Experimental study of the quantum driven pendulum and its classical analog in atom optics

We present experimental results for the dynamics of cold atoms in a far detuned amplitude-modulated optical standing wave. Phase-space resonances constitute distinct peaks in the atomic momentum distribution containing up to 65% of all atoms resulting from a mixed quantum chaotic phase space. We characterize the atomic behavior in classical and quantum regimes and we present the applicable quantum and classical theory, which we have developed and refined. We show experimental proof that the size and the position of the resonances in phase space can be controlled by varying several parameters, such as the modulation frequency, the scaled well depth, the modulation amplitude, and the scaled Planck’s constant of the system. We have found a surprising stability against amplitude noise. We present methods to accurately control the momentum of an ensemble of atoms using these phase-space resonances which could be used for efficient phase-space state preparation.

Special issue on advances in data mining and its applications

Data mining is the process to identify valid, implicit, previously unknown, potentially useful and understandable information from large databases. It is an important step in the process of knowledge discovery in databases, (Olaru & Wehenkel, 1999). In a data mining process, input data can be structured, seme-structured, or unstructured. Data can be in text, categorical or numerical values. One of the important characteristics of data mining is its ability to deal data with large volume, distributed, time variant, noisy, and high dimensionality. A large number of data mining algorithms have been developed for different applications. For example, association rules mining can be useful for market basket problems, clustering algorithms can be used to discover trends in unsupervised learning problems, classification algorithms can be applied in decision-making problems, and sequential and time series mining algorithms can be used in predicting events, fault detection, and other supervised learning problems (Vapnik, 1999). Classification is among the most important tasks in the data mining, particularly for data mining applications into engineering fields. Together with regression, classification is mainly for predictive modelling. So far, there have been a number of classification algorithms in practice. According to (Sebastiani, 2002), the main classification algorithms can be categorized as: decision tree and rule based approach such as C4.5 (Quinlan, 1996); probability methods such as Bayesian classifier (Lewis, 1998); on-line methods such as Winnow (Littlestone, 1988) and CVFDT (Hulten 2001), neural networks methods (Rumelhart, Hinton & Wiliams, 1986); example-based methods such as k-nearest neighbors (Duda & Hart, 1973), and SVM (Cortes & Vapnik, 1995). Other important techniques for classification tasks include Associative Classification (Liu et al, 1998) and Ensemble Classification (Tumer, 1996).

Regulation of photosynthetic pigments in micro-algae by multiple environmental factors: a dynamic balance hypothesis

Environmental effects on the concentration of photosynthetic pigments in micro-algae can be explained by dynamics of photosystem synthesis and deactivation. A model that couples photosystem losses to the relative cellular rates of energy harvesting (light absorption) and assimilation predicts optimal concentrations of light-harvesting pigments and balanced energy flow under environmental conditions that affect light availability and metabolic rates. Effects of light intensity, nutrient supply and temperature on growth rate and pigment levels were similar to general patterns observed across diverse micro-algal taxa. Results imply that dynamic behaviour associated with photophysical stress, and independent of gene regulation, might constitute one mechanism for photo-acclimation of photosynthesis.

Amino acid synthesis in the symbiotic sea anemone Aiptasia pulchella

Symbiotic Aiptasia pulchella and freshly isolated zooxanthellae were incubated in (NaHCO3)-C-14 and NH4Cl for 1 to 240 min, and samples were analysed by reverse-phase high-performance liquid chromatography (HPLC) and an online radiochemical detector. NH4+ was first assimilated into C-14-glutamate and C-14-glutamine in the zooxanthellae residing in A. pulchella. The specific activities (dpm nmol(-1)) of C-14-glutamate and C-14-glutamine in vivo, were far greater in the zooxanthellae than in the host tissue, indicating that NH4+ was principally incorporated into the glutamate and glutamine pools of the zooxanthellae. C-14-alpha-ketoglutarate was taken up from the medium by intact A. pulchella and assimilated into a small amount of C-14-glutamate in the host tissue, but no C-14-glutamine was detected in the host fraction. The C-14-glutamate that was synthesized was most likely produced from transamination reactions as opposed to the direct assimilation of NH4+. The free aminoacid composition of the host tissue and zooxanthellae of A. pulchella was also measured. The results presented here demonstrate that NH4+ was initially assimilated by the zooxanthellae of A. pulchella.

