Integrative computational biology for cancer research

Over the past two decades, high-throughput (HTP) technologies such as microarrays and mass spectrometry have fundamentally changed clinical cancer research. They have revealed novel molecular markers of cancer subtypes, metastasis, and drug sensitivity and resistance. Some have been translated into the clinic as tools for early disease diagnosis, prognosis, and individualized treatment and response monitoring. Despite these successes, many challenges remain: HTP platforms are often noisy and suffer from false positives and false negatives; optimal analysis and successful validation require complex workflows; and great volumes of data are accumulating at a rapid pace. Here we discuss these challenges, and show how integrative computational biology can help diminish them by creating new software tools, analytical methods, and data standards

Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging

An algorithm for determining networks from gene expression data enables the identification of genes potentially linked to aging in worms

Great desire for extended life and health amongst the American public

People want to live long, healthy lives. Previous surveys suggest very limited interest in much longer lifespans, but we show that stipulating good health changes responses to favor longer lives by an order of magnitude. Advances in aging research hold out hope for greatly slowed aging with associated good health. Understanding the public's desires correctly is important to avoid misallocation of resources for research

Atmospheric Circulation of Hot Jupiters: A Shallow Three-Dimensional Model

Remote observing of exoplanetary atmospheres is now possible, offering us access to circulation regimes unlike any of the familiar Solar System cases. Atmospheric circulation models are being developed to study these new regimes but model validations and intercomparisons are needed to establish their consistency and accuracy. To this end, we present a simple Earth-like validation of the pseudo-spectral solver of meteorological equations called IGCM (Intermediate General Circulation Model), based on Newtonian relaxation to a prescribed latitudinal profile of equilibrium temperatures. We then describe a straightforward and idealized model extension to the atmospheric flow on a hot Jupiter with the same IGCM solver. This shallow, three-dimensional hot Jupiter model is based on Newtonian relaxation to a permanent day-night pattern of equilibrium temperatures and the absence of surface drag. The baroclinic regime of the Earth's lower atmosphere is contrasted with the more barotropic regime of the simulated hot Jupiter flow. For plausible conditions at the 0.1-1 bar pressure level on HD 209458b, the simulated flow is characterized by unsteadiness, subsonic wind speeds, a zonally-perturbed superrotating equatorial jet and large scale polar vortices. Violation of the Rayleigh-Kuo inflexion point criterion on the flanks of the accelerating equatorial jet indicates that barotropic (horizontal shear) instabilities may be important dynamical features of the simulated flow. Similarities and differences with previously published simulated hot Jupiter flows are briefly noted.Comment: 31 pages, 9 figures, accepted for publication in ApJ. Version with hi-res figures: http://www.astro.columbia.edu/~kristen/Hires/hotjup.3d.shallow.ps.g

Radiation-Hydrodynamics of Hot Jupiter Atmospheres

Radiative transfer in planetary atmospheres is usually treated in the static limit, i.e., neglecting atmospheric motions. We argue that hot Jupiter atmospheres, with possibly fast (sonic) wind speeds, may require a more strongly coupled treatment, formally in the regime of radiation-hydrodynamics. To lowest order in v/c, relativistic Doppler shifts distort line profiles along optical paths with finite wind velocity gradients. This leads to flow-dependent deviations in the effective emission and absorption properties of the atmospheric medium. Evaluating the overall impact of these distortions on the radiative structure of a dynamic atmosphere is non-trivial. We present transmissivity and systematic equivalent width excess calculations which suggest possibly important consequences for radiation transport in hot Jupiter atmospheres. If winds are fast and bulk Doppler shifts are indeed important for the global radiative balance, accurate modeling and reliable data interpretation for hot Jupiter atmospheres may prove challenging: it would involve anisotropic and dynamic radiative transfer in a coupled radiation-hydrodynamical flow. On the bright side, it would also imply that the emergent properties of hot Jupiter atmospheres are more direct tracers of their atmospheric flows than is the case for Solar System planets. Radiation-hydrodynamics may also influence radiative transfer in other classes of hot exoplanetary atmospheres with fast winds.Comment: 25 pages, 4 figures, accepted for publication in ApJ (minor revisions

Magnetic Scaling Laws for the Atmospheres of Hot Giant Exoplanets

We present scaling laws for advection, radiation, magnetic drag and ohmic dissipation in the atmospheres of hot giant exoplanets. In the limit of weak thermal ionization, ohmic dissipation increases with the planetary equilibrium temperature (T_eq >~ 1000 K) faster than the insolation power does, eventually reaching values >~ 1% of the insolation power, which may be sufficient to inflate the radii of hot Jupiters. At higher T_eq values still, magnetic drag rapidly brakes the atmospheric winds, which reduces the associated ohmic dissipation power. For example, for a planetary field strength B=10G, the fiducial scaling laws indicate that ohmic dissipation exceeds 1% of the insolation power over the equilibrium temperature range T_eq ~ 1300-2000 K, with a peak contribution at T_eq ~ 1600 K. Evidence for magnetically dragged winds at the planetary thermal photosphere could emerge in the form of reduced longitudinal offsets for the dayside infrared hotspot. This suggests the possibility of an anticorrelation between the amount of hotspot offset and the degree of radius inflation, linking the atmospheric and interior properties of hot giant exoplanets in an observationally testable way. While providing a useful framework to explore the magnetic scenario, the scaling laws also reveal strong parameter dependencies, in particular with respect to the unknown planetary magnetic field strength.Comment: 23 pages, 5 figures, accepted for publication in Ap

