bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation of sample sizes for pooled faecal sampling for detection of Salmonella in pigs
Authors: ARNOLD M. E. , COOK A. J. C.
Published: May 2009

Salmonella infection in breeding pigs was the subject of a European survey in 2008. The prevalence of pig-breeding holdings infected with Salmonella was determined by microbiological culture of pooled pen faecal samples. The objective of this study was to estimate the sensitivity of pooled faecal sampling and to calculate the required sample sizes. To do this, individual and pooled faecal samples were collected from a sample of pens from nine farms. Bayesian methods were used to estimate the sensitivity of individual and pooled faecal sampling, and the degree of clustering of Salmonella at the pen level. Sample sizes were then calculated for various values of design prevalence, taking into account the clustering. Pooling was highly efficient compared to individual sampling, e.g. with 18 pooled samples required to detect a 10% prevalence with 95% certainty, compared to 35 individual rectal samples. We recommend that pooled sampling is used for detection of Salmonella in pigs. Results were influenced by the degree of clustering at pen level, and it is important to take this into account both in the estimation of appropriate sample sizes and the estimation of prevalence from pooled sample data.
Complementarity demand functions and pricing models for multi-product markets
Authors: SOON WANMEI , ZHAO GONGYUN , ZHANG JIEPING
Published: May 2009

In contrast to single-product pricing models, multi-product pricing models have been much less studied because of the complexity of multi-product demand functions. It is highly non-trivial to construct a multi-product demand function on the entire set of non-negative prices, not to mention approximating the real market demands to a desirable accuracy. Thus, many decision makers use incomplete demand functions which are defined only on a restricted domain, e.g. the set where all components of demand functions are non-negative. In the first part of this paper, we demonstrate the necessity of defining demand functions on the entire set of non-negative prices through some examples. Indeed, these examples show that incomplete demand functions may lead to inferior pricing models. Then we formulate a type of demand functions using a Nonlinear Complementarity Problem (NCP). We call it a Complementarity-Constrained Demand Function (CCDF). We will show that such demand functions possess certain desirable properties, such as monotonicity. In the second part of the paper, we consider an oligopolistic market, where producers/sellers are playing a non-cooperative game to determine the prices of their products. When a CCDF is incorporated into the best response problem of each producer/seller involved, it leads to a complementarity constrained pricing problem facing each producer/seller. Some basic properties of the pricing models are presented. In particular, we show that, under certain conditions, the complementarity constraints in this pricing model can be eliminated, which tremendously simplifies the computation and theoretical analysis.
Assessment of three generations of mice derived by ICSI using freeze-dried sperm
Authors: Li Ming-Wen , Willis Brandon J. , Griffey Stephen M. , Spearow Jimmy L. , Lloyd K. C. Kent
Published: May 2009

Although the derivation of mice by intracytoplasmic sperm injection (ICSI) using freeze-dried sperm has been demonstrated previously, a comprehensive analysis of their viability, health, and fertility has not. The purpose of the present study was to determine the extent to which ICSI using freeze-dried sperm stored at 4 °C for 1–2 months from mice on either an inbred (C57BL/6J) or hybrid (B6D2F1/J) genetic background results in genomic instability and/or phenotypic abnormality in mice and two generations of their progeny. Fertilization rates (number of 2-cells per injected oocytes) using ICSI of fresh and freeze-dried sperm were similar within and between mouse strains, although fewer freeze-dried sperm-derived embryos than fresh sperm-derived embryos developed to blastocystsin vitro(C57BL/6J and B6D2F1/J) and liveborn pupsin vivo(B6D2F1/J only). Nevertheless, once born, mice derived by ICSI using freeze-dried sperm in both mouse strains were healthy and reproductively sound. No major differences in litter size, weaning rate, and sex ratio were noted in the two generations of progeny (F2 and F3) of ICSI-derived offspring using freeze-dried sperm compared with that in the natural mating (control) group. Further, there was no evidence that either ICSI or freeze drying induced genomic instability, as determined by microsatellite analysis of the derived mice and subsequent generations when compared with both parental genotypes, nor were there differences in the number or types of pathological changes in any of the three generations of progeny. We conclude that viable, healthy and genomically stable mice can be derived by ICSI using freeze-dried mouse sperm stored in the refrigerator for at least 2 months. Further, because freeze drying is a simpler and more economical technique compared with embryo and sperm cryopreservation, the results of this study justify additional research to continue to develop and enhance the technique for the preservation, storage, and sharing of genetically altered mice.
Development and spindle formation in rat somatic cell nuclear transfer (SCNT) embryos in vitro using porcine recipient oocytes
Authors: Sugawara Atsushi , Sugimura Satoshi , Hoshino Yumi , Sato Eimei
Published: May 2009

