A mass action model of a fibroblast growth factor signaling pathway and its simplification

We consider a kinetic law of mass action model for Fibroblast Growth Factor (FGF) signaling, focusing on the induction of the RAS-MAP kinase pathway via GRB2 binding. Our biologically simple model suffers a combinatorial explosion in the number of differential equations required to simulate the system. In addition to numerically solving the full model, we show that it can be accurately simplified. This requires combining matched asymptotics, the quasi-steady state hypothesis, and the fact subsets of the equations decouple asymptotically. Both the full and simplified models reproduce the qualitative dynamics observed experimentally and in previous stochastic models. The simplified model also elucidates both the qualitative features of GRB2 binding and the complex relationship between SHP2 levels, the rate SHP2 induces dephosphorylation and levels of bound GRB2. In addition to providing insight into the important and redundant features of FGF signaling, such work further highlights the usefulness of numerous simplification techniques in the study of mass action models of signal transduction, as also illustrated recently by Borisov and co-workers (Borisov et al. in Biophys. J. 89, 951–66, 2005, Biosystems 83, 152–66, 2006; Kiyatkin et al. in J. Biol. Chem. 281, 19925–9938, 2006). These developments will facilitate the construction of tractable models of FGF signaling, incorporating further biological realism, such as spatial effects or realistic binding stoichiometries, despite a more severe combinatorial explosion associated with the latter

PCR for the detection of pathogens in neonatal early onset sepsis.

BACKGROUND: A large proportion of neonates are treated for presumed bacterial sepsis with broad spectrum antibiotics even though their blood cultures subsequently show no growth. This study aimed to investigate PCR-based methods to identify pathogens not detected by conventional culture. METHODS: Whole blood samples of 208 neonates with suspected early onset sepsis were tested using a panel of multiplexed bacterial PCRs targeting Streptococcus pneumoniae, Streptococcus agalactiae (GBS), Staphylococcus aureus, Streptococcus pyogenes (GAS), Enterobacteriaceae, Enterococcus faecalis, Enterococcus faecium, Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis and Mycoplasma genitalium, a 16S rRNA gene broad-range PCR and a multiplexed PCR for Candida spp. RESULTS: Two-hundred and eight samples were processed. In five of those samples, organisms were detected by conventional culture; all of those were also identified by PCR. PCR detected bacteria in 91 (45%) of the 203 samples that did not show bacterial growth in culture. S. aureus, Enterobacteriaceae and S. pneumoniae were the most frequently detected pathogens. A higher bacterial load detected by PCR was correlated positively with the number of clinical signs at presentation. CONCLUSION: Real-time PCR has the potential to be a valuable additional tool for the diagnosis of neonatal sepsis

Upward Three-Dimensional Grid Drawings of Graphs

A \emph{three-dimensional grid drawing} of a graph is a placement of the vertices at distinct points with integer coordinates, such that the straight line segments representing the edges do not cross. Our aim is to produce three-dimensional grid drawings with small bounding box volume. We prove that every $n$-vertex graph with bounded degeneracy has a three-dimensional grid drawing with $O(n^{3/2})$ volume. This is the broadest class of graphs admiting such drawings. A three-dimensional grid drawing of a directed graph is \emph{upward} if every arc points up in the z-direction. We prove that every directed acyclic graph has an upward three-dimensional grid drawing with $(n^3)$ volume, which is tight for the complete dag. The previous best upper bound was $O(n^4)$. Our main result is that every $c$-colourable directed acyclic graph ($c$ constant) has an upward three-dimensional grid drawing with $O(n^2)$ volume. This result matches the bound in the undirected case, and improves the best known bound from $O(n^3)$ for many classes of directed acyclic graphs, including planar, series parallel, and outerplanar

On some problems involving Hardy's function

Some problems involving the classical Hardy function $$Z(t) := \zeta(1/2+it)\bigl(\chi(1/2+it)\bigr)^{-1/2}, \quad \zeta(s) = \chi(s)\zeta(1-s)$$ are discussed. In particular we discuss the odd moments of $Z(t)$, the distribution of its positive and negative values and the primitive of $Z(t)$. Some analogous problems for the mean square of $|\zeta(1/2+it)|$ are also discussed.Comment: 15 page

On Recognizing Transparent Objects in Domestic Environments Using Fusion of Multiple Sensor Modalities

Current object recognition methods fail on object sets that include both diffuse, reflective and transparent materials, although they are very common in domestic scenarios. We show that a combination of cues from multiple sensor modalities, including specular reflectance and unavailable depth information, allows us to capture a larger subset of household objects by extending a state of the art object recognition method. This leads to a significant increase in robustness of recognition over a larger set of commonly used objects.Comment: 12 page

The third moment of quadratic Dirichlet L-functions

We study the third moment of quadratic Dirichlet L-functions, obtaining an error term of size $O(X^{3/4 + \varepsilon})$.Comment: 27 pages. v2: modified a remark on p.

User's guide for the Solar Backscattered Ultraviolet (SBUV) and the Total Ozone Mapping Spectrometer (TOMS) RUT-S and RUT-T data sets: October 31, 1978 to November 1, 1980

Raw data from the Solar Backscattered Ultrviolet/Total Ozone Mapping Spectrometer (SBUV/TOMS) Nimbus 7 operation are available on computer tape. These data are contained on two separate sets of RUTs (Raw Units Tapes) for SBUV and TOMS, labelled RUT-S and RUT-T respectively. The RUT-S and RUT-T tapes contain uncalibrated radiance and irradiance data, housekeeping data, wavelength and electronic calibration data, instrument field-of-view location and solar ephemeris information. These tapes also contain colocated cloud, terrain pressure and snow/ice thickness data, each derived from an independent source. The "RUT User's Guide" describes the SBUV and TOMS experiments, the instrument calibration and performance, operating schedules, and data coverage, and provides an assessment of RUT-S and -T data quality. It also provides detailed information on the data available on the computer tapes

Electron Transport through a Molecular Conductor with Center-of-Mass Motion

The linear conductance of a molecular conductor oscillating between two metallic leads is investigated numerically both for Hubbard interacting and noninteracting electrons. The molecule-leads tunneling barriers depend on the molecule displacement from its equilibrium position. The results present an interesting interference which leads to a conductance dip at the electron-hole symmetry point, that could be experimentally observable. It is shown that this dip is caused by the destructive interference between the purely electronic and phonon-assisted tunneling channels, which are found to carry opposite phases. When an internal vibrational mode is also active, the electron-hole symmetry is broken but a Fano-like interference is still observed

Tunable dipolar magnetism in high-spin molecular clusters

We report on the Fe17 high-spin molecular cluster and show that this system is an exemplification of nanostructured dipolar magnetism. Each Fe17 molecule, with spin S=35/2 and axial anisotropy as small as D=-0.02K, is the magnetic unit that can be chemically arranged in different packing crystals whilst preserving both spin ground-state and anisotropy. For every configuration, molecular spins are correlated only by dipolar interactions. The ensuing interplay between dipolar energy and anisotropy gives rise to macroscopic behaviors ranging from superparamagnetism to long-range magnetic order at temperatures below 1K.Comment: Replaced with version accepted for publication in Physical Review Letter