203 research outputs found
Unravelling the Yeast Cell Cycle Using the TriGen Algorithm
Analyzing microarray data represents a computational challenge
due to the characteristics of these data. Clustering techniques are
widely applied to create groups of genes that exhibit a similar behavior
under the conditions tested. Biclustering emerges as an improvement of
classical clustering since it relaxes the constraints for grouping allowing
genes to be evaluated only under a subset of the conditions and not under
all of them. However, this technique is not appropriate for the analysis of
temporal microarray data in which the genes are evaluated under certain
conditions at several time points. In this paper, we present the results of
applying the TriGen algorithm, a genetic algorithm that finds triclusters
that take into account the experimental conditions and the time points,
to the yeast cell cycle problem, where the goal is to identify all genes
whose expression levels are regulated by the cell cycle
Solar Wind and its Evolution
By using our previous results of magnetohydrodynamical simulations for the
solar wind from open flux tubes, I discuss how the solar wind in the past is
different from the current solar wind. The simulations are performed in fixed
one-dimensional super-radially open magnetic flux tubes by inputing various
types of fluctuations from the photosphere, which automatically determines
solar wind properties in a forward manner. The three important parameters which
determine physical properties of the solar wind are surface fluctuation,
magnetic field strengths, and the configuration of magnetic flux tubes.
Adjusting these parameters to the sun at earlier times in a qualitative sense,
I infer that the quasi-steady-state component of the solar wind in the past was
denser and slightly slower if the effect of the magneto-centrifugal force is
not significant. I also discuss effects of magneto-centrifugal force and roles
of coronal mass ejections.Comment: 6 pages, 1 figure, Earth, Planets, & Space in press (based on 5th
Alfven Conference) correction of discussion on a related pape
4pi Models of CMEs and ICMEs
Coronal mass ejections (CMEs), which dynamically connect the solar surface to
the far reaches of interplanetary space, represent a major anifestation of
solar activity. They are not only of principal interest but also play a pivotal
role in the context of space weather predictions. The steady improvement of
both numerical methods and computational resources during recent years has
allowed for the creation of increasingly realistic models of interplanetary
CMEs (ICMEs), which can now be compared to high-quality observational data from
various space-bound missions. This review discusses existing models of CMEs,
characterizing them by scientific aim and scope, CME initiation method, and
physical effects included, thereby stressing the importance of fully 3-D
('4pi') spatial coverage.Comment: 14 pages plus references. Comments welcome. Accepted for publication
in Solar Physics (SUN-360 topical issue
Sharp changes of solar wind ion flux and density within and outside current sheets
Analysis of the Interball-1 spacecraft data (1995-2000) has shown that the
solar wind ion flux sometimes increases or decreases abruptly by more than 20%
over a time period of several seconds or minutes. Typically, the amplitude of
such sharp changes in the solar wind ion flux (SCIFs) is larger than 0.5x10^8
cm^-2 s^-1. These sudden changes of the ion flux were also observed by the
Solar Wind Experiment (SWE), on board the WIND spacecraft, as the solar wind
density increases and decreases with negligible changes in the solar wind
velocity. SCIFs occur irregularly at 1 AU, when plasma flows with specific
properties come to the Earth's orbit. SCIFs are usually observed in slow,
turbulent solar wind with increased density and interplanetary magnetic field
strength. The number of times SCIFs occur during a day is simulated using the
solar wind density, magnetic field, and their standard deviations as input
parameters for a period of 5 years. A correlation coefficient of ~0.7 is
obtained between the modelled and the experimental data. It is found that SCIFs
are not associated with coronal mass ejections (CMEs), corotating interaction
regions (CIRs), or interplanetary shocks; however, 85% of the sector boundaries
are surrounded by SCIFs. The properties of the solar wind plasma for days with
5 or more SCIF observations are the same as those of the solar wind plasma at
the sector boundaries. One possible explanation for the occurrence of SCIFs
(near sector boundaries) is magnetic reconnection at the heliospheric current
sheet or local current sheets. Other probable causes of SCIFs (inside sectors)
are turbulent processes in the slow solar wind and at the crossings of flux
tubes.Comment: 33 pages, 8 figures, 6 tables, Solar Physics 2011, in pres
Selectivity control in Pt-catalyzed cinnamaldehyde hydrogenation
Chemoselectivity is a cornerstone of catalysis, permitting the targeted modification of specific functional groups within complex starting materials. Here we elucidate key structural and electronic factors controlling the liquid phase hydrogenation of cinnamaldehyde and related benzylic aldehydes over Pt nanoparticles. Mechanistic insight from kinetic mapping reveals cinnamaldehyde hydrogenation is structure-insensitive over metallic platinum, proceeding with a common Turnover Frequency independent of precursor, particle size or support architecture. In contrast, selectivity to the desired cinnamyl alcohol product is highly structure sensitive, with large nanoparticles and high hydrogen pressures favoring C=O over C=C hydrogenation, attributed to molecular surface crowding and suppression of sterically-demanding adsorption modes. In situ vibrational spectroscopies highlight the role of support polarity in enhancing C=O hydrogenation (through cinnamaldehyde reorientation), a general phenomenon extending to alkyl-substituted benzaldehydes. Tuning nanoparticle size and support polarity affords a flexible means to control the chemoselective hydrogenation of aromatic aldehydes
A multi-species synthesis of physiological mechanisms in drought-induced tree mortality
Widespread tree mortality associated with drought 92 has been observed on all forested continents, and global change is expected to exacerbate vegetation vulnerability. Forest mortality has implications for future biosphere-atmosphere interactions of carbon, water, and energy balance, and is poorly represented in dynamic vegetation models. Reducing uncertainty requires improved mortality projections founded on robust physiological processes. However, the proposed mechanisms of drought-induced mortality, including hydraulic failure and carbon starvation, are unresolved. A growing number of empirical studies have investigated these mechanisms, but data have not been consistently analyzed across species and biomes using a standardized physiological framework. Here we show that xylem hydraulic failure was ubiquitous across multiple tree taxa at drought induced mortality. All species assessed had 60% or higher loss of xylem hydraulic conductivity, consistent with proposed theoretical and modelled survival thresholds. We found diverse responses in non-structural carbohydrate reserves at mortality, indicating that evidence supporting carbon starvation was not universal. Reduced non-structural carbohydrates were more common for gymnosperms than angiosperms, associated with xylem hydraulic vulnerability, and may have a role in reducing hydraulic function. Our finding that hydraulic failure at drought-induced mortality was persistent across species indicates that substantial improvement in vegetation modelling can be achieved using thresholds in hydraulic function
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