Cloning that uses somatic cell nuclear transfer (SCNT) technology with gene targeting could be a potential alternative approach to obtain valuable rat models. In the present study, we determined the developmental competence of rat SCNT embryos constructed using murine and porcine oocytes at metaphase II (MII). Further, we assessed the effects of certain factors, such as: (i) the donor cell type (fetal fibroblasts or cumulus cells); and (ii) premature chromosome condensation (PCC) with normal spindle formation, on the developmental competence of rat interspecies SCNT (iSCNT) embryos. iSCNT embryos that had been constructed using porcine oocytes developed to the blastocyst stage, while those embryos made using murine MII oocytes did not. Rat iSCNT embryos constructed with green fluorescent protein (GFP)-expressing fetal fibroblasts injected into porcine oocytes showed considerable PCC with a normal bipolar spindle formation. The total cell number of iSCNT blastocyst derived from GFP-expressing fetal fibroblasts was higher than the number derived from cumulus cells. In addition, these embryos expressed GFP at the blastocyst stage. This paper is the first report to show that rat SCNT embryos constructed using porcine MII oocytes have the potential to develop to the blastocyst stage in vitro. Thus the iSCNT technique, when performed using porcine MII oocytes, could provide a new bioassay system for the evaluatation of the developmental competence of rat somatic cells.
Church of the In-Between God: Recovering an Ecclesial Sense of Place Down-under
Authors: Pickard Stephen
Published: May 2009

This article examines the significance of ‘place’ as a theme in ecclesiology in the interests of developing an ecclesial sense of place within my own context of Australian Anglicanism. To talk about ecclesiology is to talk about place, about God’s place, about our placement in the world, about how and why our social life operates as it does, about what engenders optimal life enhancing community. From this perspective, place can be a critical concept through which theology, ecclesiology, mission and ministry can be organized and better understood. The primary discipline that has deployed the concept of place is geography. Accordingly, in this article, I consider the theme of place as it is discussed in professional geography and briefly examine some implications for being church and the Anglican Church in particular. This provides the framework for consideration of place within an Australian cultural and ecclesial context. In doing so, I examine the motif of verandah as a depiction of ecclesial place down-under. The key concept of the ‘in-between place’ to depict a post-colonial way of being church is deployed in order to recover an ecclesial sense of place down-under. Underpinning such an approach is the theological concept of the in-between God.
Church Tradition and Psychological Type Preferences among Anglicans in England
Authors: Village Andrew , Francis Leslie J. , Craig Charlotte
Published: May 2009

A sample of 290 individuals attending Evangelical Anglican churches and Anglo-Catholic churches in central England completed the Keirsey Temperament Sorter, a measure of psychological type preferences. Overall, there were clear preferences for sensing over intuition, for feeling over thinking, and for judging over perceiving, which is consistent with the findings of two earlier studies profiling the psychological type of Anglican churchgoers. However, there was also a significantly higher proportion of intuitives among Anglo-Catholics than among Evangelical Anglicans, which is consistent with the greater emphasis in Anglo-Catholic churches on mystery, awe, and the centrality of sacraments in worship which may resonate with the intuitive predisposition. The implications of these findings are discussed for the benefits of breadth and diversity within Anglicanism.
Datenanalyse: Das Null-Ritual und der Umgang mit Effekten in der Zeitschrift für Sportpsychologie
Authors: Conzelmann Achim , Raab Markus
Published: May 2009

