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Item11th Intelligent Systems for Molecular Biology 2003 (ISMB2003)(Hindawi, 2003-09) Abbott, Catherine AnneThis report profiles the keynote talks given at ISMB03 in Brisbane, Australia by Ron Shamir, David Haussler, John Mattick, Yoshihide Hayashizaki, Sydney Brenner, theOverton Prize winner, Jim Kent, and the ISCB Senior Accomplishment Awardee,David Sankov. ItemAn 180 MHz 16 bit multiplier using asynchronous logic design techniques(Institute of Electrical and Electronics Engineers Computer Society (IEEE Publishing), 1994) Burford, Richard G; Fan, Xingcha; Bergmann, Neil WA CMOS digital logic design technique is described which exploits the advantages of fast precharged logic and efficient latch design commonly used in synchronous systems while maintaining the features of localized control inherent in asynchronous design. A pipelined sixteen bit multiplier is presented and its performance compared with several previously reported asynchronous and synchronous designs. ItemThe 7Li(p,n)7 Be Reaction as a Source of Fast Neutrons for Smaller Compact Cyclotrons(Institute of Electrical and Electronics Engineers Computer Society (IEEE Publishing), 1979) Chaudhri, M Anwar; Templer, J.; Rouse, J LThe usefulness of the 7Li(p,n)7Be reaction as a fast neutron source for applications, such as neutron therapy etc., using smaller compact cyclotrons (proton energies of up to 15-18 MeV) has been investigated by measuring thin and thick target neutron spectra, absolute cross sections and angular distributions of various neutron groups produced in this reaction at 10.45 MeV. Our results indicate that the forward direction is still the preferred one for obtaining the most suitable fast neutron beam for biomedical application, and that moderately thick, rather than infinitely thick, target would provide higher mean energy. Moreover, it has also been shown that the 7Li(p,n)7 Be reaction is more suited for producing neutron beams for therapy than proton and deuteron induced reactions on Be at corresponding energies, and that a therapeutically useful neutron beam can be produced even with smaller compact cyclotrons. ItemA biolistic method for high-throughput production of transgenic wheat plants with single gene insertions(BioMed Central, 2018-06-26) Ismagul, Ainur; Yang, Nannan; Maltseva, Elina; Iskakova, Gulnur; Mazonka, Inna; Skiba, Yuri; Bi, Huihui; Eliby, Serik; Jatayev, Satyvaldy; Shavrukov, Yuri; Borisjuk, Nikolai; Langridge, PeterBackground The relatively low efficiency of biolistic transformation and subsequent integration of multiple copies of the introduced gene/s significantly complicate the genetic modification of wheat (Triticum aestivum) and other plant species. One of the key factors contributing to the reproducibility of this method is the uniformity of the DNA/gold suspension, which is dependent on the coating procedure employed. It was also shown recently that the relative frequency of single copy transgene inserts could be increased through the use of nanogram quantities of the DNA during coating. Results A simplified DNA/gold coating method was developed to produce fertile transgenic plants, via microprojectile bombardment of callus cultures induced from immature embryos. In this method, polyethyleneglycol (PEG) and magnesium salt solutions were utilized in place of the spermidine and calcium chloride of the standard coating method, to precipitate the DNA onto gold microparticles. The prepared microparticles were used to generate transgenics from callus cultures of commercial bread wheat cv. Gladius resulting in an average transformation frequency of 9.9%. To increase the occurrence of low transgene copy number events, nanogram amounts of the minimal expression cassettes containing the gene of interest and the hpt gene were used for co-transformation. A total of 1538 transgenic wheat events were generated from 15,496 embryos across 19 independent experiments. The variation of single copy insert frequencies ranged from 16.1 to 73.5% in the transgenic wheat plants, which compares favourably to published results. Conclusions The DNA/gold coating procedure presented here allows efficient, large scale transformation of wheat. The use of nanogram amounts of vector DNA improves the frequency of single copy transgene inserts in transgenic wheat plants. ItemA-band methyl halide dissociation via electronic curve crossing as studied by electron energy loss spectroscopy(American Institute of Physics, 2010) Kato, Hisaaki; Masui, Hisashi; Hoshino, Masahiro; Cho, Hyuck; Ingolfsson, Oddur; Brunger, Michael James; Limao-Vieira, Paulo; Tanaka, HiroshiExcitation of the A-band low-lying electronic states in the methyl halides, CH3I, CH3Br, CH3Cl, and CH3F, has been investigated for the (n→σ∗) transitions, using electron energy loss spectroscopy (EELS) in the range of 3.5–7.5 eV. For the methyl halides, CH3I, CH3Br, and CH3Cl, three components of the Q complex (3Q1, 3Q0, and 1Q1) were directly observed, with the exception of methyl fluoride, in the optically forbidden EELS experimental conditions of this