Partial bisulfite conversion for unique template sequencing

We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone

Advanced experimental applications for x-ray transmission gratings Spectroscopy using a novel grating fabrication method

A novel fabrication method for soft x-ray transmission grating and other optical elements is presented. The method uses Focused-Ion-Beam (FIB) technology to fabricate high-quality free standing grating bars on Transmission Electron Microscopy grids (TEM-grid). High quality transmission gratings are obtained with superb accuracy and versatility. Using these gratings and back-illuminated CCD camera, absolutely calibrated x-ray spectra can be acquired for soft x-ray source diagnostics in the 100-3000 eV spectral range. Double grating combinations of identical or different parameters are easily fabricated, allowing advanced one-shot application of transmission grating spectroscopy. These applications include spectroscopy with different spectral resolutions, bandwidths, dynamic ranges, and may serve for identification of high-order contribution, and spectral calibrations of various x-ray optical elements

Mapping the Spatial Distribution of a Disease-Transmitting Insect in the Presence of Surveillance Error and Missing Data

Maps of the distribution of epidemiological data often ignore surveillance error or possible correlations between missing information and outcomes. We analyse presence–absence data at the household level (12050 points) of a disease‐carrying insect in Mariano Melgar, Peru, collected as part of the Arequipan Ministry of Health\u27s efforts to control Chagas disease. We construct a Bayesian hierarchical model to locate regions that are vulnerable to under‐reporting due to surveillance error, accounting for variability in participation due to infestation status. The spatial correlation in the data allows us to identify relative inspector sensitivity and to elucidate the relationship between participation and infestation. We show that naive estimates of prevalence would be biased by surveillance error and missingness at random assumptions. We validate our results through simulations and observe how randomized inspector assignments may improve prevalence estimates. Our results suggests that bias due to imperfect observations and missingness at random can be assessed and corrected in prevalence estimates of spatially auto-correlated binary variables

Adaptive Investment Strategies For Periodic Environments

In this paper, we present an adaptive investment strategy for environments with periodic returns on investment. In our approach, we consider an investment model where the agent decides at every time step the proportion of wealth to invest in a risky asset, keeping the rest of the budget in a risk-free asset. Every investment is evaluated in the market via a stylized return on investment function (RoI), which is modeled by a stochastic process with unknown periodicities and levels of noise. For comparison reasons, we present two reference strategies which represent the case of agents with zero-knowledge and complete-knowledge of the dynamics of the returns. We consider also an investment strategy based on technical analysis to forecast the next return by fitting a trend line to previous received returns. To account for the performance of the different strategies, we perform some computer experiments to calculate the average budget that can be obtained with them over a certain number of time steps. To assure for fair comparisons, we first tune the parameters of each strategy. Afterwards, we compare the performance of these strategies for RoIs with different periodicities and levels of noise.Comment: Paper submitted to Advances in Complex Systems (November, 2007) 22 pages, 9 figure

Major impact of dust deposition on the productivity of the Arabian Sea

In the Arabian Sea (AS), spatiotemporal nutrient limitation patterns of primary production and the possible role of nutrient inputs from the atmosphere are still not well understood. Using a biogeochemical model forced by modeled aerosol deposition, we show that without high atmospheric iron inputs through dust deposition during the summer monsoon, primary production over the AS would be reduced by half. Atmospheric iron deposition also supports most of the nitrogen fixation over the AS. However, our ocean biogeochemistry modeling results suggest that dinitrogen fixation constitutes a negligible fraction of the primary production. Finally, we show that atmospheric inputs of nitrogen, mostly from anthropogenic activities in India, have a negligible impact on primary production

Effect of Pt substitution on the electronic structure of AuTe2

We report a photoemission and x-ray absorption study on Au1-xPtxTe2 (x = 0 and 0.35) triangular lattice in which superconductivity is induced by Pt substitution for Au. Au 4f and Te 3d core-level spectra of AuTe2 suggests a valence state of Au2+(Te2)2-, which is consistent with its distorted crystal structure with Te-Te dimers and compressed AuTe6 otahedra. On the other hand, valence-band photoemission spectra and pre-edge peaks of Te 3d absorption edge indicate that Au 5d bands are almost fully occupied and that Te 5p holes govern the transport properties and the lattice distortion. The two apparently conflicting pictures can be reconciled by strong Au 5d/Au 6s-Te 5p hybridization. Absence of a core-level energy shift with Pt substitution is inconsistent with the simple rigid band picture for hole doping. The Au 4f core-level spectrum gets slightly narrow with Pt substitution, indicating that the small Au 5d charge modulation in distorted AuTe2 is partially suppressed.Comment: 13 pages, 4 figures, accepted by Physical Review