Zusammenfassung. Ziel dieses Beitrages ist die Analyse der Anwendung empirischer Tests in der deutschsprachigen Sportpsychologie. Die Ergebnisse vergleichbarer Analysen, bspw. in der Psychologie, zeigen, dass zwischen Anforderungen aus Testkonzepten und empirischer Realität Unterschiede existieren, die bislang für die Sportpsychologie nicht beschrieben und bewertet worden sind. Die Jahrgänge 1994–2007 der Zeitschrift für Sportpsychologie (früher psychologie und sport) wurden danach untersucht, ob Forschungsfragen formuliert, welche Stichprobenart gewählt, welches Testkonzept verwendet, welches Signifikanzniveau benutzt und ob statistische Probleme diskutiert wurden. 83 Artikel wurden von zwei unabhängigen Bewertern nach diesen Aspekten kategorisiert. Als Ergebnis ist festzuhalten, dass in der sportpsychologischen Forschung überwiegend eine Mischung aus Fishers Signifikanztesten sowie Neyman-Pearsons-Hypothesentesten zur Anwendung kommt,das sogenannte „Hybrid-Modell” oder „Null-Ritual”. Die Beschreibung der Teststärke ist kaum zu beobachten. Eine zeitliche Analyse der Beiträge zeigt, dass vor allem die Benutzung von Effektgrößen in den letzten Jahren zugenommen hat. Abschließend werden Ansätze zur Verbesserung und der Vereinheitlichung der Anwendung empirischer Tests vorgeschlagen und diskutiert.
Die Bedeutung von Wohlbefinden im Zusammenhang zwischen Sportengagement und Gewaltverhalten bei Jugendlichen
Authors: Moesch Karin , Birrer Daniel , Schmid Jürg , Seiler Roland
Published: May 2009

Zusammenfassung. Obschon normative Erwartungen an Sport als Freizeitbeschäftigung mit gewaltpräventiver Wirkung immer wieder postuliert werden, sind empirische Befunde zum Zusammenhang zwischen Sport und Gewalt inkonsistent. Einhellig werden jedoch positive Auswirkungen des Sporttreibens auf das Wohlbefinden berichtet, ebenso wie negative Assoziationen zwischen Wohlbefinden und Gewaltverhalten. Vor einem sozialisations- und stresstheoretischen Hintergrund wird in der vorliegenden querschnittlichen Befragung von 1664 Schweizer Jugendlichen im Alter von 12 bis 18 Jahren die Annahme geprüft, ob ein indirekter Zusammenhang zwischen Sportengagement und Gewaltverhalten besteht, der durch das Wohlbefinden vermittelt wird. Die mit Strukturgleichungsmodellen gewonnenen Ergebnisse liefern schwache Unterstützung für diese Annahme. Allerdings sind die Pfadkoeffizienten klein (Sport – Wohlbefinden: β = .39; Wohlbefinden – Gewaltverhalten: β = −.13) und der indirekte Effekt entsprechend gering (−.05). Es wird gefolgert, dass Sportangebote für Jugendliche deren Bedürfnisse nach Autonomie, Kompetenz und sozialem Anschluss befriedigen müssen, um Wohlbefinden zu erhalten bzw. zu fördern, welches wiederum als Ressource gegen deviantes Verhalten dienen kann.
Fore‐arc motion and Cocos Ridge collision in Central America
Authors: LaFemina Peter , Dixon Timothy H. , Govers Rob , Norabuena Edmundo , Turner Henry , Saballos Armando , Mattioli Glen , Protti Marino , Strauch Wilfried
Published: May 2009

We present the first regional surface velocity field for Central America, showing crustal response to interaction of the Cocos and Caribbean plates. Elastic half‐space models for interseismic strain accumulation on the dipping subduction plate boundary fit the GPS data well and show strain accumulation offshore and beneath the Nicoya and Osa peninsulas in Costa Rica but not in Nicaragua. Since large subduction zone earthquakes occur in Nicaragua, we suggest that interseismic locking in Nicaragua and some other parts of Central America occurs but is mainly shallow, <20 km depth, too far offshore to be detected by our on‐land GPS measurements. Our data also show significant trench‐parallel motion for most of the region, generally interpreted as due to oblique convergence and strong mechanical coupling between subducting and overriding plates. However, trench‐parallel motion is also observed in central Costa Rica, where plate convergence is normal to the trench, and in the Nicaraguan fore arc, where trench‐parallel motion is fast, up to 9 mm a−1, but mechanical coupling is low. A finite element model of collision (as opposed to subduction) involving the aseismic Cocos Ridge also fits the GPS surface velocity field, most significantly reproducing the pattern of trench‐parallel motion. We infer that buoyant, thickened CNS‐2‐Cocos Ridge crust resists normal subduction and instead acts as an indenter to the Caribbean plate, driving crustal shortening in southern Costa Rica and contributing to trench‐parallel fore‐arc motion in Costa Rica and perhaps Nicaragua as a type of tectonic escape.
Collisional model for rapid fore‐arc block rotations, arc curvature, and episodic back‐arc rifting in subduction settings
Authors: Wallace Laura M. , Ellis Susan , Mann Paul
Published: May 2009

