Periodicity in the autocorrelation function as a mechanism for regularly occurring zero crossings or extreme values of a Gaussian process

The problem of zero crossings is of great historical prevalence and promises extensive application. The challenge is to establish precisely how the autocorrelation function or power spectrum of a one-dimensional continuous random process determines the density function of the intervals between the zero crossings of that process. This paper investigates the case where periodicities are incorporated into the autocorrelation function of a smooth process. Numerical simulations, and statistics about the number of crossings in a fixed interval, reveal that in this case the zero crossings segue between a random and deterministic point process depending on the relative time scales of the periodic and nonperiodic components of the autocorrelation function. By considering the Laplace transform of the density function, we show that incorporating correlation between successive intervals is essential to obtaining accurate results for the interval variance. The same method enables prediction of the density function tail in some regions, and we suggest approaches for extending this to cover all regions. In an ever-more complex world, the potential applications for this scale of regularity in a random process are far reaching and powerful

An Efficient Molecular Dynamics Scheme for Predicting Dopant Implant Profiles in Semiconductors

We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational overhead, plus a rare event algorithm to give statistical accuracy over several orders of magnitude change in the dopant concentration. The code uses a molecular dynamics (MD) model, instead of the binary collision approximation (BCA) used in implant simulators such as TRIM and Marlowe, to describe ion-target interactions. Atomic interactions are described by a combination of `many-body' and screened Coulomb potentials. Inelastic energy loss is accounted for using a Firsov model, and electronic stopping is described by a Brandt-Kitagawa model which contains the single adjustable parameter for the entire scheme. Thus, the program is easily extensible to new ion-target combinations with the minimum of tuning, and is predictive over a wide range of implant energies and angles. The scheme is especially suited for calculating profiles due to low energy, large angle implants, and for situations where a predictive capability is required with the minimum of experimental validation. We give examples of using our code to calculate concentration profiles and 2D `point response' profiles of dopants in crystalline silicon, silicon-germanium blends, and gallium-arsenide. We can predict the experimental profile over five orders of magnitude for and channeling and for non-channeling implants at energies up to hundreds of keV.Comment: 10 pages, 7 figures. Proceedings of COSIRES98. Accepted for publication in Nucl. Instrum. and Meth. B. See http://bifrost.lanl.gov/~reed

The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 angstrom resolution

Maturation of tRNA precursors into functional tRNA molecules requires trimming of the primary transcript at both the 5' and 3' ends. Cleavage of nucleotides from the 3' stem of tRNA precursors, releasing nucleotide diphosphates, is accomplished in Bacillus by a phosphate-dependent exoribonuclease, Rph. The crystal structure of this enzyme from B. anthracis has been solved by molecular replacement to a resolution of 1.7 angstrom and refined to an R factor of 19.3%. There is one molecule in the asymmetric unit; the crystal packing reveals the assembly of the protein into a hexamer arranged as a trimer of dimers. The structure shows two sulfate ions bound in the active-site pocket, probably mimicking the phosphate substrate and the phosphate of the 3'-terminal nucleotide of the tRNA precursor. Three other bound sulfate ions point to likely RNA-binding sites

Simple Synchronous Detector for Spectroscopic Studies

Lock-in-amplifiers are used in many applications for signal processing and offer the ability to discriminate high levels of noise. While these instruments are very powerful and offer many features, they are not portable and are expensive. An economical and easy to use alternative circuit is presented which incorporates pre-amplification, reference, and synchronous detection on one circuit board. The design can be used in laboratory or process control situations where its small size and low cost are advantageous. The circuit was successfully applied to moderate and high level signals as seen in flame infrared emission detection and in a portable radiometer for rocket plume studies

An endogenous inhibitor of angiogenesis downregulated by hypoxia in human aortic valve stenosis promotes disease pathogenesis

Acknowledgements The authors would like to acknowledge the NHS Grampian Biorepository for their support and assistance with all immunohistochemistry. Sources of funding This work was generously funded by the British Heart Foundation, UK (FS/17/28/32807) and Grampian NHS Endowments.Peer reviewedPublisher PD

Signal Processing and Propagation for Aeroacoustic Sensor Networking,” Ch

Passive sensing of acoustic sources is attractive in many respects, including the relatively low signal bandwidth of sound waves, the loudness of most sources of interest, and the inherent difficulty of disguising or concealing emitted acoustic signals. The availability of inexpensive, low-power sensing and signal-processing hardware enables application of sophisticated real-time signal processing. Among th

An Estimate of Nest Loss in Canada Due to Industrial Forestry Operations

Annual loss of nests by industrial (nonwoodlot) forest harvesting in Canada was estimated using two avian point-count data sources: (1) the Boreal Avian Monitoring Project (BAM) dataset for provinces operating in this biome and (2) available data summarized for the major (nonboreal) forest regions of British Columbia. Accounting for uncertainty in the proportion of harvest occurring during the breeding season and in avian nesting densities, our estimate ranges from 616 thousand to 2.09 million nests. Estimates of the impact on numbers of individuals recruited into the adult breeding population were made based on the application of survivorship estimates at various stages of the life cycle. Future improvements to this estimate are expected as better and more extensive avian breeding pair density estimates become available and as provincial forestry statistics become more refined, spatially and temporally. The effect of incidental take due to forestry is not uniform and is disproportionately centered in the southern boreal. Those species whose ranges occur primarily in these regions are most at risk for industrial forestry in general and for incidental take in particular. Refinements to the nest loss estimate for industrial forestry in Canada will be achieved primarily through the provision of more accurate estimates of the area of forest harvested annually during the breeding season stratified by forest type and Bird Conservation Region (BCR). A better understanding of survivorship among life-history stages for forest birds would also allow for better modeling of the effect of nest loss on adult recruitment. Finally, models are needed to project legacy effects of forest harvesting on avian populations that take into account forest succession and accompanying cumulative effects of landscape change

Draft Genome Sequences of Helicobacter pylori Strains Isolated from Regions of Low and High Gastric Cancer Risk in Colombia

The draft genome sequences of six Colombian Helicobacter pylori strains are presented. These strains were isolated from patients from regions of high and low gastric cancer risk in Colombia and were characterized by multilocus sequence typing. The data provide insights into differences between H. pylori strains of different phylogeographic origins.National Institutes of Health (U.S.) (grant P01CA028842)National Institutes of Health (U.S.) (grant P01CA026731)National Institutes of Health (U.S.) (grant P30ES002109

Dual Requirement for Yeast hnRNP Nab2p in mRNA poly(A) Tail Length Control and Nuclear Export

Recent studies of mRNA export factors have provided additional evidence for a mechanistic link between mRNA 3′‐end formation and nuclear export. Here, we identify Nab2p as a nuclear poly(A)‐binding protein required for both poly(A) tail length control and nuclear export of mRNA. Loss of NAB2 expression leads to hyperadenylation and nuclear accumulation of poly(A)+ RNA but, in contrast to mRNA export mutants, these defects can be uncoupled in a nab2 mutant strain. Previous studies have implicated the cytoplasmic poly(A) tail‐binding protein Pab1p in poly(A) tail length control during polyadenylation. Although cells are viable in the absence of NAB2 expression when PAB1 is overexpressed, Pab1p fails to resolve the nab2Δ hyperadenylation defect even when Pab1p is tagged with a nuclear localization sequence and targeted to the nucleus. These results indicate that Nab2p is essential for poly(A) tail length control in vivo, and we demonstrate that Nab2p activates polyadenylation, while inhibiting hyperadenylation, in the absence of Pab1p in vitro. We propose that Nab2p provides an important link between the termination of mRNA polyadenylation and nuclear export