investigation. The effect of electronic-state curve crossing emerged in the transition probabilities for the 3Q0 and 1Q1 states, with spin-orbit splitting observed and quantified against results from recent ab initio studies. ItemAbsolute cross sections for dissociative electron attachment and dissociative ionization of cobalt tricarbonyl nitrosyl in the energy range from 0 eV to 140 eV(American Institute of Physics, 2013-01-24) Engmann, Sarah; Stano, Michal; Papp, Peter; Brunger, Michael James; Matejcik, Stefan; Ingolfsson, OddurWe report absolute dissociative electron attachment (DEA) and dissociative ionization (DI) cross sections for electron scattering from the focused electron beam induced deposition (FEBID) precursor Co(CO)3NO in the incident electron energy range from 0 to 140 eV. We find that DEA leads mainly to single carbonyl loss with a maximum cross section of 4.1 × 10−16 cm2, while fragmentation through DI results mainly in the formation of the bare metal cation Co+ with a maximum cross section close to 4.6 × 10−16 cm2 at 70 eV. Though DEA proceeds in a narrow incident electron energy range, this energy range is found to overlap significantly with the expected energy distribution of secondary electrons (SEs) produced in FEBID. The DI process, on the other hand, is operative over a much wider energy range, but the overlap with the expected SE energy distribution, though significant, is found to be mainly in the threshold region of the individual DI processes. ItemActive heat pulse sensing of 3-D-flow fields in streambeds(Copernicus Publications on behalf of the European Geosciences Union, 2018-03-20) Banks, Edward Wallace; Shanafield, Margaret; Noorduijn, Saskia; McCallum, James; Lewandowski, Jorg; Batelaan, OkkeProfiles of temperature time series are commonly used to determine hyporheic flow patterns and hydraulic dynamics in the streambed sediments. Although hyporheic flows are 3-D, past research has focused on determining the magnitude of the vertical flow component and how this varies spatially. This study used a portable 56-sensor, 3-D temperature array with three heat pulse sources to measure the flow direction and magnitude up to 200 mm below the water–sediment interface. Short, 1 min heat pulses were injected at one of the three heat sources and the temperature response was monitored over a period of 30 min. Breakthrough curves from each of the sensors were analysed using a heat transport equation. Parameter estimation and uncertainty analysis was undertaken using the differential evolution adaptive metropolis (DREAM) algorithm, an adaption of the Markov chain Monte Carlo method, to estimate the flux and its orientation. Measurements were conducted in the field and in a sand tank under an extensive range of controlled hydraulic conditions to validate the method. The use of short-duration heat pulses provided a rapid, accurate assessment technique for determining dynamic and multi-directional flow patterns in the hyporheic zone and is a basis for improved understanding of biogeochemical processes at the water–streambed interface. ItemActive vibration absorber design via sliding mode control(Institute of Electrical and Electronics Engineers Computer Society (IEEE Publishing), 2000) Cao, Tri-Tan Van; Chen, Lei; He, Fangpo; Sammut, KarlA new, simple control method for vibration absorber design is presented. A nonlinear robust control scheme based on a variable structure is designed and simulated. Robust synthesis of the discontinuity surface based on classical frequency loop-shaping and the edge theorem is discussed. The proposed control scheme has two advantages over the current existing vibration absorber design methodologies: 1) it is completely insensitive to changes in the stiffness and damping of the absorber, and strongly robust against parametric uncertainties of the primary vibrating structure; and 2) it is capable of suppressing both cyclic and random vibrations over a very wide range of frequencies. ItemAcute effects of chlorogenic acids on endothelial function and blood pressure in healthy men and women(Royal Society of Chemistry, 2016-04-19) Ward, Natalie C; Hodgson, Jonathan M; Woodman, Richard John; Zimmermann, D; Poquet, L; Leveques, A; Actis-Goretta, L; Puddey, I B; Croft, K DCoffee is a rich source of polyphenols, primarily chlorogenic acids (CGA). Certain polyphenols and polyphenol-rich foods and beverages have been shown to improve endothelial function and lower blood pressure (BP). The aim of the present study was to investigate the acute effect of two doses of CGA (5-CGA) on endothelial function and BP. In a cross-over study, 16 healthy men and women received: (i) 0 mg purified 5-CGA (control group); (ii) 450 mg purified 5-CGA; (iii) 900 mg purified 5-CGA; and (iv) 200 mg purified (−)-epicatechin (positive control) in random order one week apart. Peak and continuous mean (60 to 240 s post ischaemia) flow-mediated dilation (FMD) was measured at baseline, 1 h and 4 h. BP was measured at baseline and every 30 min to 4 h. Plasma CGA and epicatechin levels were significantly increased at both 1 h and 4 h post their