We review geophysical and geological data from 23 active and ancient plate boundaries to document a compelling spatial and temporal relationship between collision, plate boundary curvature, rapid tectonic rotations, and the occurrence of back‐arc rifting. Our observations support a conceptual model where the change from subduction to collision causes rapid fore‐arc rotation (when viewed in a reference frame relative to the bounding tectonic plates), leading to marked plate boundary curvature. Our global compilation reveals that most active back‐arc rifts are associated with rapidly rotating fore arcs and nearby collisions. Thus, we propose that collision and rapid fore‐arc rotations play a major role in the evolution and kinematics of back‐arc basins. We conduct numerical modeling to better understand the physical processes behind these observed rapid tectonic rotations at convergent margins. Our results suggest that the presence of an indentor or choke point in the subduction system (e.g., collision) can generate rapid rotation of the fore arc about a nearby pole and lead to back‐arc rifting. The rate of fore‐arc rotation and back‐arc rifting depends on the incoming indentor velocity and can be greatly enhanced by slab rollback and the presence of a low‐viscosity back arc. Where viscosity of the back arc is low, fore‐arc rotation dominates; where back‐arc viscosity is high, the formation of strike‐slip faults and tectonic escape dominates. Our observational and model‐derived results illustrate that shallow crustal forces produced by the entry of buoyant features into subduction zones are a fundamental mechanism for the generation of fore‐arc block rotations, plate boundary curvature, back‐arc rift evolution, and tectonic escape in subduction systems. Rollback of the subducting slab within the mantle will certainly enhance the processes we describe but it is not the only driving force.
Source regions for Antarctic MLT non‐migrating semidiurnal tides
Authors: Murphy D. J. , Aso T. , Fritts D. C. , Hibbins R. E. , McDonald A. J. , Riggin D. M. , Tsutsumi M. , Vincent R. A.
Published: May 2009

Source regions for the westward propagating zonal wavenumber one and three components of the semidiurnal tide observed in the summer mesosphere and lower thermosphere over Antarctica are identified by correlating local tidal variations with global planetary wave one activity in the stratosphere and lower mesosphere. The advantages of using zonal wavenumber resolved tidal amplitudes for such a study are described. The results support the prediction of a source region in the northern hemisphere.
Analysis of variations of cloud and aerosol properties associated with active and break spells of Indian summer monsoon using MODIS data
Authors: Ravi Kiran V. , Rajeevan M. , Vijaya Bhaskara Rao S. , Prabhakara Rao N.
Published: May 2009

Indian summer monsoon exhibits significant intra‐seasonal variations with active and break monsoon spells. Using MODIS data of 8 years (2000–2007), variations of cloud and aerosol properties over the Indian region associated with the active and break spells were examined. The study shows statistically significant variations of cloud properties (cloud optical depth, cloud fraction and cloud top pressure) between active and break monsoon days over central and northeast India and the equatorial Indian Ocean. During the monsoon break spells, associated with the anomalous circulation, aerosol loading from the north Arabian Sea is transported to central India. This increase in aerosol content decreases the cloud effective radii, suggesting the indirect effect of aerosols on cloud properties. There is also an inverse relationship of cloud properties over the monsoon zone over central India and the southeast equatorial Indian Ocean, suggesting possible role of southeast equatorial Indian Ocean on the development of active‐break cycles.
Joule heating and nitric oxide in the thermosphere
Authors: Barth C. A. , Lu G. , Roble R. G.
Published: May 2009

