bluuebunny/crossref_metadata_2025 huggingface dataset:
Zaprinast, a well‐known cyclic guanosine monophosphate‐specific phosphodiesterase inhibitor, is an agonist for GPR35
Authors: Taniguchi Yasuhito , Tonai-Kachi Hiroko , Shinjo Katsuhiro
Published: August 2006

We found that zaprinast, a well‐known cyclic guanosine monophosphate‐specific phosphodiesterase inhibitor, acted as an agonist for a G protein‐coupled receptor, GPR35. In our intracellular calcium mobilization assay, zaprinast activated rat GPR35 strongly (geometric mean EC50 value of 16 nM), whereas it activated human GPR35 moderately (geometric mean EC50 value of 840 nM). We also demonstrated that GPR35 acted as a Gαi/o‐ and Gα16‐coupled receptor for zaprinast when heterologously expressed in human embryonic kidney 293 (HEK 293) cells. These findings will facilitate the research on GPR35 and the drug discovery of the GPR35 modulators.
A novel salmonid myoD gene is distinctly regulated during development and probably arose by duplication after the genome tetraploidization
Authors: Macqueen Daniel J. , Johnston Ian A.
Published: August 2006

A novel myoD paralogue was characterised in Salmo salar (smyoD1c) and S. trutta (btmyoD1c). SmyoD1c had 78.2/90.6% protein sequence identity to smyoD1a/smyoD1b, respectively. Each paralogue was differentially expressed throughout somitogenesis. In adult fish, smyoD1a was the predominant gene expressed in fast muscle, whereas smyoD1c was 2–3 times upregulated in slow muscle compared to smyoD1a/1b. A maximum likelihood analysis indicated that myoD1c arose by duplication of myoD1b after the salmonid tetraploidization. Another myoD paralogue (myoD2) is present in at least some teleosts, reflecting a more ancient genome duplication. To accommodate these findings we propose a simplified teleost‐myoD nomenclature.
Climate regime shifts and community reorganization in the Gulf of Alaska: how do recent shifts compare with 1976/1977?
Authors: Litzow Michael A.
Published: August 2006

Climate regime shifts have recently occurred in the North Pacific (1998–1999) and the Arctic (2000), but the nature of biological reaction to these events is poorly understood. An index of local climate (1960–2005), and data from commercial fishery catches (1960–2004) and from small-mesh trawl surveys (1972–2005) are used to assess the impacts of these climate events in the Subarctic Gulf of Alaska. Non-linear regression showed that survey catch composition strongly responded to local climate at lags of 2 and 4 years, providing evidence of rapid ecological response to climate change in the system. A sequential regime shift detection method identified rapid change in local climate, and in survey and commercial catches following the well-documented regime shift to a positive state of the Pacific Decadal Oscillation (PDO) in 1976/1977. However, the analysis failed to detect the 1998/1999 regime shift in local climate, or in survey or commercial catches. This result is consistent with the view that the 1998/1999 climate regime shift did not represent a reversion to a negative PDO state. Local temperature increased and local sea level pressure decreased in the Gulf of Alaska during the years 2001–2005, consistent with anthropogenic warming and recent spatial reorganization in Arctic climate. There was no evidence of community reorganization following this climate event. Further observation will be required to evaluate the persistence of this new climate pattern, and the nature of community reaction to it.
Feeding of Atlantic salmon (Salmo salar L.) post-smolts in the Northeast Atlantic
Authors: Haugland Monika , Holst Jens Christian , Holm Marianne , Hansen Lars Petter
Published: August 2006

Stomach samples from 1384 Atlantic salmon, collected from 1991 to 2003 in the Northeast Atlantic, were analysed to fill the gap between studies on post-smolt diet in fjords and coastal areas of the Northeast Atlantic and studies on the diet of pre-adults and adults in the Norwegian Sea. The post-smolts fed largely on 0-group fish. Blue whiting was an important prey only in the slope current transporting the larvae from the spawning areas west of the United Kingdom into the North and Norwegian Seas. Sandeel and herring were important or present in the stomachs throughout most of the area studied. Unusually large quantities of 0-group herring in the Norwegian Sea in summer 2002 coincided with a high condition factor of post-smolts that year. The forage ratio of the post-smolts was positively related to the proportion of herring in the stomachs and the abundance of herring recruits. Despite these findings, the most productive period for Atlantic salmon on record, the 1970s, coincided with the collapse of the Norwegian spring-spawning herring, which raises the question as to whether herring is more important as a competitor than as a food source. Hyperiid amphipods were more important prey than krill, in contrast to the situation for other pelagic fish species.
A refined fish consumption model for lactating Cape fur seals (Arctocephalus pusillus pusillus), based on scat analyses
Authors: Mecenero Silvia , Kirkman Stephen P. , Roux Jean-Paul
Published: August 2006