respective treatments. Peak FMD was not significantly altered by either dose of 5-CGA or the epicatechin, relative to control (p > 0.05). Relative to control, effects on continuous mean FMD response following 450 mg 5-CGA and 900 mg of 5-CGA (0.47 ± 0.16%, p = 0.016 and 0.65 ± 0.16%, p < 0.001, respectively) at 1 h and (0.18 ± 0.17%, p = 0.99 and 0.44 ± 0.16%, p < 0.05, respectively) at 4 h. There was no significant effect of any of the treatments on BP. In conclusion, the present study has found no significant effect of 5-CGA, at 450 and 900 mg, on peak FMD response. However, there were significant improvements in mean post-ischaemic FMD response, particularly at the 1 h time point in this group of healthy individuals. ItemAdabook and Multibook: adaptive boosting with chance correction(2013-09) Powers, David MartinThere has been considerable interest in boosting and bagging, including the combination of the adaptive techniques of AdaBoost with the random selection with replacement techniques of Bagging. At the same time there has been a revisiting of the way we evaluate, with chance-corrected measures like Kappa, Informedness, Correlation or ROC AUC being advocated. This leads to the question of whether learning algorithms can do better by optimizing an appropriate chance corrected measure. Indeed, it is possible for a weak learner to optimize Accuracy to the detriment of the more reaslistic chance-corrected measures, and when this happens the booster can give up too early. This phenomenon is known to occur with conventional Accuracy-based AdaBoost, and the MultiBoost algorithm has been developed to overcome such problems using restart techniques based on bagging. This paper thus complements the theoretical work showing the necessity of using chance-corrected measures for evaluation, with empirical work showing how use of a chance-corrected measure can improve boosting. We show that the early surrender problem occurs in MultiBoost too, in multiclass situations, so that chance-corrected AdaBook and Multibook can beat standard Multiboost or AdaBoost, and we further identify which chance-corrected measures to use when. ItemAdaptive Asymptotical Synchronization for Stochastic Complex Networks with Time-Delay and Markovian Switching(Hindawi, 2014-06-04) Jiang, Xueling; Qin, Shuijie; Tong, Dongbing; Wang, LipingThe problem of adaptive asymptotical synchronization is discussed for the stochastic complex dynamical networks with time-delay and Markovian switching. By applying the stochastic analysis approach and the M-matrix method for stochastic complex networks, several sufficient conditions to ensure adaptive asymptotical synchronization for stochastic complex networks are derived. Through the adaptive feedback control techniques, some suitable parameters update laws are obtained. Simulation result is provided to substantiate the effectiveness and characteristics of the proposed approach. ItemAdaptive integral sliding mode control for active vibration absorber design(Institute of Electrical and Electronics Engineers Computer Society (IEEE Publishing), 2000) Cao, Tri-Tan Van; Chen, Lei; He, Fangpo; Sammut, KarlA new tuning method for active vibration absorber design is presented in this paper. A robust, adaptive control scheme based on a variable structure with an adaptive discontinuity surface is designed and simulated. Robust synthesis of an adaptive discontinuity surface based on an augmented state-space is discussed. The proposed tuning scheme has three superior features compared with the existing counterparts in that: (i) it is completely insensitive to changes in the stiffness and damping of the absorber, (ii) it is capable of suppressing cyclic vibrations over a wide range of frequencies, (iii) its real-time operation requires only one adjustable gain. ItemAdaptive order-statistics multi-shell filtering for bad pixel correction within CFA demosaicking(Institute of Electrical and Electronics Engineers Computer Society (IEEE Publishing), 2009) Li, Jimmy Siu; Randhawa, SharmilAs today's digital cameras contain millions of image sensors, it is highly probable that the image sensors will contain a few defective pixels due to errors in the fabrication process. While these bad pixels would normally be mapped out in the manufacturing process, more defective pixels, known as hot pixels, could appear over time with camera usage. Since some hot pixels can still function at normal settings, they need not be permanently mapped out because they will only appear on a long exposure and/or at high ISO settings. In this paper, we apply an adaptive order-statistics multi-shell filter within CFA demosaicking to filter out only bad pixels whilst preserving the rest of the image. The CFA image containing bad pixels is first demosaicked to produce a full colour image. The adaptive filter is then only applied to the actual sensor pixels within the colour image for bad pixel correction. Demosaicking is then re-applied at those bad pixel locations to produce the final full colour image free of defective pixels. It has been shown that our proposed method outperforms