The effect of Joule heating on the density of nitric oxide in the thermosphere was studied using observations from the Student Nitric Oxide Explorer (SNOE) satellite and model calculations from the Thermospheric Ionosphere Electrodynamics General Circulation Model for a Joule heating event that occurred on 25 September 1998. Model results and SNOE observations from fifteen orbits were compared in the latitude range 82°S to 82°N over the altitude range 100–150 km. Joule heating which occurred in the 55°‐ to 60°‐latitude region produced a meridional wind blowing equatorward and a gravity wave propagating equatorward, which caused an increase in the temperature of the thermosphere in the 20°‐ to 75°‐latitude region. When the heated thermosphere was illuminated by solar radiation, the density of nitric oxide increased over this entire latitude region because of a temperature‐sensitive reaction between ground state nitrogen atoms and molecular oxygen. In the 24 hours following the Joule heating event, the increased nitric oxide diffused downward from the 150‐km region to the 110‐km level of the thermosphere.
A unified model of solar energetic particle transport in structured solar wind
Authors: Kocharov L. , Pizzo V. J. , Odstrcil D. , Zwickl R. D.
Published: May 2009

Solar energetic particle (SEP) fluxes, after their propagation from the particles' source to the Earth's orbit, depend on the state of solar wind, which is known to be highly variable in both time and space. Commonly used SEP transport models are based on the assumption of the standard interplanetary magnetic field, which would be the case for a uniform, steady state expansion of solar wind. Modeling of SEP transport in the standard solar wind can be facilitated by the use of a corotating reference frame, wherein the solar wind speed is parallel to interplanetary magnetic field at each point and the magnetic field is static. However, this approach is not possible in the realistic solar wind. This necessitates development of a more general SEP model applicable to particle transport in arbitrarily structured solar wind and in interplanetary coronal mass ejections, magnetic clouds, and shocks. In the framework of focused transport theory, we formulate a practical model of SEP transport in an evolving, structured solar wind. This unified model accommodates the results of three‐dimensional MHD modeling of solar wind based on observations of the sun, solar wind, and SEPs in a particular event. A relation between the generalized focused transport model and the diffusion‐convection equation of cosmic ray transport is discussed.
Survey of magnetospheric line radiation events observed by the DEMETER spacecraft
Authors: Němec F. , Parrot M. , Santolík O. , Rodger C. J. , Rycroft M. J. , Hayosh M. , Shklyar D. , Demekhov A.
Published: May 2009

Magnetospheric line radiation (MLR) events are electromagnetic waves in the frequency range between about 1 and 8 kHz that, when presented as a frequency‐time spectrogram, take the form of nearly parallel and clearly defined lines, which sometimes drift slightly in frequency. They have been observed both by satellites and ground‐based instruments, but their origin is still unclear. We present a survey of these MLR waves observed by the DEMETER spacecraft (at an altitude of about 700 km). Three years of VLF Survey mode data were manually searched for MLR events, creating the largest event satellite database of about 650 events, which was then used to investigate the wave properties and geographical occurrence. Finally, the most favorable geomagnetic conditions (Kp and Dst indices) for the occurrence of MLR events have been found. It is shown that MLR events occur mostly at L > 2 (upper limit is given by a limitation of the spacecraft), they occur primarily inside the plasmasphere, and there is a lower number of events occurring over the Atlantic Ocean than elsewhere on the globe. The MLR events occur more often during the day and usually during, or after, periods of higher magnetic activity. Their frequencies usually lay between about 2 and 6 kHz, with the total frequency bandwidth of an observation being below 2 kHz in the majority of cases. Moreover, it is shown that the longitudinal dimensions of the MLR events can be as large as 100° and they can last for up to a few hours. Finally, we discuss a possibility that MLR events may be triggered by power line harmonic radiation (PLHR) and we report an event supporting this hypothesis.
Desalination processes of sea ice revisited
Authors: Notz Dirk , Worster M. Grae
Published: May 2009

We reexamine five processes that have been suggested to be important for the loss of salt from sea ice. These processes are the initial fractionation of salt at the ice‐ocean interface, brine diffusion, brine expulsion, gravity drainage, and flushing with surface meltwater. We present results from analytical and numerical studies, as well as from laboratory and field experiments, that show that, among these processes, only gravity drainage and flushing contribute to any measurable net loss of salt. We show that during ice growth the salinity field is continuous across the ice‐ocean interface. Hence there is no immediate segregation of salt at the advancing front.
High‐resolution open‐ocean temperature spectra
Authors: van Haren Hans , Gostiaux Louis
Published: May 2009

