Application of the WEPP model with digital geographic information

The Water Erosion Prediction Project (WEPP) is a process-based continuous simulation erosion model that can be applied to hillslope profiles and small watersheds. One limitation to application of WEPP (or other models) to the field or farm scale is the difficulty in determining the watershed structure, which may be composed of multiple channels and profiles (and potentially other features as well). This presentation describes current efforts to link the WEPP model with Geographic Information Systems (GIS) and utilize Digital Elevation Model (DEM) data to generate the necessary topographic inputs for erosion model simulations. Two automated approaches for applying the WEPP model have been developed and compared to manual application of the model. The first approach (named the Hillslope method) uses information from a DEM to delineate the watershed boundary, channel and hillslope locations, and then configure "representative" hillslope slope profiles from the myriad flowpath data. The second approach (named the Flowpath method) also uses DEM information to delineate the watershed boundary, but then runs WEPP model simulations on every flowpath within a watershed. For a set of research watersheds, the automatic Hillslope method performed as well as a manual application of WEPP by an expert user in predictions of runoff and sediment loss. Tests also showed that the Hillslope and Flowpath methods were not significantly different than each other or different from manual model applications in predictions of hillslope erosion. Additional research work ongoing at the National Soil Erosion Research Laboratory is examining the feasibility of using commonly available digital elevation data (for example from on-vehicle Geographical Positioning Systems (GPS)) to provide input for the automated techniques for driving the erosion model

Transcriptional implications of intragenic DNA methylation in the oestrogen receptor alpha gene in breast cancer cells and tissues

Background DNA methylation variability regions (MVRs) across the oestrogen receptor alpha (ESR1) gene have been identified in peripheral blood cells from breast cancer patients and healthy individuals. In contrast to promoter methylation, gene body methylation may be important in maintaining active transcription. This study aimed to assess MVRs in ESR1 in breast cancer cell lines, tumour biopsies and exfoliated epithelial cells from expressed breast milk (EBM), to determine their significance for ESR1 transcription. Methods DNA methylation levels in eight MVRs across ESR1 were assessed by pyrosequencing bisulphite-converted DNA from three oestrogen receptor (ER)-positive and three ER-negative breast cancer cell lines. DNA methylation and expression were assessed following treatment with DAC (1 μM), or DMSO (controls). ESR1 methylation levels were also assayed in DNA from 155 invasive ductal carcinoma biopsies provided by the Breast Cancer Campaign Tissue Bank, and validated with DNA methylation profiles from the TCGA breast tumours (n = 356 ER-pos, n = 109 ER-neg). DNA methylation was profiled in exfoliated breast epithelial cells from EBM using the Illumina 450 K (n = 36) and pyrosequencing in a further 53 donor samples. ESR1 mRNA levels were measured by qRT-PCR. Results We show that ER-positive cell lines had unmethylated ESR1 promoter regions and highly methylated intragenic regions (median, 80.45%) while ER-negative cells had methylated promoters and lower intragenic methylation levels (median, 38.62%). DAC treatment increased ESR1 expression in ER-negative cells, but significantly reduced methylation and expression of ESR1 in ER-positive cells. The ESR1 promoter was unmethylated in breast tumour biopsies with high levels of intragenic methylation, independent of ER status. However, ESR1 methylation in the strongly ER-positive EBM DNA samples were very similar to ER-positive tumour cell lines. Conclusion DAC treatment inhibited ESR1 transcription in cells with an unmethylated ESR1 promoter and reduced intragenic DNA methylation. Intragenic methylation levels correlated with ESR1 expression in homogenous cell populations (cell lines and exfoliated primary breast epithelial cells), but not in heterogeneous tumour biopsies, highlighting the significant differences between the in vivo tumour microenvironment and individual homogenous cell types. These findings emphasise the need for care when choosing material for epigenetic research and highlights the presence of aberrant intragenic methylation levels in tumour tissue

Recent glitches detected in the Crab pulsar

From 2000 to 2010, monitoring of radio emission from the Crab pulsar at Xinjiang Observatory detected a total of nine glitches. The occurrence of glitches appears to be a random process as described by previous researches. A persistent change in pulse frequency and pulse frequency derivative after each glitch was found. There is no obvious correlation between glitch sizes and the time since last glitch. For these glitches $\Delta\nu_{p}$ and $\Delta\dot{\nu}_{p}$ span two orders of magnitude. The pulsar suffered the largest frequency jump ever seen on MJD 53067.1. The size of the glitch is $\sim$ 6.8 $\times 10^{-6}$ Hz, $\sim$ 3.5 times that of the glitch occured in 1989 glitch, with a very large permanent changes in frequency and pulse frequency derivative and followed by a decay with time constant $\sim$ 21 days. The braking index presents significant changes. We attribute this variation to a varying particle wind strength which may be caused by glitch activities. We discuss the properties of detected glitches in Crab pulsar and compare them with glitches in the Vela pulsar.Comment: Accepted for publication in Astrophysics & Space Scienc

