Practical Algorithms For Mean Velocity Estimation In Pulse Doppler Weather Radars Using A Small Number Of Samples

Doppler weather radars with fast scanning rates must estimate spectral moments based on a small number of echo samples. This paper concerns the estimation of mean Doppler velocity in a coherent radar using a short complex time series. Specific results are presented based on 16 samples. A wide range of signal-to-noise ratios are considered, and attention is given to ease of implementation. It is shown that FFT estimators fare poorly in low SNR and/or high spectrum-width situations. Several variants of a vector pulse-pair processor are postulated and an algorithm is developed for the resolution of phase angle ambiguity. This processor is found to be better than conventional processors at very low SNR values. A feasible approximation to the maximum entropy estimator is derived as well as a technique utilizing the maximization of the periodogram. It is found that a vector pulse-pair processor operating with four lags for clear air observation and a single lag (pulse-pair mode) for storm observation may be a good way to estimate Doppler velocities over the entire gamut of weather phenomena.

Small-amplitude cyclic voltammetry: Part I. A simple fourier synthesis approach

Current-potential relationships are derived for small-amplitude periodic inputs for linear electrochemical systems using a Fourier synthesis procedure. Specific results have been obtained for a triangular potential waveform for two simple model systems.

"Small-particle limit" the second harmonic generation from noble metal nanoparticles

In this paper, we have probed the origin of SHG in copper nanoparticles by polarization-resolved hyper-Rayleigh scattering (HRS). Results obtained with various sizes of copper nanoparticles at four different wavelengths covering the wavelength range 738-1907 nm reveal that the origin of second harmonic generation (SHG) in these particles is purely dipolar in nature as long as the size (d) of the particles remains smaller compared to the wavelength (;.) of light ("small-particle limit"). However, contribution of the higher order multipoles coupled with retardation effect becomes apparent with an increase in the d/lambda ratio. We have identified the "small-particle limit" in the second harmonic generation from noble metal nanoparticles by evaluating the critical d/lambda ratio at which the retardation effect sets in the noble metal nanoparticles. We have found that the second-order nonlinear optical property of copper nanoparticles closely resembles that of gold, but not that of silver. (C) 2009 Elsevier B.V. All rights reserved.

Conformational analysis of small disulfide loops. Spectroscopic and theoretical studies on a synthetic cyclic tetrapeptide containing cystine

The conformational analysis of the synthetic peptide Boc-Cys-Pro-Val-Cys-NHMe has been carried out, as a model for small disulfide loops, in biologically active polypeptides. 'H NMR studies (270 MHz) establish that the Val(3) and Cys(4) NH groups are solvent shielded, while 13C studies establish an all-trans peptide backbone. Circular dichroism and Raman spectroscopy provide evidence for a right-handed twist of the disulfide bond. Analysis of the vicinal (JaB)c oupling constants for the two Cys residues establishes that XI - *60° for Cys(4), while some flexibility is suggested at Cys( 1). Conformational energy calculations, imposing intramolecular hydrogen bonding constraints, favor a P-turn (type I) structure with Pro(2)-Va1(3) as the corner residues. Theoretical and spectroscopic results are consistent with the presence of a transannular 4 - 1 hydrogen bond between Cys( 1) CO and Cys(4) NH groups, with the Val NH being sterically shielded from the solvent environment.

Estimating the efficiency of a small beam trawl for sampling tiger prawns Penaeus esculentus and P. semisulcatus in seagrass by removal experiments

The efficiency with which a small beam trawl (1 x 0.5 m mouth) sampled postlarvae and juveniles of tiger prawns Penaeus esculentus and P, semisulcatus at night was estimated in 3 tropical seagrass communities (dominated by Thalassia hemprichii, Syringodium isoetifolium and Enhalus acoroides, respectively) in the shallow waters of the Gulf of Carpentaria in northern Australia. An area of seagrass (40 x 3 m) was enclosed by a net and the beam trawl was repeatedly hand-hauled over the substrate. Net efficiency (q) was calculated using 4 methods: the unweighted Leslie, weighted Leslie, DeLury and Maximum-likelihood (ML) methods. The Maximum-likelihood is the preferred method for estimating efficiency because it makes the fewest assumptions and is not affected by zero catches. The major difference in net efficiencies was between postlarvae (mean ML q +/- 95% confidence limits = 0.66 +/- 0.16) and juveniles of both species (mean q for juveniles in water less than or equal to 1.0 m deep = 0.47 +/- 0.05), i.e. the beam trawl was more efficient at capturing postlarvae than juveniles. There was little difference in net efficiency for P, esculentus between seagrass types (T, hemprichii versus S. isoetifolium), even though the biomass and morphologies of seagrass in these communities differed greatly (biomasses were 54 and 204 g m(-2), respectively). The efficiency of the net appeared to be the same for juveniles of the 2 species in shallow water, but was lower for juvenile P, semisulcatus at high tide when the water was deeper (1.6 to 1.9 m) (0.35 +/- 0.08). The lower efficiency near the time of high tide is possibly because the prawns are more active at high than low tide, and can also escape above the net. Factors affecting net efficiency and alternative methods of estimating net efficiency are discussed.