a separate process of CFA demosaicking followed by bad pixel removal. ItemThe adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes(John Wiley & Sons, 2016) McCairns, R J Scott; Smith, Steve; Sasaki, Minami; Bernatchez, L; Beheregaray, Luciano BellagambaWhilst adaptation and phenotypic plasticity might buffer species against habitat degradation associated with global climate change, few studies making such claims also possess the necessary and sufficient data to support them. Doing so requires demonstration of heritable variation in traits affecting fitness under new environmental conditions. We address this issue using an emerging aquatic system to study adaptation to climate change, the crimson-spotted rainbowfish (Melanotaenia duboulayi), a freshwater species from a region of eastern Australia projected to be affected by marked temperature increases. Captive born M. duboulayi of known pedigree were used to assess the long-term effects of contemporary and 2070-projected summer temperatures on the expression of genes previously identified in a climate change transcriptomics (RNA-Seq) experiment. Nearly all genes responded to increasing temperature. Significant additive genetic variance explained a moderate proportion of transcriptional variation for all genes. Most genes also showed broad-sense genetic variation in transcriptional plasticity. Additionally, molecular pathways of candidate genes co-occur with genes inferred to be under climate-mediated selection in wild M. duboulayi populations. Together, these results indicate the presence of existing variation in important physiological traits, and the potential for adaptive responses to a changing thermal environment. ItemAdsorption behavior of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin on pristine and doped black phosphorene: A DFT study(Elsevier, 2017-07-03) Zhang, Hong-ping; Hou, Jia-liang; Wang, Yaobin; Tang, Ping-ping; Zhang, Ya-ping; Lin, Xiao-yan; Liy, Changsheng; Tang, YouhongPolychlorinated dibenzo-p-dioxins (PCDDs) are highly toxic to humans. The search for novel and effective methods and materials for detecting or removing these gas pollutants is becoming more important and urgent. With its high specific surface area, abundance, and variety of potential applications, phosphorene has attracted much research interest. In this study, density functional theory was used to study the interactions between a doped phosphorene sheet and a tetrachlorodibenzo-p-dioxin (TCDD) molecule. The initial configurations of the TCDD and metallic (Ca or Ti) or nonmetallic (S and Se) dopants were investigated during the TCDD–phosphorene interaction study. Adsorption energy, isosurface of electron density difference, and density of states analysis were utilized to explore the interactions between TCDD and phosphorene. The results indicated that Ca dopant effectively improved the interaction between TCDD and phosphorene. Se dopant reduced the interaction between TCDD and phosphorene. Combining interactions between TCDD and the pristine, Ca-doped, and Se-doped phosphorenes, phosphorene could be a promising candidate for TCDD sensing and removal. ItemAdvances in Carbon Nanotube n-type Doping: Methods, Analysis and Applications(Elsevier, 2018-01-01) Brownlie, Liam; Shapter, Joseph GeorgeGreat advances in semiconductor technologies continue to be made with the demand for cheap, non-toxic, easily processed and environmentally friendly technologies on the rise. Single-walled carbon nanotubes (SWCNTs) are viewed as a promising candidate that satisfies these criteria however proper doping of the SWCNTs to provide n-type behaviour has been a persistent issue. In recent years, great advances have been made in providing air stable and efficient n-type doping of SWCNTs. This review presents the most recent and promising methods of n-type doping SWCNTs highlighted for their simplicity and quality of electrical properties. The analysis and major applications of these semiconductors with a focus on thermoelectric devices and transistors are discussed. ItemAge and quality stratification of groundwater in the Triassic Sherwood Sandstone aquifer of South Yorkshire and the East Midlands, UK(Elsevier, 2018-08-09) Smedley, Pauline L; Shand, Paul; Butcher, Andrew SGroundwater from the Triassic Sherwood Sandstone aquifer of the English East Midlands shows a well-documented evolution in chemistry and residence time as it flows downgradient from shallow unconfined conditions to greater depths, confined by Mercia Mudstone. The flow path covers a lateral distance of some 40 km and depths approaching 800 m. The presence of fresh groundwater (Cl = 15 mg/L, Na = 17 mg/L, SO4 = 144 mg/L, TDS = 500 mg/L) of likely Pleistocene age can be demonstrated down to about 500 m depth in the aquifer, some 10 km downgradient of its confined/unconfined interface. This is amongst the deepest fresh groundwater identified in the UK. Beyond that zone, salinity increases in response to dissolution of gypsum or anhydrite, giving Ca-SO4 groundwater. Further downgradient still, saline groundwater (TDS = 10 g/L) is encountered in the deepest