Removing batch effects for prediction problems with frozen surrogate variable analysis

Batch effects are responsible for the failure of promising genomic prognos- tic signatures, major ambiguities in published genomic results, and retractions of widely-publicized findings. Batch effect corrections have been developed to re- move these artifacts, but they are designed to be used in population studies. But genomic technologies are beginning to be used in clinical applications where sam- ples are analyzed one at a time for diagnostic, prognostic, and predictive applica- tions. There are currently no batch correction methods that have been developed specifically for prediction. In this paper, we propose an new method called frozen surrogate variable analysis (fSVA) that borrows strength from a training set for individual sample batch correction. We show that fSVA improves prediction ac- curacy in simulations and in public genomic studies. fSVA is available as part of the sva Bioconductor package

Light weight fire resistant graphite composites

Composite structures with a honeycomb core and characterized by lightweight and excellent fire resistance are provided. These sandwich structures employ facesheets made up of bismaleimide-vinyl styrylpyridine copolymers with fiber reinforcement such as carbon fiber reinforcement. In preferred embodiments the facesheets are over layered with a decorative film. The properties of these composites make them attractive materials of construction aircraft and spacecraft

Direct versus Delayed pathways in Strong-Field Non-Sequential Double Ionization

We report full-dimensionality quantum and classical calculations for double ionization of laser-driven helium at 390 nm. Good qualitative agreement is observed. We show that the classical double ionization trajectories can be divided into two distinct pathways: direct and delayed. The direct pathway, with an almost simultaneous ejection of both electrons, emerges from small laser intensities. With increasing intensity its relative importance, compared to the delayed ionization pathway, increases until it becomes the predominant pathway for total electron escape energy below around 5.25 $U_{p}$. However the delayed pathway is the predominant one for double ionization above a certain cut-off energy at all laser intensities

Relation between Tunneling and Particle Production in Vacuum Decay

The field-theoretical description of quantum fluctuations on the background of a tunneling field $\sigma$ is revisited in the case of a functional Schrodinger approach. We apply this method in the case when quantum fluctuations are coupled to the $\sigma$ field through a mass-squared term, which is 'time-dependent' since we include the dynamics of $\sigma$ . The resulting mode functions of the fluctuation field, which determine the quantum state after tunneling, display a previously unseen resonance effect when their mode number is comparable to the curvature scale of the bubble. A detailed analysis of the relation between the excitations of the field about the true vacuum (interpreted as particle creation) and the phase shift coming from tunneling is presented.Comment: 20 pages, 4 figures, submitted to PR

Acceleration of the universe, vacuum metamorphosis, and the large-time asymptotic form of the heat kernel

We investigate the possibility that the late acceleration observed in the rate of expansion of the universe is due to vacuum quantum effects arising in curved spacetime. The theoretical basis of the vacuum cold dark matter (VCDM), or vacuum metamorphosis, cosmological model of Parker and Raval is revisited and improved. We show, by means of a manifestly nonperturbative approach, how the infrared behavior of the propagator (related to the large-time asymptotic form of the heat kernel) of a free scalar field in curved spacetime causes the vacuum expectation value of its energy-momentum tensor to exhibit a resonance effect when the scalar curvature R of the spacetime reaches a particular value related to the mass of the field. we show that the back reaction caused by this resonance drives the universe through a transition to an accelerating expansion phase, very much in the same way as originally proposed by Parker and Raval. Our analysis includes higher derivatives that were neglected in the earlier analysis, and takes into account the possible runaway solutions that can follow from these higher-derivative terms. We find that the runaway solutions do not occur if the universe was described by the usual classical FRW solution prior to the growth of vacuum energy-density and negative pressure (i.e., vacuum metamorphosis) that causes the transition to an accelerating expansion of the universe in this theory.Comment: 33 pages, 3 figures. Submitted to Physical Review D15 (Dec 23, 2003). v2: 1 reference added. No other change