Cloning Of Rice Dna And Identification Of Transfer-Rna Gene Clones

THE rapid development of recombinant DNA technology has brought forth a revolution in biology'>", it aids us to have a closer look at the 'way genes are organized, eS11 ecially in the complex eucaryotic genornes'<", Although many animal and yeast genes have been studied in detail using recombinant DNA technology, plant genes have seldom been targets for such studie., Germination is an ideal process to study gene expression .because it effects a . shift in the metabolic status of seeds from a state of 'dormancy to an active one. AJ;l understanding of gene organization and regulation darin.g germination can be accomplblted by molecular cloning of DNA from seeds lik.e rice. To study the status of histone, rRNA tRNA and other genes in the rice genome, a general method was developed to clone eucarvotic DNA in a' plasmid vector pBR 322. This essentially ~ involves the following steps. The rice embryo and plasmid pBR 322 DNAs were cut witll restriction endonuclease Bam Hi to generate stick.Y ends, The plasmid DNA was puosphatased, the DNA~ ware a~·tnealed and joined 'by T4 phage DNA ligase. The recombinant DNA molecules thus produced were transjerred into E. coli and colonies containing them Were selected by their sensitivity to tetracycline and resistance to ampicillin, Two clones were identified . 2S haVing tRNA genes by hybridization of the DNA in the clones \vitl1 32P-la.belled rice tRNAs.

Temperature characteristics of the billet and the dies in a small batch forging production

The work reported herein is part of an on-going programme to develop a computer code which, given the geometrical, process and material parameters of the forging operation, is able to predict the die and the billet cooling/heating characteristics in forging production. The code has been experimentally validated earlier for a single forging cycle and is now validated for a small batch production. To facilitate a step-by-step development of the code, the billet deformation has so far been limited to its surface layers, a situation akin to coining. The code has been used here to study the effects of die preheat-temperature, machine speed and rate of deformation the cooling/heating of the billet and the dies over a small batch of 150 forgings. The study shows: that there is a pre-heat temperature at which the billet temperature changes little from one forging to the next; that beyond a particular number of forgings, the machine speed ceases to have any pronounced influence on the temperature characteristics of the billet; and that increasing the rate of deformation reduces the heat loss from the billet and gives the billet a stable temperature profile with respect to the number of forgings. The code, which is simple to use, is being extended to bulk-deformation problems. Given a practical range of possible machine, billet and process specifics, the code should be able to arrive at a combination of these parameters which will give the best thermal characteristics of the die-billet system. The code is also envisaged as being useful in the design of isothermal dies and processes.

Genetic association analysis of miRNA SNPs implicates MIR145 in breast cancer susceptibility

Background MicroRNAs (miRNAs) are important small non-coding RNA molecules that regulate gene expression in cellular processes related to the pathogenesis of cancer. Genetic variation in miRNA genes could impact their synthesis and cellular effects and single nucleotide polymorphisms (SNPs) are one example of genetic variants studied in relation to breast cancer. Studies aimed at identifying miRNA SNPs (miR-SNPs) associated with breast malignancies could lead towards further understanding of the disease and to develop clinical applications for early diagnosis and treatment. Methods We genotyped a panel of 24 miR-SNPs using multiplex PCR and chip-based matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis in two Caucasian breast cancer case control populations (Primary population: 173 cases and 187 controls and secondary population: 679 cases and 301 controls). Association to breast cancer susceptibility was determined using chi-square (X 2 ) and odds ratio (OR) analysis. Results Statistical analysis showed six miR-SNPs to be non-polymorphic and twelve of our selected miR-SNPs to have no association with breast cancer risk. However, we were able to show association between rs353291 (located in MIR145) and the risk of developing breast cancer in two independent case control cohorts (p = 0.041 and p = 0.023). Conclusions Our study is the first to report an association between a miR-SNP in MIR145 and breast cancer risk in individuals of Caucasian background. This finding requires further validation through genotyping of larger cohorts or in individuals of different ethnicities to determine the potential significance of this finding as well as studies aimed to determine functional significance. Keywords: Association analysis; Breast cancer; microRNA; miR-SNPs; MIR145