A refined fish consumption model for lactating Cape fur seals in Namibia during the eight-month lactation period, which allows for spatio-temporal variation in the diet as determined by scat analyses, has been developed. Previous estimates of prey consumption by Cape fur seals have been based mostly on coarse diet composition models. Sensitivity analyses showed that the energetic requirement and mass of lactating females (bioenergetic variables), as well as the energetic density of prey (diet variable), contributed most to the uncertainty in consumption estimates. Uncertainty in the remaining input variables had minimal effects on the estimates of food consumption. The consumption of commercial prey (horse mackerel, hake and pelagic fish) was greatest by the colony at Cape Cross. The model estimated that a female of average mass 55 kg ingested, on average, 11% of her body mass per day. This model is easily applied to other age/sex classes of the seal population. It permits improvement of the estimates of prey consumption by seals, which are useful for assessing levels of competitive interactions between seals and fisheries or other predators, or the impacts of seals on prey species.
Instrument Comparison for Dna Genotyping by Amplicon Melting
Authors: Herrmann Mark G. , Durtschi Jacob D. , Voelkerding Karl V. , Wittwer Carl T.
Published: August 2006

DNA melting analysis for the identification of sequence is increasingly used in molecular diagnostics. Recent advances in DNA melting analysis, including high-resolution instrumentation and specialized fluorescent DNA-binding dyes, allow genotyping by whole amplicon melting without probes. With the popularity of melting analysis as a diagnostic tool, there is a need to characterize the ability of commercially available real-time PCR instruments to perform high-resolution amplicon melting analyses. Four real-time instruments varying in sample format, throughput, and heat transfer (Cepheid's SmartCycler, Idaho Technology's HR-1, and Roche's LightCycler 1.2 and LightCycler 2.0) were evaluated for their ability to differentiate homozygous genotypes at the human β-globin sickle cell locus. The melting transition was monitored by including the dye LCGreen Plus in the PCR, and the data were uniformly analyzed with custom in-house software. The wild-type and mutant homozygous genotypes differed by a theoretical Tm of 0.09°C and were best discriminated by the high-resolution HR-1 instrument. All instruments could identify a double single nucleotide polymorphism heterozygote by the heteroduplexes formed. However, signal-to-noise ratios varied from 260 to 3500, suggesting that melting instrument design (data acquisition, data density, thermal control) determines the accuracy of genotyping by amplicon melting. (JALA 2006;11:273-7)
Novel Data Analysis for in Vitro Electrophysiological Assays in HTS
Authors: Miu Peter , Fomenko Igor , Durst Mark , Balaban David
Published: August 2006

Recent development in automated patch-clamp platforms has transformed the preclinical drug development landscape by incorporating electrophysiological assays at early stages of drug screening. PatchXpress 7000A, an automated 16-channel parallel patch-clamp platform, has a higher throughput than the conventional whole cell patch clamp. We developed and optimized assay conditions for the human ether-a-go-go channel (hERG) on an automated patch-clamp system such as PatchXpress 7000A. We applied nonlinear mixed models to quantify the consistency of the assay from cell to cell and to provide an accurate measure of drug potency over the population of the same cell type. The well-known hERG blocker quinidine was used in the experiments. The results of this novel statistical approach are the estimate of the average potency for the population of the cells with high degree of accuracy and the estimate of the potency variability from cell to cell. This method revealed no significant difference in the potency estimates for our assay and for conventional patch-clamp platform. We suggest that the novel data analysis can accurately predict compound potency when the assay protocols may have a small number of test concentrations and repeated measurements. (JALA 2006;11:195–202)
Debunking the Myth: Validation of Fluorescein for Testing the Precision of Nanoliter Dispensing
Authors: Harris David L. , Mutz Mitchell
Published: August 2006

Acoustic energy can precisely and accurately eject a droplet of liquid from a reservoir, enabling delivery of picoliter and nanoliter volumes (Ellson, R.; Mutz, M.; Browning, B.; Lee, L.; Miller, M.; Papen, R. Transfer of low nanoliter volumes between microplates using focused acoustics—automation considerations. Journal of the Association for Laboratory Automation 2003, 8(5), 29–34). Acoustic droplet ejection has been shown to be extremely precise (coefficients of variation < 2%) over a wide range of dispensed volumes (Ellson, R.; Mutz, M.; Browning, B.; Lee, L.; Miller, M.; Papen, R. Transfer of low nanoliter volumes between microplates using focused acoustics—automation considerations. Journal of the Association for Laboratory Automation 2003, 8(5), 29–34). However, measuring the performance of low-volume fluid transfers can be difficult because the data are often masked by variability in bulk dispensers and fluorescence readers used as part of the overall measurement process (Petersen, J.; Nguyen, J. Comparison of absorbance and fluorescence methods for determining liquid dispensing precision. Journal of the Association for Laboratory Automation 2005, 10(2), 82–87; Rhode, H.; Schulze, M.; Renard, S.; Zimmerman, P.; Moore, T.; Cumme, G.; Horn, A. An improved method for checking HTS/uHTS liquid handling systems. Journal of Biomolecular Screening 2004, 9, 726–733). The fluorophore used must also be stable so that thermal bleaching and photobleaching do not contribute additional variability to the measurements. This study assesses the suitability of fluorescein to measure the precision of fluid transfers of 2.5-nL DMSO droplets. The short-term and long-term stabilities of fluorescein are first qualified using a reference standard. Next, we determine the noise contribution of the filler and reader. Lastly, data are presented for the precision of 5- and 50-nL fluid transfers using this fluorescein measurement process. (JALA 2006;11:233–9)
Extending Near-Field Scanning Optical Microscopy for Biological Studies
Authors: Mooren Olivia L. , Erickson Elizabeth S. , Dickenson Nicholas E. , Dunn Robert C.
Published: August 2006

