A general purpose subroutine for fast fourier transform on a distributed memory parallel machine

One issue which is central in developing a general purpose Fast Fourier Transform (FFT) subroutine on a distributed memory parallel machine is the data distribution. It is possible that different users would like to use the FFT routine with different data distributions. Thus, there is a need to design FFT schemes on distributed memory parallel machines which can support a variety of data distributions. An FFT implementation on a distributed memory parallel machine which works for a number of data distributions commonly encountered in scientific applications is presented. The problem of rearranging the data after computing the FFT is also addressed. The performance of the implementation on a distributed memory parallel machine Intel iPSC/860 is evaluated

Current-induced two-level fluctuations in pseudo spin-valves (Co/Cu/Co) nanostructures

Two-level fluctuations of the magnetization state of pseudo spin-valve pillars Co(10 nm)/Cu(10 nm)/Co(30 nm) embedded in electrodeposited nanowires (~40 nm in diameter, 6000 nm in length) are triggered by spin-polarized currents of 10^7 A/cm^2 at room temperature. The statistical properties of the residence times in the parallel and antiparallel magnetization states reveal two effects with qualitatively different dependences on current intensity. The current appears to have the effect of a field determined as the bias field required to equalize these times. The bias field changes sign when the current polarity is reversed. At this field, the effect of a current density of 10^7 A/cm^2 is to lower the mean time for switching down to the microsecond range. This effect is independent of the sign of the current and is interpreted in terms of an effective temperature for the magnetization.Comment: 4 pages, 5 figures, revised version, to be published in Phys. Rev. Let

Prevalence and co-infection of Toxoplasma gondii and Neospora caninum in Apodemus sylvaticus in an area relatively free of cats

The protozoan parasite Toxoplasma gondii is prevalent worldwide and can infect a remarkably wide range of hosts despite felids being the only definitive host. As cats play a major role in transmission to secondary mammalian hosts, the interaction between cats and these hosts should be a major factor determining final prevalence in the secondary host. This study investigates the prevalence of T. gondii in a natural population of Apodemus sylvaticus collected from an area with low cat density (<2·5 cats/km2). A surprisingly high prevalence of 40·78% (95% CI: 34·07%–47·79%) was observed despite this. A comparable level of prevalence was observed in a previously published study using the same approaches where a prevalence of 59% (95% CI: 50·13%–67·87%) was observed in a natural population of Mus domesticus from an area with high cat density (>500 cats/km2). Detection of infected foetuses frompregnant dams in both populations suggests that congenital transmission may enable persistence of infection in the absence of cats. The prevalences of the related parasite, Neospora caninum were found to be low in both populations (A. sylvaticus: 3·39% (95% CI: 0·12%–6·66%); M. domesticus: 3·08% (95% CI: 0·11%–6·05%)). These results suggest that cat density may have a lower than expected effect on final prevalence in these ecosystems

Recovering Grammar Relationships for the Java Language Specification

Grammar convergence is a method that helps discovering relationships between different grammars of the same language or different language versions. The key element of the method is the operational, transformation-based representation of those relationships. Given input grammars for convergence, they are transformed until they are structurally equal. The transformations are composed from primitive operators; properties of these operators and the composed chains provide quantitative and qualitative insight into the relationships between the grammars at hand. We describe a refined method for grammar convergence, and we use it in a major study, where we recover the relationships between all the grammars that occur in the different versions of the Java Language Specification (JLS). The relationships are represented as grammar transformation chains that capture all accidental or intended differences between the JLS grammars. This method is mechanized and driven by nominal and structural differences between pairs of grammars that are subject to asymmetric, binary convergence steps. We present the underlying operator suite for grammar transformation in detail, and we illustrate the suite with many examples of transformations on the JLS grammars. We also describe the extraction effort, which was needed to make the JLS grammars amenable to automated processing. We include substantial metadata about the convergence process for the JLS so that the effort becomes reproducible and transparent

\u3cem\u3eSarcocystis Neurona\u3c/em\u3e Diagnostic Primer and Its Use in Methods of Equine Protozoal Myeloencephalitis Diagnosis

An amplification primer and probe which can be used in an in vitro diagnostic test for the presence of S. neurona in equine blood or cerebrospinal fluid. Sarcocystis neurona is responsible for the equine condition of protozoal myelitis. The amplification primer is seventeen nucleotides in length and complementary to a unique section of the small ribosomal subunit of Sarcocystis neurona. The primer encompasses nucleotide positions 1470-1487 of the small ribosomal subunit of S. neurona. The primer has the sequence 5\u27 CCATTCCGGACGCGGGT SEQ ID NO:1