Nitrogen relations of natural and disturbed plant communities in tropical Australia

Nitrogen relations of natural and disturbed tropical plant communities in northern Australia (Kakadu National Park) were studied. Plant and soil N characteristics suggested that differences in N source utilisation occur at community and species level. Leaf and xylem sap N concentrations of plants in different communities were correlated with the availability of inorganic soil N (NH4+ and NO3-). In general, rates of leaf NO3- assimilation were low. Even in communities with a higher N status, including deciduous monsoon forest, disturbed wetland, and a revegetated mine waste rock dump, levels of leaf nitrate reductase, xylem and leaf NO3 levels were considerably lower than those that have been reported for eutrophic communities. Although NO3- assimilation in escarpment and eucalypt woodlands, and wetland, was generally low, within these communities there was a suite of species that exhibited a greater capacity for NO3- assimilation. These high-NO3- species were mainly annuals, resprouting herbs or deciduous trees that had leaves with high N contents. Ficus, a high-NO3- species, was associated with soil exhibiting higher rates of net mineralisation and net nitrification. Low-NO3- species were evergreen perennials with low leaf N concentrations. A third group of plants, which assimilated NO3- (albeit at lower rates than the high-NO3- species), and had high-N leaves, were leguminous species. Acacia species, common in woodlands, had the highest leaf N contents of all woody species. Acacia species appeared to have the greatest potential to utilise the entire spectrum of available N sources. This versatility in N source utilisation may be important in relation to their high tissue N status and comparatively short life cycle. Differences in N utilisation are discussed in the context of species life strategies and mycorrhizal associations.

Role of phosphorylation in the conformation of tau peptides implicated in Alzheimer's disease

A series of peptides corresponding to isolated regions of Tau (tau) protein have been synthesized and their conformations determined by H-1 NMR spectroscopy. Immunodominant peptides corresponding to tau(224-240) and a bisphosphorylated derivative in which a single Thr and a single Ser are phosphorylated at positions 231 and 235 respectively, and which are recognized by an Alzheimer's disease-specific monoclonal antibody, were the main focus of the study. The nonphosphorylated peptide adopts essentially a random coil conformation in aqueous solution, but becomes slightly more ordered into P-type structure as the hydrophobicity of the solvent is increased by adding up to 50% trifluoroethanol (TFE). Similar trends are observed for the bisphosphorylated peptide, with a somewhat stronger tendency to form an extended structure, There is tentative NMR evidence for a small population of species containing a turn at residues 229-231 in the phosphorylated peptide, and this is strongly supported by CD spectroscopy. A proposal that the selection of a bioactive conformation from a disordered solution ensemble may be an important step (in either tubulin binding or in the formation of PHF) is supported by kinetic data on Pro isomerization. A recent study showed that Thr231 phosphorylation affected the rate of prolyl isomerization and abolished tubulin binding. This binding was restored by the action of the prolyl isomerase Pin1. In the current study, we find evidence for the existence of both trans and cis forms of tau peptides in solution but no difference in the equilibrium distribution of cis-trans isomers upon phosphorylation. Increasing hydrophobicity decreases the prevalence of cis forms and increases the major trans conformation of each of the prolines present in these molecules. We also synthesized mutant peptides containing Tyr substitutions preceding the Pro residues and found that phosphorylation of Tyr appears to have an effect on the equilibrium ratio of cis-trans isomerization and decreases the cis content.

Cryptococcus nyarrowii sp nov., a basidiomycetous yeast from Antarctica

in December 1997,196 soil and snow samples were collected from Vestvold Hills, Davis Base, Antarctica. Two isolates, CBS 8804 T (pink colonies) and CBS 8805 (yellow colonies), were shown by proteome analysis and DNA sequencing to represent the same species. Results from the sequencing of the D1/D2 region of the large rDNA subunit placed this species in the hymenomycetous tree in a unique sister clade to the Trichosporonalles and the Tremellalles. The clade consists of Holtermannia corniformis CBS 6979 and CBS strains 8804(T) 8805, 8016, 7712, 7713 and 7743. Morphological and physiological characteristics placed this species in the genus Cryptococcus, with characteristics including the assimilation Of D-glucuronate and myo-inositol, no fermentation, positive Diazonium blue B and urease reactions, absence of sexual reproduction and production of starch-like compounds. Fatty acid analysis identified large proportions of polyunsaturated lipids, mainly linolleic (C-18.2) and, to a lesser extent, linolenic (C-18.3) acids. On the basis of the physiological and phylogenetic data, isolates CBS 8804(T) and CBS 8805 are described as Cryptococcus nyarrowii sp. nov.