Near-field scanning optical microscopy (NSOM) is a scanning probe technique that enables optical measurements to be conducted with nanometric spatial resolution. In addition to high-resolution optical information, NSOM yields a topographic mapping of sample features that enables a direct comparison to be made between surface topography and the optical signal. For the biological sciences, where sophisticated fluorescence labeling protocols have been developed, the simultaneously collected fluorescence and topography information measured with NSOM offers a potentially powerful tool. The progress in implementing NSOM on unfixed, viable samples, however, has been slowed over concerns regarding sample heating and problems associated with damaging forces generated during imaging. Here, we discuss recent measurements that show sample heating to be modest and not limiting for NSOM applications on viable tissues. In addition, we highlight recent work on developing new NSOM probes that have been demonstrated to be amenable with imaging unfixed samples under buffered conditions. These developments now enable the high resolution of NSOM to be applied to areas in the biological sciences that were previously inaccessible. (JALA 2006;11:268–72)
Automated Generation of Animl Documents by Analytical Instruments
Authors: Roth Alexander , Jopp Ronny , Schäfer Reinhold , Kramer Gary W.
Published: August 2006

The scope of this project covers the storing of result data produced by generic laboratory devices during processing of analytical experiments, the data describing the examination methods, and the audit trail using the Analytical Information Markup Language (AnIML) standard. This project also considers the integration of generic devices in automated laboratory environments.

AnIML is an upcoming ASTM standard format for recording analytical data and workflows with accompanying experimental metadata. Adapting this standard to existing instruments currently requires manual intervention. The goal of this project is to automate as many steps as possible in generating an AnIML document with all its essential information supplied directly by the analytical instrument. Software with such functionality could be integrated into analytical instruments or reside in firmware boxes hooked to the instruments. This would allow a smooth transition to the new standard even in complex existing environments. A set of prerequisites have to be fulfilled before the feasibility of this approach can be shown.

The prototype application we describe here integrates the generic description of an instrument using the Laboratory Equipment Control Interface Specification, Object Management Group (LECIS OMG) Device Capability Dataset. Information about the device's commands and the device's data stream with its semantics can be found there. The experiment's metadata are provided by the test order. In both cases, XML schemas contain the information syntax. Using this information, we developed a generic interface that maps the result stream semantically and then transforms it into an AnIML document without manual intervention. At this time, we have completed and tested a prototype implementation and are working to support the full functionality of both the LECIS OMG and the ASTM AnIML standards. (JALA 2006;11:247–53)
Label-Free Profiling of Ligands for Endogenous Gpcrs Using a Cell-Based High-Throughput Screening Technology
Authors: Li Guangshan , Ferrie Ann M. , Fang Ye
Published: August 2006

This article reports the use of Corning Epic system— a label-free and noninvasive optical system that is centered on resonant waveguide grating biosensors—to profile endogenous G protein-coupled receptors (GPCRs) in living cells under physiologically relevant conditions. The endogenous GPCRs examined were bradykinin B2receptor in A431 cells and protease-activated receptor subtype 1 (PAR1) in Chinese hamster ovary (CHO) cells. The activation of either receptor led to Gq-mediated signaling in the respective cells, as confirmed by Fluo-3 assays. Stimulation of CHO cells with thrombin, a PAR1natural agonist, resulted in an optical response relating to dynamic mass redistribution that is similar to that induced by bradykinin in A431 cells. Based on the kinetics of agonist-mediated optical signatures, two time points, one before and another 5 min after the stimulation, were chosen to develop high-throughput (HT) screening assays. Results showed that such endpoint measurements enable not only HT screening of compounds using endogenous GPCRs, but also determining the efficacies of agonists. Those results suggested that the Corning Epic label-free system is an easily scaleable biosensor, amenable as an HTS platform for GPCR drug discovery and deorphanization. (JALA 2006;11:181–7)
Verifying Liquid-Handler Performance for Complex or Nonaqueous Reagents: A New Approach
Authors: Albert Keith J. , Bradshaw John Thomas , Knaide Tanya R. , Rogers Alexis L.
Published: August 2006

Multichannel volume dispensing devices, such as automated liquid handlers, are widely used in drug discovery assays and other high-throughput screening processes. The performance of these systems is heavily based on the ability to deliver proper volumes of specific reagents. For instance, because concentrations of species within an assay are volume dependent, assay integrity and the subsequent interpretation of assay results are directly tied to liquid-handler performance. When liquid handlers are used to aspirate/dispense aqueous-based reagents, there are many accepted methodologies used to calibrate/verify the system's ability to properly perform within a user's tolerance window. In other situations, however, liquid handlers are used to dispense complex or nonaqueous reagents, such as dimethyl sulfoxide (DMSO), serum, and aqueous-based mixtures with detergents, for which there may not be standard, or simple, methodologies to verify liquid-handler performance. Discussed herein is the recent research on broadening existing methods for accurately assessing liquid-handler performance when dispensing complex or nonaqueous reagents. Accurate and reliable adjustment of liquidhandler protocols for varied reagent types could have farreaching adoption in all scientific communities. Using this methodology, target aliquots of multiple solutions were dispensed with a calibrated syringe and subsequently validated via dual-dye ratiometric photometry. Various custom sample solutions were prepared to incorporate (a) 75–90% DMSO (v/v), (b) 20% glycerol (v/v), and (c) 50% ethanol (v/v). (JALA 2006;11:172-80)
A Buoyancy-Driven Compact Thermocycler for Rapid PCR
Authors: Agrawal Nitin , Ugaz Victor M.
Published: August 2006