Three-Dimensional Atmospheric Circulation Models of HD 189733b and HD 209458b with Consistent Magnetic Drag and Ohmic Dissipation

We present the first three-dimensional circulation models for extrasolar gas giant atmospheres with geometrically and energetically consistent treatments of magnetic drag and ohmic dissipation. Atmospheric resistivities are continuously updated and calculated directly from the flow structure, strongly coupling the magnetic effects with the circulation pattern. We model the hot Jupiters HD 189733b (Teq \approx 1200 K) and HD 209458b (Teq \approx 1500 K) and test planetary magnetic field strengths from 0 to 30 G. We find that even at B = 3 G the atmospheric structure and circulation of HD 209458b are strongly influenced by magnetic effects, while the cooler HD 189733b remains largely unaffected, even in the case of B = 30 G and super-solar metallicities. Our models of HD 209458b indicate that magnetic effects can substantially slow down atmospheric winds, change circulation and temperature patterns, and alter observable properties. These models establish that longitudinal and latitudinal hot spot offsets, day-night flux contrasts, and planetary radius inflation are interrelated diagnostics of the magnetic induction process occurring in the atmospheres of hot Jupiters and other similarly forced exoplanets. Most of the ohmic heating occurs high in the atmosphere and on the day side of the planet, while the heating at depth is strongly dependent on the internal heat flux assumed for the planet, with more heating when the deep atmosphere is hot. We compare the ohmic power at depth in our models, and estimates of the ohmic dissipation in the bulk interior (from general scaling laws), to evolutionary models that constrain the amount of heating necessary to explain the inflated radius of HD 209458b. Our results suggest that deep ohmic heating can successfully inflate the radius of HD 209458b for planetary magnetic field strengths of B \geq 3 - 10 G.Comment: 35 pages, 12 figures, minimal revisions due to referee's comments, ApJ accepte

Three Dimensional Modeling of Hot Jupiter Atmospheric Flows

We present a three dimensional hot Jupiter model, extending from 200 bar to 1 mbar, using the Intermediate General Circulation Model from the University of Reading. Our horizontal spectral resolution is T31 (equivalent to a grid of 48x96), with 33 logarithmically spaced vertical levels. A simplified (Newtonian) scheme is employed for the radiative forcing. We adopt a physical set up nearly identical to the model of HD 209458b by Cooper & Showman (2005,2006) to facilitate a direct model inter-comparison. Our results are broadly consistent with theirs but significant differences also emerge. The atmospheric flow is characterized by a super-rotating equatorial jet, transonic wind speeds, and eastward advection of heat away from the dayside. We identify a dynamically-induced temperature inversion ("stratosphere") on the planetary dayside and find that temperatures at the planetary limb differ systematically from local radiative equilibrium values, a potential source of bias for transit spectroscopic interpretations. While our model atmosphere is quasi-identical to that of Cooper & Showman (2005,2006) and we solve the same meteorological equations, we use different algorithmic methods, spectral-implicit vs. grid-explicit, which are known to yield fully consistent results in the Earth modeling context. The model discrepancies identified here indicate that one or both numerical methods do not faithfully capture all of the atmospheric dynamics at work in the hot Jupiter context. We highlight the emergence of a shock-like feature in our model, much like that reported recently by Showman et al. (2009), and suggest that improved representations of energy conservation may be needed in hot Jupiter atmospheric models, as emphasized by Goodman (2009).Comment: 25 pages, 6 figures, minor revisions, ApJ accepted, version with hi-res figures: http://www.astro.columbia.edu/~kristen/Hires/hotjup.3d.deep.ps.g

A General Circulation Model for Gaseous Exoplanets with Double-Gray Radiative Transfer

We present a new version of our code for modeling the atmospheric circulation on gaseous exoplanets, now employing a "double-gray" radiative transfer scheme, which self-consistently solves for fluxes and heating throughout the atmosphere, including the emerging (observable) infrared flux. We separate the radiation into infrared and optical components, each with its own absorption coefficient, and solve standard two-stream radiative transfer equations. We use a constant optical absorption coefficient, while the infrared coefficient can scale as a powerlaw with pressure. Here we describe our new code in detail and demonstrate its utility by presenting a generic hot Jupiter model. We discuss issues related to modeling the deepest pressures of the atmosphere and describe our use of the diffusion approximation for radiative fluxes at high optical depths. In addition, we present new models using a simple form for magnetic drag on the atmosphere. We calculate emitted thermal phase curves and find that our drag-free model has the brightest region of the atmosphere offset by ~12 degrees from the substellar point and a minimum flux that is 17% of the maximum, while the model with the strongest magnetic drag has an offset of only ~2 degrees and a ratio of 13%. Finally, we calculate rates of numerical loss of kinetic energy at ~15% for every model except for our strong-drag model, where there is no measurable loss; we speculate that this is due to the much decreased wind speeds in that model.Comment: 29 pages, 12 figures, 2 tables, submitted to Ap