, so that we eliminate the need for a common, fixed-resolution index system. We discuss future directions in extending the current analysis to late-type galaxies.Comment: 36 Pages, 13 Figures, 4 Tables. AJ Accepte

The size distribution of galaxies in the Sloan Digital Sky Survey

abridged: We use a complete sample of about 140,000 galaxies from the Sloan Digital Sky Survey (SDSS) to study the size distribution of galaxies and its dependence on their luminosity, stellar mass, and morphological type. The large SDSS database provides statistics of unprecedented accuracy. For each type of galaxy, the size distribution at given luminosity (or stellar mass) is well described by a log-normal function, characterized by its median $\bar{R}$ and dispersion $\sigma_{\ln R}$. For late-type galaxies, there is a characteristic luminosity at $M_{r,0}\sim -20.5$ (assuming $h=0.7$) corresponding to a stellar mass M_0\sim 10^{10.6}\Msun. Galaxies more massive than $M_0$ have $\bar{R}\propto M^{0.4}$ and $\sigma_{\ln R}\sim 0.3$, while less massive galaxies have $\bar{R}\propto M^{0.15}$ and $\sigma_{\ln R}\sim 0.5$. For early-type galaxies, the $\bar{R}$ - $M$ relation is significantly steeper, $\bar{R}\propto M^{0.55}$, but the $\sigma_{\ln R}$ - $M$ relation is similar to that of late-type galaxies. Faint red galaxies have sizes quite independent of their luminosities.Comment: 42 pages, 18 figures, 2 tables; replaced with the version accepted by MNRA

Large Scale Clustering of Sloan Digital Sky Survey Quasars: Impact of the Baryon Density and the Cosmological Constant

We report the first result of the clustering analysis of Sloan Digital Sky Survey (SDSS) quasars. We compute the two-point correlation function (2PCF) of SDSS quasars in redshift space at $8h^{-1}{\rm Mpc} < s < 500h^{-1}{\rm Mpc}$, with particular attention to its baryonic signature. Our sample consists of 19986 quasars extracted from the SDSS Data Release 4 (DR4). The redshift range of the sample is $0.72 \le z \le 2.24$ (the mean redshift is $\bar z = 1.46$) and the reddening-corrected $i$-band apparent magnitude range is $15.0 \le m_{i,{\rm rc}} \le 19.1$. Due to the relatively low number density of the quasar sample, the bump in the power spectrum due to the baryon density, $\Omega_{\rm b}$, is not clearly visible. The effect of the baryon density is, however, to distort the overall shape of the 2PCF.The degree of distortion makes it an interesting alternate measure of the baryonic signature. Assuming a scale-independent linear bias and the spatially flat universe, i.e., $\Omega_{\rm b} + \Omega_{\rm d} + \Omega_\Lambda =1$, where $\Omega_{\rm d}$ and $\Omega_\Lambda$ denote the density parameters of dark matter and the cosmological constant, we combine the observed quasar 2PCF and the predicted matter 2PCF to put constraints on $\Omega_{\rm b}$ and $\Omega_\Lambda$. Our result is fitted as $0.80- 2.8\Omega_{\rm b} < \Omega_\Lambda < 0.90 - 1.4\Omega_{\rm b}$ at the 2$\sigma$ confidence level, which is consistent with results from other cosmological observations such as WMAP. (abridged)Comment: 26 pages, 12 figures, Accepted for publication in the PAS