We have designed a novel convective flow-based thermocycling system capable of performing high-speed DNA amplification via the polymerase chain reaction in a simplified and inexpensive format. Successful amplification of a 191 bp influenza-A target is demonstrated within 25 min using a 10 μL reaction volume with no modification to standard laboratory protocols. The system is simple to assemble and can be readily integrated with existing laboratory instrumentation for automated operation. (JALA 2006;11:217–21)
The Effects of Small Molecule and Protein Solutes on Acoustic Drop Ejection
Authors: Shieh Jean , Ellson Richard N. , Olechno Joseph
Published: August 2006

Increasing the solute concentration of a solution alters the speed of sound in the solution in addition to changing the fluid viscosity and surface tension. For liquid handling devices that transfer fluids with acoustic energy, the change in sound speed can impact the focus of the acoustic energy and ultimately the accuracy of the transfer volume. To determine the effects of increasing solute concentration on transfer accuracy and precision, we studied the change in sound speed in dimethyl sulfoxide with the addition of low-molecular weight compounds and in phosphate-buffered saline with protein. The impact of compound and protein concentration on transfer precision and accuracy was found to be minimal and ADE can be used to transfer fluids regardless of these additions. (JALA 2006;11:227–32)
Improving IC50 Results with Acoustic Droplet Ejection
Authors: Olechno Joseph , Shieh Jean , Ellson Richard
Published: August 2006

IC50 analyses are typically sample, time, and labor intensive. They commonly require multiple dilution steps and consume significant amounts of sample compound. Aqueous intermediate dilutions of concentrated stock solutions can lead to rapid sample precipitation and the generation of false negatives (Spicer, T.; Fitzgerald, Y.; Burford, N.; Matson, S.; Chatterjee, M.; Gilchrist, M.; Myslik, J.; O'Connell, J. Pharmacological evaluation of different compound dilution and transfer paradigms on an enzyme assay in low volume 384-well format, Poster presented at Drug Discovery Technology, August 2005, Boston, MA). Hydrophobic compounds may stick to pipette tips or intermediate dilution vessels, reducing the concentration of the analyte in the dilution and also increasing the possibility of cross contamination. The requirement for multiple serial dilutions in common IC50 analyses causes significant accumulated error. Concentrations of dimethyl sulfoxide (DMSO), the typical solvent used to solubilize compound libraries, as low as 1% in the final assay solution can significantly affect the results of the experiment. Finally, the cost of pipette tips and intermediate dilution vessels, and the frequency of the DMSO washes of tips grows significantly as the number of compounds being analyzed is increased.

A system incorporating acoustic droplet ejection of compounds improves IC50 results by reducing the amount of sample used in the analysis to nanoliters, eliminating intermediate aqueous dilutions and accumulated pipetting error, lowering DMSO concentrations in the final assay to below 1%, and reducing costs of consumables (plastics, solvents, and their disposal). (JALA 2006;11:240–6)
Power and persuasion: Nonviolent strategies to influence state security forces in Serbia (2000) and Ukraine (2004)
Authors: Binnendijk Anika Locke , Marovic Ivan
Published: August 2006

During the Serbian Otpor movement to oust Milosevic (2000) and the Ukrainian “Orange Revolution” (2004), the organizers developed explicit strategies to increase the costs of repression and to undermine the willingness of state security forces to engage in violent acts against them. By employing varying combinations of persuasion and deterrence tailored to the particular institutions they were addressing, the movements were able to successfully avoid a major crackdown.
RESIDUAL EFFECTIVENESS OF MINJINGU PHOSPHATE ROCK AND FALLOW BIOMASS ON CROP YIELDS AND FINANCIAL RETURNS IN WESTERN KENYA
Authors: NDUNG'U K. W. , OKALEBO J. R. , OTHIENO C. O. , KIFUKO M. N. , KIPKOECH A. K. , KIMENYE L. N.
Published: August 2006

In western Kenya, severe nutrient depletion, especially that of nitrogen and phosphorus, has drastically reduced crop yields over the past two to three decades. The potential effects of P application, with a single direct application of Minjingu phosphate rock (MPR) at 20, 40 and 60 kg P ha−1, and fallow biomass in terms of nutrient replenishment on maize and bean yields were investigated on N and P deficient soils of western Kenya for six cropping seasons (three years). The agro-forestry shrubs tested were one season (six months) Crotalaria grahamiana and Tephrosia vogelii followed by maize monocrop. These fallow species were intercropped with beans in the 2000 long rains season to provide a food benefit to the farmer. Soil samples were taken at the end of each season and analyzed for soil pH and extractable P. The results showed that soil available P increased significantly following application of MPR. Significant increases in bean yields were obtained when 60 kg P ha−1 as MPR were applied, and contributed to a 260 % increase above the control. Significant maize grain yield increases were obtained when MPR was applied alone or in combination with fallow biomass as compared with treatments with either no external nutrient addition (control) or with fallow biomass alone in all seasons. The 60 kg P ha −1 MPR rate gave the highest cumulative maize grain yields (9.6 t ha−1) over the five consecutive maize growing seasons, followed by 40 kg P ha−1 (8.8 t ha−1). The residual benefits of MPR at modest rates of application (60 kg P ha−1) were found to persist in the soil for only three cropping seasons. Thereafter, there was a steady decline in soil chemical properties (pH and available P), grain yields and net benefits. The study demonstrated the need for frequent additions of P especially in the fourth consecutive season to ensure sustained availability of P, favorable pH, and increased crop yields and net benefits on the nutrient-depleted soils of western Kenya.
YIELD EFFICIENCY IN PROGENY TRIALS WITH COCOA
Authors: PANG JOE THAU-YIN
Published: August 2006