Inferring Loop Invariants using Postconditions

One of the obstacles in automatic program proving is to obtain suitable loop invariants. The invariant of a loop is a weakened form of its postcondition (the loop's goal, also known as its contract); the present work takes advantage of this observation by using the postcondition as the basis for invariant inference, using various heuristics such as "uncoupling" which prove useful in many important algorithms. Thanks to these heuristics, the technique is able to infer invariants for a large variety of loop examples. We present the theory behind the technique, its implementation (freely available for download and currently relying on Microsoft Research's Boogie tool), and the results obtained.Comment: Slightly revised versio

Post-Newtonian SPH calculations of binary neutron star coalescence. I. Method and first results

We present the first results from our Post-Newtonian (PN) Smoothed Particle Hydrodynamics (SPH) code, which has been used to study the coalescence of binary neutron star (NS) systems. The Lagrangian particle-based code incorporates consistently all lowest-order (1PN) relativistic effects, as well as gravitational radiation reaction, the lowest-order dissipative term in general relativity. We test our code on sequences of single NS models of varying compactness, and we discuss ways to make PN simulations more relevant to realistic NS models. We also present a PN SPH relaxation procedure for constructing equilibrium models of synchronized binaries, and we use these equilibrium models as initial conditions for our dynamical calculations of binary coalescence. Though unphysical, since tidal synchronization is not expected in NS binaries, these initial conditions allow us to compare our PN work with previous Newtonian results. We compare calculations with and without 1PN effects, for NS with stiff equations of state, modeled as polytropes with $\Gamma=3$. We find that 1PN effects can play a major role in the coalescence, accelerating the final inspiral and causing a significant misalignment in the binary just prior to final merging. In addition, the character of the gravitational wave signal is altered dramatically, showing strong modulation of the exponentially decaying waveform near the end of the merger. We also discuss briefly the implications of our results for models of gamma-ray bursts at cosmological distances.Comment: RevTeX, 37 pages, 17 figures, to appear in Phys. Rev. D, minor corrections onl

Observation of Orbitally Excited B_s Mesons

We report the first observation of two narrow resonances consistent with states of orbitally excited (L=1) B_s mesons using 1 fb^{-1} of ppbar collisions at sqrt{s} = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron. We use two-body decays into K^- and B^+ mesons reconstructed as B^+ \to J/\psi K^+, J/\psi \to \mu^+ \mu^- or B^+ \to \bar{D}^0 \pi^+, \bar{D}^0 \to K^+ \pi^-. We deduce the masses of the two states to be m(B_{s1}) = 5829.4 +- 0.7 MeV/c^2 and m(B_{s2}^*) = 5839.7 +- 0.7 MeV/c^2.Comment: Version accepted and published by Phys. Rev. Let

Global Search for New Physics with 2.0/fb at CDF

Data collected in Run II of the Fermilab Tevatron are searched for indications of new electroweak-scale physics. Rather than focusing on particular new physics scenarios, CDF data are analyzed for discrepancies with the standard model prediction. A model-independent approach (Vista) considers gross features of the data, and is sensitive to new large cross-section physics. Further sensitivity to new physics is provided by two additional algorithms: a Bump Hunter searches invariant mass distributions for "bumps" that could indicate resonant production of new particles; and the Sleuth procedure scans for data excesses at large summed transverse momentum. This combined global search for new physics in 2.0/fb of ppbar collisions at sqrt(s)=1.96 TeV reveals no indication of physics beyond the standard model.Comment: 8 pages, 7 figures. Final version which appeared in Physical Review D Rapid Communication

Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization

Wave function of the radion with a bulk scalar field

The behaviour of the distance between two branes (the `radion') in a braneworld model with a bulk scalar field is investigated. We show that the BPS conditions of supergravity ensure that the dynamics of the scalar field and the radion are not independent; we derive the four-dimensional effective action, showing that the effective theory is of scalar-tensor nature, coupling the radion to four-dimensional gravit