Genetic variability of Tomato spotted wilt virus in Australia and validation of real time RT-PCR for its detection in single and bulked leaf samples

The potential for large-scale use of a sensitive real time reverse transcription polymerase chain reaction (RT-PCR) assay was evaluated for the detection of Tomato spotted wilt virus (TSWV) in single and bulked leaf samples by comparing its sensitivity with that of DAS-ELISA. Using total RNA extracted with RNeasy® or leaf soak methods, real time RT-PCR detected TSWV in all infected samples collected from 16 horticultural crop species (including flowers, herbs and vegetables), two arable crop species, and four weed species by both assays. In samples in which DAS-ELISA had previously detected TSWV, real time RT-PCR was effective at detecting it in leaf tissues of all 22 plant species tested at a wide range of concentrations. Bulk samples required more robust and extensive extraction methods with real time RT-PCR, but it generally detected one infected sample in 1000 uninfected ones. By contrast, ELISA was less sensitive when used to test bulked samples, once detecting up to 1 infected in 800 samples with pepper but never detecting more than 1 infected in 200 samples in tomato and lettuce. It was also less reliable than real time RT-PCR when used to test samples from parts of the leaf where the virus concentration was low. The genetic variability among Australian isolates of TSWV was small. Direct sequencing of a 587 bp region of the nucleoprotein gene (S RNA) of 29 isolates from diverse crops and geographical locations yielded a maximum of only 4.3% nucleotide sequence difference. Phylogenetic analysis revealed no obvious groupings of isolates according to geographic origin or host species. TSWV isolates, that break TSWV resistance genes in tomato or pepper did not differ significantly in the N gene region studied, indicating that a different region of the virus genome is responsible for this trait.

Peanut stripe potyvirus resistance in peanut (Arachis hypogaea L.) plants carrying viral coat protein gene sequences

Peanut (Arachis hypogaea L.) lines exhibiting high levels of resistance to peanut stripe virus (PStV) were obtained following microprojectile bombardment of embryogenic callus derived from mature seeds. Fertile plants of the commercial cultivars Gajah and NC7 were regenerated following co-bombardmentwith the hygromycin resistance gene and one of two forms of the PStV coat protein (CP) gene, an untranslatable, full length sequence (CP2) or a translatable gene encoding a CP with an N-terminal truncation (CP4). High level resistance to PStV was observed for both transgenes when plants were challenged with the homologous virus isolate. The mechanism of resistance appears to be RNA-mediated, since plants carrying either the untranslatable CP2 or CP4 had no detectable protein expression, but were resistant or immune (no virus replication). Furthermore, highly resistant, but not susceptible CP2 T0 plants contained transgene-specific small RNAs. These plants now provide important germplasm for peanut breeding, particularly in countries where PStV is endemic and poses a major constraint to peanut production.

Host range, symptom expression and RNA 3 sequence analyses of six Australian strains of Cucumber mosaic virus

We have characterised six Australian Cucumber mosaic virus (CMV) strains belonging to different subgroups, determined by the sequence of their complete RNA 3 and by their host range and the symptoms they cause on species in the Solanaceae, Cucurbitaceae and on sweet corn. These data allowed classification of strains into the known three CMV subgroups and identification of plant species able to differentiate the Australian strains by symptoms and host range. Western Australian strains 237 and Twa and Queensland strains 207 and 242 are closely related members of CMV subgroup IA, which cause similar severe symptoms on Nicotiana species. Strains 207 and 237 (subgroup IA) were the only strains tested which systemically infected sweet corn. Strain 243 caused the most severe symptoms of all strains on Nicotiana species, tomato and capsicum and appears to be the first confirmed subgroup IB strain reported in Australia. Based on pair-wise distance analysis and phylogeny of RNA 3, as well as mild disease symptoms on Nicotiana species, CMV 241 was assigned to subgroup II, as the previously described Q-CMV and LY-CMV.