Yield efficiency of cocoa, defined as yield over a period of time divided by the increment in trunk cross-sectional area over that period, was estimated in four factorial matings in Sabah, Malaysia, evaluated at a single planting density. The parents were 18 seedlings of Upper Amazon Forastero type, broadly representative of Peruvian Amazon material, and 15 clones of Trinitario type, selected from cultivated cocoa in Ecuador, Trinidad and Papua New Guinea. Both the Upper Amazon and Trinitario parents varied in general combining ability (gca) for yield efficiency, with strong evidence of additive inheritance of the trait. Some of the Upper Amazon parents showed higher yield efficiency than many of the Trinitarios. Correlations between gcas for yield efficiency and yield were inconsistent. This is thought to be because the parents differed markedly in optimal planting density, which is higher for many of the Upper Amazons with high gca for yield efficiency than it is for some of the Trinitarios. At the current stage of cocoa breeding, selection for adaptation to planting density is a higher priority than selection for yield efficiency.
COMPARISON OF FIELD PERFORMANCE BETWEEN DASHEEN MOSAIC VIRUS-FREE AND VIRUS-INFECTED IN VITRO PLANTS OF COCOYAM (XANTHOSOMA SPP.) IN NICARAGUA
Authors: REYES G. , RÖNNBERG-WÄSTLJUNG A. C. , NYMAN M.
Published: August 2006

Cocoyam (Xanthosoma spp.) is the most important export crop of all the root and tuber crops grown in Nicaragua. Despite its importance, the total planted area and yield have significantly decreased during the past few years, a decrease that is mainly due to diseases that are disseminated through the planting material. In this study virus-free (NI) and virus-infected (I) in vitro plants from three genotypes were established in a non-traditional production area. The aim was to evaluate their agronomic performance, and to study the re-infection of dasheen mosaic virus (DsMV) and its effect on yield. Repeated measurements of morphological traits were made during the experimental period. The height of the plants, the diameter of the pseudo-stem and the leaf area increased continuously up to 217 days after planting after which the growth curves declined. The genotypes differed in all yield components, except in yield per plant. Regardless of genotype, the NI plants produced a larger number of cormels that were heavier and longer than the cormels produced by I plants. This resulted in a higher yield from NI plants (18.2 t ha−1) compared with I plants (13.6 t ha−1). Seven months after planting between 60 and 90 % of the NI plants, depending on genotype, were infected with DsMV. Aphis gossypii was the only aphid observed in the field trial and is therefore most probably the vector responsible for the transmission of the virus.
DISTINGUISHING THE EFFECTS OF GENOTYPE AND SEED PHYSIOLOGICAL AGE ON LOW TEMPERATURE TOLERANCE OF RICE (ORYZA SATIVA L.)
Authors: ALI M. G. , NAYLOR R. E. L. , MATTHEWS S.
Published: August 2006

When differences are observed between genotypes in their response to low temperatures at germination, it has been generally assumed these are purely genetic. Laboratory experiments were carried out to evaluate the effects of physiological age on the temperature responses of 13 rice genotypes from Bangladesh in order to clarify whether (a) differences in seed germination at low temperature represented genetic differences or differences in the physiological state of the particular seed lot used and (b) whether genotype performance at higher temperatures was indicative of performance at lower temperatures. A higher initial seed moisture content (mc) was associated with lower initial viability (Ki). The base temperature for germination differed by less than 1 °C between genotypes. Seeds remaining ungerminated at low temperatures usually germinated when transferred to 21 °C. The thermal time requirement to reach t50 (θ) differed widely between genotypes. Lower optimum temperatures for germination were associated with lower thermal time requirements. Ageing seeds for 24 hours at 24 % mc and 45 °C significantly reduced final germination on a thermal gradient table at all temperatures below 20.8 °C in genotype BR29 but only below 16.5 °C in BR11. The rates of germination (seeds d−1) of aged seeds were also lower at all temperatures. Germination of high quality seeds of four genotypes were compared at 21 °C and 11 °C both before and after ageing (at 24 % mc and 45 °C). Ageing consistently reduced the rates of germination at both 21 °C and 11 °C. Increased ageing time progressively reduced the rate of germination of all seed lots at both temperatures. The rates of germination at 11 °C and 21 °C were positively and significantly (p < 0.01) related to final germination at the lower temperature of 11 °C. These results demonstrate that seed physiological quality as well as genotype might influence the final germination and rate of germination of rice genotypes at low temperatures. This information will be useful for breeders involved in selection of lines suitable for growing in cooler seasons.
A survey of statistical user simulation techniques for reinforcement-learning of dialogue management strategies
Authors: SCHATZMANN JOST , WEILHAMMER KARL , STUTTLE MATT , YOUNG STEVE
Published: August 2006

Within the broad field of spoken dialogue systems, the application of machine-learning approaches to dialogue management strategy design is a rapidly growing research area. The main motivation is the hope of building systems that learn through trial-and-error interaction what constitutes a good dialogue strategy. Training of such systems could in theory be done using human users or using corpora of human–computer dialogue, but in practice the typically vast space of possible dialogue states and strategies cannot be explored without the use of automatic user simulation tools.