Deconvolving the delta O-18 seawater component from subseasonal coral delta O-18 and Sr/Ca at Rarotonga in the southwestern subtropical Pacific for the period 1726 to 1997

To reconstruct oceanographic variations in the subtropical South Pacific, 271-year long subseasonal time series of Sr/Ca and delta(18)O were generated from a coral growing at Rarotonga (21.5degreesS, 159.5degreesW). In this case, coral Sr/Ca appears to be an excellent proxy for sea surface temperature (SST) and coral delta(18)O is a function of both SST and seawater delta(18)O composition (delta(18)O(sw)). Here, we focus on extracting the delta(18)O(sw) signal from these proxy records. A method is presented assuming that coral Sr/Ca is solely a function of SST and that coral delta(18)O is a function of both SST and delta(18)O(sw). This method separates the effects of delta(18)O(sw) from SST by breaking the instantaneous changes of coral delta(18)O into separate contributions by instantaneous SST and delta(18)O(sw) changes, respectively. The results show that on average delta(18)O(sw) at Rarotonga explains similar to39% of the variance in delta(18)O and that variations in SST explains the remaining similar to61% of delta(18)O variance. Reconstructed delta(18)O(sw) shows systematic increases in summer months (December-February) consistent with the regional pattern of variations in precipitation and evaporation. The delta(18)O(sw) also shows a positive linear correlation with satellite-derived estimated salinity for the period 1980 to 1997 (r = 0.72). This linear correlation between reconstructed delta(18)O(sw) and salinity makes it possible to use the reconstructed delta(18)O(sw) to estimate the past interannual and decadal salinity changes in this region. Comparisons of coral delta(18)O and delta(18)O(sw) at Rarotonga with the Pacific decadal oscillation index suggest that the decadal and interdecadal salinity and SST variability at Rarotonga appears to be related to basin-scale decadal variability in the Pacific. Copyright (C) 2002 Elsevier Science Ltd.

Solution structure of χ-conopeptide MrIA, a modulator of the human norepinephrine transporter

The chi-conopeptides MrIA and MrIB are 13-residue peptides with two disulfide bonds that inhibit human and rat norepinephrine transporter systems and are of significant interest for the design of novel drugs involved in pain treatment. In the current study we have determined the solution structure of MrIA using NMR spectroscopy. The major element of secondary structure is a hairpin with the two strands connected by an inverse gamma-turn. The residues primarily involved in activity have previously been shown to be located in the turn region (Sharpe, I. A.; Palant, E.: Schroder, C. L; Kaye, D. M.; Adams, D. I.; Alewood, P. F.; Lewis, R. J. J Biol Client 2003, 278, 40317-40323), which appears to be more flexible than the beta-strands based on disorder in the ensemble of calculated structures. Analogues of MrIA with N-terminal truncations indicate that the N-terminal residues play a role in defining a stable conformation and the native disulfide connectivity. In particular, noncovalent interactions between Val3 and Hypl2 are likely to be involved in maintaining a stable conformation. The N-terminus also affects activity, as a single N-terminal deletion introduced additional pharmacology at rat vas deferens, while deleting the first two amino acids reduced chi-conopeptide potency. This article was originally published online as an accepted preprint. The Published Online date corresponds to the preprint version. You can request a copy of the preprint by entailing the Biopolymers editorial office at biopolymers@wiley.com (c) 2005 Wiley Periodicals, Inc.

Environmental control of potential yield of sunflower in the subtropics

A simple framework was used to analyse the determinants of potential yield of sunflower (Helianthus annuus L.) in a subtropical environment. The aim was to investigate the stability of the determinants crop duration, canopy light interception, radiation use efficiency (RUE), and harvest index (HI) at 2 sowing times and with 3 genotypes differing in crop maturity and stature. Crop growth, phenology, light interception, yield, prevailing temperature, and radiation were recorded and measured throughout the crop cycle. Significant differences in grain yield were found between the 2 sowings, but not among genotypes within each sowing. Mean yields (0% moisture) were 6 . 02 and 2 . 17 t/ha for the first sowing, on 13 September (S1), and the second sowing, on 5 March (S2), respectively. Exceptionally high yields in S1 were due to high biomass assimilation associated with the high radiation environment, high light interception owing to a greater leaf area index, and high RUE (1 . 47-1 . 62 g/MJ) across genotypes. It is proposed that the high RUE was caused by high levels of available nitrogen maintained during crop growth by frequent applications of fertiliser and sewage effluent as irrigation. In addition to differences in the radiation environment, the assimilate partitioned to grain was reduced in S2 associated with a reduction in the duration of grain-filling. Harvest index was 0 . 40 in S1 and 0 . 25 in S2. It is hypothesised that low minimum temperatures experienced in S2 reduced assimilate production and partitioning, causing premature maturation.