part of the confined aquifer. Downgradient geochemical evolution and increasing residence time are also observed in the South Yorkshire section of the aquifer, to the north of the East Midlands flow path. Here, analogous sequential geochemical changes are observed, controlled by carbonate and sulphate mineral reactions, redox changes and silicate hydrolysis, with evidence of increased inputs of e.g. Na, Cl and SO4 from modern pollution at shallow depths in the unconfined aquifer. Redox conditions are more variable in the western part of the South Yorkshire aquifer, due to local confinement or semi-confinement by fine-grained Quaternary deposits overlying the Sherwood Sandstone. Ratios of δ13C in this section of aquifer increase from −14‰ at outcrop to −11‰ in Mercia-Mudstone-confined conditions as a result of gradual equilibration with aquifer carbonate under closed-system conditions. Ratios of δ18O and δ2H become more depleted, reaching −9‰ and −61‰ respectively, suggesting recharge under climatic conditions significantly cooler than the modern era. Increasing residence time is also indicated by increasing concentrations of a number of trace elements (e.g. Li, Rb, Sr, Mo). These transitions are also observed vertically within investigated boreholes in unconfined and semi-confined sections of the aquifer. Deep groundwater (160–170 m depth) from a borehole within the unconfined aquifer of South Yorkshire has δ18O and δ2H ratios as depleted as −9.2‰ and −67‰ respectively. Such depth stratification indicates that good-quality palaeowater, likely of Pleistocene age, can exist at depth even in the unconfined Sherwood Sandstone aquifer, and that vertical hydraulic conductivity is much lower than lateral. A paucity of boreholes in the Mercia-Mudstone-confined section of the South Yorkshire aquifer makes estimation of the lateral extent of fresh groundwater there more problematic, though brackish groundwater (Cl = 1300 mg/L, TDS = 5.5 g/L) has been identified 12 km east of the aquifer's confined margin. ItemAggregation-disaggregation algorithm for e2-singularly perturbed limiting average Markov control problems(Institute of Electrical and Electronic Engineers, 1991) Abbad, Mohammed; Filar, Jerzy AIn this paper we consider a singular perturbation of order 2 for a Markov decision process with the limiting average reward criterion. We define a singular perturbation of order 2 in the following sense: we assume that the underlying process is composed of n separate irreducible processes, and that a small e-perturbation is such that it ”unites” these processes into m separate irreducible processes. Then another small e2-perturbation is such that it “unites” these latter processes into a single irreducible process. The present paper is organized as follows: In Section 2, we formulate the singular perturbation of order 2. In Section 3, we give explicitly the limit Markov Control Problem (limit MCP), that is entirely different from the original unperturbed MDP, which forms an appropriate asymptotic approximation to a whole family of perturbed problems. Thus only the single limit MCP needs to be solved. ItemAggregation-induced emission fluorogens as biomarkers to assess the viability of microalgae in aquatic ecosystems(Royal Society of Chemistry, 2015-09-29) Guo, Feng; Gai, Wei Ping; Hong, Y; Tang, B Z; Qin, Jianguang; Tang, YouhongMicroalgae can be a valuable indicator for monitoring water pollution due to their sensitivity to the changes induced by pollutants in the environment. In this study, an aggregation-induced emission fluorogen was used as a novel tool to differentiate dead and live microalgae and quantify the link between live algal concentration and fluorogen intensity. Protein in the cell protoplasm is the key component contributing to fluorescence emission in algae. ItemAgricultural Land Fragmentation at Urban Fringes: An Application of Urban-To-Rural Gradient Analysis in Adelaide(MDPI, 2017-04-16) Wadduwage, Suranga; Millington, Andrew; Crossman, Neville David; Sandhu, HarpinderOne of the major consequences of expansive urban growth is the degradation and loss of productive agricultural land and agroecosystem functions. Four landscape metrics—Percentage of Land (PLAND), Mean Parcel Size (MPS), Parcel Density (PD), and Modified Simpson’s Diversity Index (MSDI)—were calculated for 1 km × 1 km cells along three 50 km-long transects that extend out from the Adelaide CBD, in order to analyze variations in landscape structures. Each transect has different land uses beyond the built-up area, and they differ in topography, soils, and rates of urban expansion. Our new findings are that zones of agricultural land fragmentation can be identified by the relationships between MPS and PD, that these occur in areas where PD ranges from 7 and 35, and that these occur regardless of distance along the transect, land use, topography, soils, or rates of urban growth. This suggests a geometry of fragmentation that may be consistent, and indicates that quantification of both land use and land-use change in zones of fragmentation is potentially important in planning.