This requirement for training statistical dialogue models has created an interesting new application area for predictive statistical user modelling and a variety of different techniques for simulating user behaviour have been presented in the literature ranging from simple Markov models to Bayesian networks. The development of reliable user simulation tools is critical to further progress on automatic dialogue management design but it holds many challenges, some of which have been encountered in other areas of current research on statistical user modelling, such as the problem of ‘concept drift’, the problem of combining content-based and collaboration-based modelling techniques, and user model evaluation. The latter topic is of particular interest, because simulation-based learning is currently one of the few applications of statistical user modelling that employs both direct ‘accuracy-based’ and indirect ‘utility-based’ evaluation techniques.

In this paper, we briefly summarize the role of the dialogue manager in a spoken dialogue system, give a short introduction to reinforcement-learning of dialogue management strategies and review the literature on user modelling for simulation-based strategy learning. We further describe recent work on user model evaluation and discuss some of the current research issues in simulation-based learning from a user modelling perspective.
Global mapping of crustal and lithospheric thickness on Venus
Authors: Anderson F. Scott , Smrekar Suzanne E.
Published: August 2006

We have produced a high‐resolution global admittance map of Venus using a spatiospectral localization technique, calculating 64,800 admittance spectra evenly spaced in latitude and longitude. We grouped the admittance spectra into 35 classes that we inverted for elastic, crustal, and lithospheric thickness using bottom‐loading, top‐loading, and short‐wavelength top‐loading models with long‐wavelength bottom‐loading (“hot spot”) models. Our best fit models identify 17 classes consistent with top loading (40% of the surface), 7 with bottom loading (39%), and 4 with a long‐wavelength bottom‐loading model (15%). The remaining seven classes (6% of the surface) generally had large‐amplitude top‐loading signatures that could not be fit with our models. For the classes that were successfully modeled the estimated range of crustal (0–90 km) and elastic thickness (0–100 km) is larger than results for most previous studies, primarily because of the incorporation of bottom loading. Nearly half of the planet has elastic thickness <20 km, which we cannot distinguish from isostasy, suggesting that these regions are tectonically inactive. A key finding is that the lithospheric properties typically vary over scales of 1000 km or less except in some plains and crustal plateau regions. Both the scale and range of crustal and elastic thickness variations indicate that Venus remains an active planet and that geologic processes may be more complex than previously recognized. In many regions the correlation with surface geology is not obvious, and this suggests that deformation of the lower lithosphere and crust may occur with little surface manifestation.
Wildfires threaten mercury stocks in northern soils
Authors: Turetsky Merritt R. , Harden Jennifer W. , Friedli Hans R. , Flannigan Mike , Payne Nicholas , Crock James , Radke Lawrence
Published: August 2006

With climate change rapidly affecting northern forests and wetlands, mercury reserves once protected in cold, wet soils are being exposed to burning, likely triggering large releases of mercury to the atmosphere. We quantify organic soil mercury stocks and burn areas across western, boreal Canada for use in fire emission models that explore controls of burn area, consumption severity, and fuel loading on atmospheric mercury emissions. Though renowned as hotspots for the accumulation of mercury and its transformation to the toxic methylmercury, boreal wetlands might soon transition to hotspots for atmospheric mercury emissions. Estimates of circumboreal mercury emissions from this study are 15‐fold greater than estimates that do not account for mercury stored in peat soils. Ongoing and projected increases in boreal wildfire activity due to climate change will increase atmospheric mercury emissions, contributing to the anthropogenic alteration of the global mercury cycle and exacerbating mercury toxicities for northern food chains.
Magnetohydrodynamic simulation of the interaction between interplanetary strong shock and magnetic cloud and its consequent geoeffectiveness
Authors: Xiong Ming , Zheng Huinan , Wang Yuming , Wang Shui
Published: August 2006

Numerical studies have been performed to interpret the observed “shock overtaking magnetic cloud (MC)” event by a 2.5 dimensional magnetohydrodynamic (MHD) model in the heliospheric meridional plane. Results of an individual MC simulation show that the MC travels with a constant bulk flow speed. The MC is injected with a very strong inherent magnetic field over that in the ambient flow and expands rapidly in size initially. Consequently, the diameter of the MC increases in an asymptotic speed while its angular width contracts gradually. Meanwhile, simulations of MC‐shock interaction are also presented, in which both a typical MC and a strong fast shock emerge from the inner boundary and propagate along the heliospheric equator, separated by an appropriate interval. The results show that the shock first catches up with the preceding MC, then penetrates through the MC, and finally merges with the MC‐driven shock into a stronger compound shock. The morphologies of shock front in interplanetary space and MC body behave as a central concave and a smooth arc, respectively. The compression and rotation of the magnetic field serve as an efficient mechanism to cause a large geomagnetic storm. The MC is highly compressed by the overtaking shock. Contrarily, the transport time of the incidental shock influenced by the MC depends on the interval between their commencements. Maximum geoeffectiveness results from when the shock enters the core of preceding MC, which is also substantiated to some extent by a corresponding simplified analytic model. Quantified by the Dst index, the specific result is that the geoeffectiveness of an individual MC is largely enhanced with 80% increment in maximum by an incidental shock.
Physical and biological contributions to the western tropical North Atlantic Ocean carbon sink formed by the Amazon River plume
Authors: Cooley S. R. , Yager P. L.
Published: August 2006