Evidence for high levels of vertical transmission in Toxoplasma gondii

Toxoplasma gondii is a highly ubiquitous and prevalent parasite. Despite the cat being the only definitive host, it is found in almost all geographical areas and warm blooded animals. Three routes of transmission are recognised: ingestion of oocysts shed by the cat, carnivory and congenital transmission. In natural populations, it is difficult to establish the relative importance of these routes. This paper reviews recent work in our laboratory which suggests that congenital transmission may be much more important than previously thought. Using PCR detection of the parasite, studies in sheep show that congenital transmission may occur in as many as 66% of pregnancies. Furthermore, in families of sheep on the same farm, exposed to the same sources of oocysts, significant divergent prevalences of Toxoplasma infection and abortion are found between different families. The data suggest that breeding from infected ewes increases the risk of subsequent abortion and infection in lambs. Congenital transmission rates in a natural population of mice were found to be 75%. Interestingly, congenital transmission rates in humans were measured at 19.8%. The results presented in these studies differ from those of other published studies and suggest that vertical transmission may be much more important than previously thought

c-FLIP regulates autophagy by interacting with Beclin-1 and influencing its stability

c-FLIP (cellular FLICE-like inhibitory protein) protein is mostly known as an apoptosis modulator. However, increasing data underline that c-FLIP plays multiple roles in cellular homoeostasis, influencing differently the same pathways depending on its expression level and isoform predominance. Few and controversial data are available regarding c-FLIP function in autophagy. Here we show that autophagic flux is less effective in c-FLIP−/− than in WT MEFs (mouse embryonic fibroblasts). Indeed, we show that the absence of c-FLIP compromises the expression levels of pivotal factors in the generation of autophagosomes. In line with the role of c-FLIP as a scaffold protein, we found that c-FLIPL interacts with Beclin-1 (BECN1: coiled-coil, moesin-like BCL2-interacting protein), which is required for autophagosome nucleation. By a combination of bioinformatics tools and biochemistry assays, we demonstrate that c-FLIPL interaction with Beclin-1 is important to prevent Beclin-1 ubiquitination and degradation through the proteasomal pathway. Taken together, our data describe a novel molecular mechanism through which c-FLIPL positively regulates autophagy, by enhancing Beclin-1 protein stability

Optical-chemical-microphysical relationships and closure studies for mixed carbonaceous aerosols observed at Jeju Island; 3-laser photoacoustic spectrometer, particle sizing, and filter analysis

Transport of aerosols in pollution plumes from the mainland Asian continent was observed in situ at Jeju, South Korea during the Cheju Asian Brown Cloud Plume-Asian Monsoon Experiment (CAPMEX) field campaign throughout August and September 2008 using a 3-laser photoacoustic spectrometer (PASS-3), chemical filter analysis, and size distributions. The PASS-3 directly measures the effects of morphology (e.g. coatings) on light absorption that traditional filter-based instruments are unable to address. Transport of mixed sulfate, carbonaceous, and nitrate aerosols from various Asian pollution plumes to Jeju accounted for 74% of the deployment days, showing large variations in their measured chemical and optical properties. Analysis of eight distinct episodes, spanning wide ranges of chemical composition, optical properties, and source regions, reveals that episodes with higher organic carbon (OC)/sulfate (SO 2-4 ) and nitrate (NO-3 )/SO2-4 composition ratios exhibit lower single scatter albedo at shorter wavelengths (!405). We infer complex refractive indices (n-ik) as a function of wavelength for the high, intermediate, and low OC/SO2-4 pollution episodes by using the observed particle size distributions and the measured optical properties. The smallest mean particle diameter corresponds to the high OC/SO2-4 aerosol episode. The imaginary part of the refractive index (k) is greater for the high OC/SO2- 4 episode at all wavelengths. A distinct, sharp increase in k at short wavelength implies enhanced light absorption by OC, which accounts for 50% of the light absorption at 405 nm, in the high OC/SO2-4 episode. Idealized analysis indicates increased absorption at 781 nm by factors greater than 3 relative to denuded black carbon in the laboratory. We hypothesize that coatings of black carbon cores are the mechanism of this enhancement. This implies that climate warming and atmospheric heating rates from black carbon particles can be significantly larger than have been estimated previously. The results of this study demonstrate ways in which atmospheric processing and mixing can amplify particle light absorption for carbonaceous aerosol, significantly at short wavelength, underscoring the need to understand and predict chemical composition effects on optical properties to accurately estimate the climate radiative forcing by mixed carbonaceous aerosols