Accurate (<1 mK) temperature sensors have been stiffly moored at ∼1450 m in the open Canary Basin for 1.5 years while sampling at 1 Hz. The sensors were in an area where regular density steps occur. In this article, we investigate the variability of internal waves in such “steppy” environment. The waves vertically move layers of persistent temperature gradients for particular temperatures. The frequency (σ) spectra of temperature, and more clearly those of inferred vertical currents w, show an internal wave band IWB that extends from 0.97f < σ < Nt, where f denotes the inertial frequency or vertical Coriolis parameter. Transition frequency Nt is higher than buoyancy frequency N, computed over large vertical scales Δz = O(100) m. The extension of IWB beyond the traditional bounds [f,N] is probably due to small‐vertical–scale layering (Δz ≈ 1 m). The associated weak stratification between such thin layers provides small‐scale Ns ≈ 4fh, where fh denotes the horizontal Coriolis parameter. This minimum stable stratification Ns is associated with tilting of vorticity away from gravity, which causes the subinertial spectral extent to 0.97f. Isothermal smoothing reveals details of coherent vertical internal wave and incoherent motions. The present w spectrum continuum of coherent IWB motions is not flat, as in previous near‐surface observations, but linearly increases from σ = f to a peak at σ ∼ 0.8N. The coherence spectrum shows a weak, significant peak at approximately twice the local buoyancy frequency for 2.5 ≤ Δz ≤ 100 m. Instead of dominant mode 1, zero phase difference, observed in IWB across the 130 m of observations, these super‐buoyancy motions show mode 2 dominance, π phase difference.
Assimilation of sea ice motion in a finite‐element sea ice model
Authors: Rollenhagen K. , Timmermann R. , Janjić T. , Schröter J. , Danilov S.
Published: May 2009

A finite‐element sea ice model (FESIM) is applied in a data assimilation study with the singular evolutive interpolated Kalman (SEIK) filter. The model has been configured for a regional Arctic domain and is forced with a combination of daily NCEP reanalysis data for 2‐m air temperature and 10‐m winds with monthly mean humidities from the ECMWF reanalysis and climatological fields for precipitation and cloudiness. We assimilate 3‐day mean ice drift fields derived from passive microwave satellite data. Based on multivariate covariances (which describe the statistical relationship between anomalies in different model fields), the sea ice drift data assimilation produces not only direct modifications of the ice drift but also updates for sea ice concentration and thickness, which in turn yield sustainable corrections of ice drift. We use observed buoy trajectories as an independent data set to validate the analyzed sea ice drift field. A good agreement between modeled and observed tracks is achieved already in the reference simulation. Application of the SEIK filter with satellite‐derived drift fields further improves the agreement. Spatial and temporal variability of ice thickness increases due to the assimilation procedure; a comparison to thickness data from a submarine‐based upward looking sonar indicates that the thickness distribution becomes more realistic. Validation with regard to satellite data shows that the velocity data assimilation has only a small effect on ice concentration, but a general improvement of the ice concentration within the pack is still evident.
On the sizes and observable effects of dust particles in polar mesospheric winter echoes
Authors: Havnes O. , Kassa M.
Published: May 2009

In the present paper, recent radar and heating experiments on the polar mesospheric winter echoes (PMWE) are analyzed with the radar overshoot model. The PMWE dust particles that influence the radar backscatter most likely have sizes around 3 nm. For dust to influence the electrons in the PMWE layers, it must be charged; therefore, we have discussed the charging of nanometer‐sized particles and found that the photodetachment effect, where photons of energy less than the work function of the dust material can remove excess electrons, probably is dominant at sunlit conditions. For moderate and low electron densities, very few of the dust smaller than ∼3 nm will be charged. We suggest that the normal requirement that disturbed magnetospheric conditions with ionizing precipitation must be present to create observable PMWE is needed mainly to create sufficiently high electron densities to overcome the photodetachment effect and charge the PMWE dust particles. We have also suggested other possible effects of the photodetachment on the occurrence rate of the PMWE. We attribute the lack of PMWE‐like radar scattering layers in the lower mesosphere during the summer not only to a lower level of turbulence than in winter but also to that dust particles are removed from these layers due to the upward wind draught in the summer mesospheric circulation system. It is likely that this last effect will completely shut off the PMWE‐like radar layers in the lower parts of the mesosphere.
Remote measurements of thundercloud electrostatic fields
Authors: Dwyer J. R. , Uman M. A. , Rassoul H. K.
Published: May 2009