Dissolved inorganic carbon (DIC) and total alkalinity (TA) were measured in the upper 1000 m of the western tropical North Atlantic Ocean (WTNA; study area 3–15°N, 40–59°W) in January–February and July–August 2001. Concentrations of DIC and TA in surface samples (0–10 m) influenced by the Amazon River plume were up to 400 μmol C kg−1 (∼20%) lower than oceanic surface samples. In this region, physical dilution by river water dominates DIC and TA inventories, driving CO2 partial pressure (pCO2) well below atmospheric levels. Nevertheless, DIC concentrations at most plume‐influenced stations were 10–90 μmol C kg−1 below levels expected from conservative mixing of seawater with low‐salinity, low‐CO2 Amazon River water. In this otherwise oligotrophic region, the diazotrophs Trichodesmium spp. and Richelia intracellularis were often abundant, supporting a link between increased carbon drawdown and nitrogen fixation in the outer plume. Net community production in the plume must surpass the fluxes of inorganic carbon from below and air‐sea CO2 replacement to leave biologically mediated DIC deficits, which is possible under observed conditions. Biological activity lowers plume pCO2 30–120 μatm below the conservative mixing line, and contributes to a CO2 deficit in the northern WTNA that outlasts the plume's physical structure.
Surface effect of rain on microwave backscatter from the ocean: Measurements and modeling
Authors: Contreras Robert F. , Plant William J.
Published: August 2006

The effect of rain on the ocean surface alters the relationship between the surface wind vector and microwave backscatter, presenting an obstacle to wind retrieval via scatterometry. To address the effect of rain on surface backscatter, we develop a physically based ocean surface wave model modified by rain. Microwave backscatter is then calculated using a multiscale scattering model. Comparisons to observations at Ku band are used to validate and tune our surface model. Simulations give insight into backscattering surface features: ring waves result primarily from the collapse of the splash‐created stalk, and the impulse responsible for the generation of ring waves has a radius roughly 5 times the drop's radius. Comparisons also show that backscatter from stationary splash features is necessary to accurately reproduce the effect of rain at Ku band. For Ku band our simulations expand upon prior measurements showing that rain increases backscatter and diminishes azimuthal variations. There is, however, a wind relative azimuthal signature in the backscatter for most rainfall rates. Simulations at Ka band, C band, and L band without the contribution from stationary splash features show that rain‐created ring waves often alter backscatter. The effects are greatest at Ka band where they mirror changes to the very high‐frequency region of the surface wave spectrum. C band backscatter is increased at moderate and high incidence angles and is sensitive to rain‐induced damping. The effect of rain on L band is to decrease backscatter at high rain rate, and it is also dependent on rain‐induced damping.
Hydrogen and carbon isotopic measurements of methane from agricultural combustion: Implications for isotopic signatures of global biomass burning sources
Authors: Yamada Keita , Ozaki Yoko , Nakagawa Fumiko , Sudo Shigeto , Tsuruta Haruo , Yoshida Naohiro
Published: August 2006

The hydrogen and carbon isotope ratios of CH4 emitted from one bonfire and two laboratory combustions of agricultural residues were determined in this study as −196 to −262‰ for δD and −19.9 to −35.1‰ for δ13C. The isotopic difference between CH4 emitted from biomass burning and fuel biomass, that is, the apparent isotopic fractionation occurring during combustion (ɛBurn), was within −101 to −174‰ for ɛBurnD and +6.9 to −8.6‰ for ɛBurn13C. That difference varied according to burning conditions: flaming and smoldering. Variation in ɛBurn is correlated with combustion efficiency (CE), defined here as the ratio of emitted CO2 to the sum of emitted CO2 and CO. In light of the previously reported global distributions of CE, the implied ɛBurn values for global biomass burning sources were −121‰ for ɛBurnD and +2.2‰ for ɛBurn13C. Using the relationship between ɛBurn and CE and global distributions of CE and isotopic ratios of fuel biomass, we estimated the global isotopic signature for biomass burning sources as −169‰ for δD and −23.6‰ for δ13C.
Liquid CO2 venting on the seafloor: Yonaguni Knoll IV hydrothermal system, Okinawa Trough
Authors: Konno Uta , Tsunogai Urumu , Nakagawa Fumiko , Nakaseama Miwako , Ishibashi Jun‐ichiro , Nunoura Takuro , Nakamura Ko‐ichi
Published: August 2006

We determined the chemical and isotopic compositions of the liquid CO2 found on Yonaguni IV knoll hydrothermal site, as well as those in hydrothermal fluid venting from the surrounding chimneys. The δ13C of both CO2 and CH4 in the liquid CO2 almost coincide with those in the hydrothermal fluid, suggesting that the liquid CO2 must be derived from the hydrothermal fluid. While showing homogeneous δ13C, the hydrothermal fluids exhibit wide variation in gas contents. Active phase separation must be taking place within the conduits. Besides, H2‐depletion in the liquid CO2 suggests formation of solid CO2‐hydrate must also precede the venting of liquid CO2. In conclusion, liquid CO2 must be produced through following subseafloor processes: phase separation of hydrothermal fluid due to boiling, formation of solid CO2‐hydrate due to cooling of vapor phase, and melting of the solid CO2‐hydrate to liquid CO2 due to a temperature increase within the sedimentary layer.
Possible source of advected water mass and residence times in the multi‐structured Sea of Japan using rare earth elements
Authors: Hatta Mariko , Zhang Jing
Published: August 2006