A universal test to determine the integrity of RNA, and its suitability for reverse transcription, in animal tissue laboratory specimens

Degradation of RNA in diagnostic specimens can cause false-negative test results and potential misdiagnosis when tests rely on the detection of specific RNA sequence. Current molecular methods of checking RNA integrity tend to be host species or group specific, necessitating libraries of primers and reaction conditions. The objective here was to develop a universal (multi-species) quality assurance tool for determining the integrity of RNA in animal tissues submitted to a laboratory for analyses. Ribosomal RNA (16S rRNA) transcribed from the mitochondrial 16S rDNA was used as template material for reverse transcription to cDNA and was amplified using polymerase chain reaction (PCR). As mitochondrial DNA has a high level of conservation, the primers used were shown to reverse transcribe and amplify RNA from every animal species tested. Deliberate degradation of rRNA template through temperature abuse of samples resulted in no reverse transcription and amplification. Samples spiked with viruses showed that single-stranded viral RNA and rRNA in the same sample degraded at similar rates, hence reverse transcription and PCR amplification of 16S rRNA could be used as a test of sample integrity and suitability for analysis that required the sample's RNA, including viral RNA. This test will be an invaluable quality assurance tool for determination of RNA integrity from tissue samples, thus avoiding erroneous test results that might occur if degraded target RNA is used unknowingly as template material for reverse transcription and subsequent PCR amplification.

Identification of small juvenile scombrids from northwest tropical Australia using mitochondrial DNA cytochrome b sequences

Small juveniles of the nine species of scombrids in Australian waters are morphologically similar to one another and, consequently, difficult to identify to species level. We show that the sequence of the mitochondrial DNA cytochrome b gene region is a powerful tool for identification of these young fish. Using this method, we identified 50 juvenile scombrids collected from Exmouth Bay, Western Australia. Six species of scombrids were apparent in this sample of fish: narrow-barred Spanish mackerel (Scomberomorus commerson), Indian mackerel (Rastrelliger kanagurta), frigate tuna (Auxis thazard), bullet tuna (Auxis rochei), leaping bonito (Cybiosarda elegans), and kawakawa (Euthynnus affinis). The presence of Indian mackerel, frigate tuna, leaping bonito, and kawakawa is the first indication that coastal waters may be an important spawning habitat for these species, although offshore spawning may also occur. The occurrence of small juvenile S. commerson was predicted from the known spawning patterns of that species, but other mackerel species (Scomberomorus munroi, Scomberomorus queenslandicus, Scomberomorus semifasiciatus) likely to be spawning during the sampling period were not detected among the 50 small juveniles analyzed here.

Development of a small-plant bioassay to assess banana grown from tissue culture for consistent infection by Fusarium oxysporum f. sp. cubense

Two reliable small-plant bioassays were developed using tissue-cultured banana, resulting in consistent symptom expression and infection by Fusarium oxysporum f. sp. cubense (Foc). One bioassay was based on providing a constant watertable within a closed pot and the second used free-draining pots. Culture medium for spore generation influenced infectivity of Foc. Inoculation of potted banana by drenching potting mix with a conidial suspension, consisting mostly of microconidia, few macroconidia and no chlamydospores, generated from one-quarter-strength potato dextrose agar + streptomycin sulfate, resulted in inconsistent infection. When a conidial suspension that consisted of all three spore types, microconidia, macroconidia and chlamydospores, prepared from spores generated on carnation leaf agar was used, all plants became infected, indicating that the spore type present in conidial suspensions may contribute to inconsistency of infection. Inconsistency of infection was not due to loss of virulence of the pathogen in culture. Millet grain precolonised by Foc as a source of inoculum resulted in consistent infection between replicate plants. Sorghum was not a suitable grain for preparation of inoculum as it was observed to discolour roots and has the potential to stunt root growth, possibly due to the release of phytotoxins. For the modified closed-pot system, a pasteurised potting mix consisting of equal parts of bedding sand, perlite and vermiculite plus 1 g/L Triabon slow release fertiliser was suitable for plant growth and promoted capillary movement of water through the potting mix profile. A suitable potting mix for the free-draining pot system was also developed.