Instability of Rotationally Tuned Dipolar Bose-Einstein Condensates

The possibility of effectively inverting the sign of the dipole-dipole interaction, by fast rotation of the dipole polarization, is examined within a harmonically trapped dipolar Bose-Einstein condensate. Our analysis is based on the stationary states in the Thomas-Fermi limit, in the corotating frame, as well as direct numerical simulations in the Thomas-Fermi regime, explicitly accounting for the rotating polarization. The condensate is found to be inherently unstable due to the dynamical instability of collective modes. This ultimately prevents the realization of robust and long-lived rotationally tuned states. Our findings have major implications for experimentally accessing this regime.Comment: 9 pages with 5 figure

The implications of alternative developer decision-making strategies on land-use and land-cover in an agent-based land market model

Land developers play a key role in land-use and land cover change, as\ud they directly make land development decisions and bridge the land and housing\ud markets. Developers choose and purchase land from rural land owners, develop\ud and subdivide land into parcel lots, build structures on lots, and sell houses to residential households. Developers determine the initial landscaping states of developed parcels, affecting the state and future trajectories of residential land cover, as well as land market activity. Despite their importance, developers are underrepresented in land use change models due to paucity of data and knowledge regarding their decision-making. Drawing on economic theories and empirical literature, we have developed a generalized model of land development decision-making within a broader agent-based model of land-use change via land markets. Developer’s strategies combine their specialty in developing of particular subdivision types, their perception of and attitude towards market uncertainty, and their learning and adaptation strategies based on the dynamics of the simulated land and housing markets. We present a new agent-based land market model that includes these elements. The model will be used to experiment with these different development decision-making methods and compare their impacts on model outputs, particularly on the quantity and spatial pattern of resultant land use changes. Coupling between the land market and a carbon sequestration model, developed for the larger SLUCE2 project, will allow us, in future work, to examine how different developer’s strategies will affect the carbon balance in residential\ud landscape

Inelastic neutron scattering studies of methyl chloride synthesis over alumina

Not only is alumina the most widely used catalyst support material in the world, it is also an important catalyst in its own right. One major chemical process that uses alumina in this respect is the industrial production of methyl chloride. This is a large scale process (650 000 metric tons in 2010 in the United States), and a key feedstock in the production of silicones that are widely used as household sealants. In this Account, we show how, in partnership with conventional spectroscopic and reaction testing methods, inelastic neutron scattering (INS) spectroscopy can provide additional insight into the active sites present on the catalyst, as well as the intermediates present on the catalyst surface.<p></p> INS spectroscopy is a form of vibrational spectroscopy, where the spectral features are dominated by modes involving hydrogen. Because of this, most materials including alumina are largely transparent to neutrons. Advantageously, in this technique, the entire “mid-infrared”, 0–4000 cm<sup>–1</sup>, range is accessible; there is no cut-off at 1400 cm<sup>–1</sup> as in infrared spectroscopy. It is also straightforward to distinguish fundamental modes from overtones and combinations. <p></p> A key parameter in the catalyst’s activity is the surface acidity. In infrared spectroscopy of adsorbed pyridine, the shifts in the ring stretching modes are dependent on the strength of the acid site. However, there is a very limited spectral range available. We discuss how we can observe the low energy ring deformation modes of adsorbed pyridine by INS spectroscopy. These modes can undergo shifts that are as large as those seen with infrared inspectroscopy, potentially enabling finer discrimination between acid sites. <p></p> Surface hydroxyls play a key role in alumina catalysis, but in infrared spectroscopy, the presence of electrical anharmonicity complicates the interpretation of the O–H stretch region. In addition, the deformations lie below the infrared cut-off. Both of these limitations are irrelevant to INS spectroscopy, and all the modes are readily observable. When we add HCl to the catalyst surface, the acid causes changes in the spectra. We can then deduce both that the surface chlorination leads to enhanced Lewis acidity and that the hydroxyl group must be threefold coordinated. <p></p> When we react η-alumina with methanol, the catalyst forms a chemisorbed methoxy species. Infrared spectroscopy clearly shows its presence but also indicates the possible coexistence of a second species. Because of INS spectroscopy’s ability to discriminate between fundamental modes and combinations, we were able to unambiguously show that there is a single intermediate present on the surface of the active catalyst. This work represents a clear example where an understanding of the chemistry at the molecular level can help rationalize improvements in a large scale industrial process with both financial and environmental benefits. <p></p&gt