The Sea of Japan is a small, fast‐acting model of global oceanic circulation. Observations from 1998 and 2001 are analyzed to clarify its circulation. New bottom water formed in early 2001 off Vladivostok was observed later that year near the southeastern edge of the Japan Basin, implying a velocity of 2.3–3.9 cm s−1. Tb–Yb patterns of rare earth elements distinguish two classes of water volume: inactive old/well‐mixed water and active relatively young water, frequently affected by the subduction of the surface water originating from Tsushima Warm Current (TWC). The proportion of TWC to old water and each residence time are: 50–75% and ∼15 years (200–400 m), and 35–80% and ∼38 years (600–1500 m). Using six strata, an improved estimate of the average residence time of Japan Sea Proper Water is >86 years; this includes the contributions from active and inactive strata.
Seasonal cycles of O3, CO, and convective outflow at the tropical tropopause
Authors: Folkins Ian , Bernath P. , Boone C. , Lesins G. , Livesey N. , Thompson A. M. , Walker K. , Witte J. C.
Published: August 2006

Measurements from the SHADOZ ozonesonde network and Aura MLS are used to show that there are seasonal cycles in ozone (O3) and carbon monoxide (CO) at the tropical tropopause (∼17 km). A simple model, driven by cloud free radiative mass fluxes, is used to investigate the origin of these seasonal cycles. The seasonal cycle in O3 is due to seasonal changes in upwelling and high altitude convective outflow. The seasonal cycle in CO at 100 hPa is influenced by both seasonal changes in dynamics and seasonal changes in CO at lower altitudes. The age of air at 17 km varies from 40 days during NH winter to 70 days during NH summer. The seasonal cycle in clear sky radiative heating at the tropical tropopause is mainly due to seasonal cycles in O3 and temperature. The seasonal cycle in O3 can be expected to amplify the seasonal cycle in cold point temperature.
Ab initio study of the composition dependence of the pressure‐induced spin transition in the (Mg1−x,Fex)O system
Authors: Persson Kristin , Bengtson Amelia , Ceder Gerbrand , Morgan Dane
Published: August 2006

We present ab initio calculations of the zero‐temperature composition dependent spin transition pressures in rocksalt (B1) (Mg1−x,Fex)O. We predict that the spin transition pressure decreases with increasing Mg content, consistent with experimental results. At high‐pressure, we find that the effective size of Mg is smaller than high‐spin Fe but quite close to low‐spin Fe, consistent with a simple compression argument for how Mg reduces the spin transition pressure. We also show that the spin transition is primarily driven by the volume difference between the high‐spin and low‐spin phases, rather than changes in the electronic structure with pressure. The volume contraction at the transition is found to depend non‐monotonically on Fe content. For FeO we predict a B1 → iB8 transition at 63 GPa, consistent with previous results. However, we also predict an unexpected reverse transition of high‐spin iB8 → low‐spin B1 at approximately 400 GPa.
An aseismic slip pulse in northern Chile and along‐strike variations in seismogenic behavior
Authors: Pritchard M. E. , Simons M.
Published: August 2006

We use interferometric synthetic aperture radar, GPS, and seismic observations spanning 5 to 18 years to reveal a detailed kinematic picture of the spatiotemporal evolution of fault slip in a region corresponding to the 30 July 1995Mw8.1 subduction zone megathrust earthquake in northern Chile. In a single area, we document a complex mosaic of phenomena including large earthquakes, postseismic afterslip with a spatial distribution that appears to be tied to variations in coastal morphology, and a completely aseismic pulse that may have triggered aMw7.1 earthquake on 30 January 1998. In contrast to simple models of fault slip behavior, this spatial heterogeneity indicates that frictional parameters on the fault do not have a systematic transition with depth and also vary rapidly along strike. The low amount of afterslip from theMw8.1 earthquake relative to other similar events suggests that postseismic behavior may be modulated by the amount of sediment subducted.
Comparison of ERA40 and NCEP/DOE near‐surface data sets with other ISLSCP‐II data sets
Authors: Betts Alan K. , Zhao Mei , Dirmeyer P. A. , Beljaars A. C. M.
Published: August 2006

The fields of 2‐m temperature, relative humidity, precipitation, downward short‐wave and long‐wave radiation, net radiation, and sensible and latent heat flux from the ERA40 and NCEP/DOE reanalyses are compared with each other and with other independent ISLSCP‐II data sets, where available. There are differences in the climatologies of the different data sets, but generally, they show consistent patterns of the major seasonal anomaly fields. The anomaly patterns are coherent, showing warm, dry seasonal biases associated with reduced precipitation and cloudiness, and the converse. This confirms that major changes in the atmospheric circulation patterns, with the associated differences in surface temperature, humidity, precipitation, cloud fields and incoming surface SW and LW radiation fluxes are captured by both reanalyses and the comparison ISLSCP‐II data sets.