Analytical and numerical models of the radio frequency emissions produced by relativistic runaway electron avalanches initiated by cosmic ray extensive air showers are presented. It is found that single‐point measurements of the distant electromagnetic fields allow the remote determination of the electrostatic field in the runaway electron avalanche region. For instance, it is possible to use ground‐based and/or remote airborne measurements of the radio frequency pulses from the runaway electron avalanches to map the magnitudes and directions of the electrostatic field within a thundercloud for regions with electric fields above the runaway avalanche threshold. Such measurements, which are difficult to perform in situ, may help answer several key questions regarding lightning initiation, such as what electric fields are usually present when lightning initiates and whether electric fields in small regions ever reach the conventional breakdown field.
One‐dimensional numerical modeling of sediment transport and bed deformation in open channels
Authors: El kadi Abderrezzak Kamal , Paquier André
Published: May 2009

A one‐dimensional numerical model for simulating unsteady flow and sediment transport in open channels is presented and tested. The flow hydrodynamics is represented by the shallow water equations, and the bed morphodynamics is represented by the Exner equation and an additional equation describing the nonequilibrium sediment transport. Sediment size distribution is represented by the median grain diameter and the standard deviation, instead of the usual modeling with multiple particle size classes. Various methods for computing bed elevation changes at a cross section due to erosion or deposition of sediment are proposed and tested, including an innovative approach that relates the spatial pattern of erosion and deposition rates to boundary shear stress distribution, which is calculated by the Merged Perpendicular Method. An explicit finite difference scheme is employed for solving the water and sediment governing equations. The pertinence of the model is examined for two hypothetical cases. The model is then tested on one set of laboratory experiments on bed degradation under steady flow, showing excellent model data fit, and indicating that incorporating a nonequilibrium sediment transport equation into the model structure is an important element in reproducing the bed degradation process. Finally, the model is applied to simulate the morphological changes taking place in the Ha!Ha! River (Quebec) after the failure of the Ha!Ha! Dyke on July 1996. Relevant results can be obtained in terms of changes in longitudinal bed profile and cross‐sectional geometry as well as water levels, although some discrepancies are obtained between the simulated and surveyed cross‐sectional geometries, mainly because bank failure and channel widening are not modeled.
Changes in hyporheic exchange flow following experimental wood removal in a small, low‐gradient stream
Authors: Wondzell Steven M. , LaNier Justin , Haggerty Roy , Woodsmith Richard D. , Edwards Richard T.
Published: May 2009

We investigated the response of hyporheic exchange flow (HEF) to wood removal in a small, low‐gradient, gravel bed stream in southeast Alaska using a series of groundwater models built to simulate HEF for the initial conditions immediately after wood removal and 1 month, 2 years, 4 years, and 16 years following wood removal. The models were based on topographic surveys of the stream channel and surrounding floodplain, and surveyed water surface elevations (WSEs) were used to assign stream boundary conditions. Using the groundwater flow model, MODFLOW, and the particle tracking model, MODPATH, we calculated hyporheic exchange fluxes, their residence time distributions, and both longitudinal and plan view spatial patterns of downwelling and upwelling zones. In the first few years, streambed scour and sediment deposition smoothed the streambed and WSE profile, reducing HEF. Also, large contiguous patches of downwelling or upwelling were fragmented, nearly doubling the total number of patches present on the streambed. As the stream continued to adjust to the loss of wood, those trends began to reverse. Accretion of sediment onto alternating bars resulted in better developed pool‐riffle morphology, enhanced HEF, and increased residence times and also resulted in downwelling and upwelling zones coalescing into elongated patches along bar margins. This study showed that the hyporheic zone is sensitive to changes in wood loading and that initial changes in HEF resulting from the direct effects of wood removal were contrary to longer‐term channel adjustments to changes in wood loading.
Hydrological properties of duff
Authors: Raaflaub Lynn , Valeo Caterina
Published: May 2009

Laboratory experiments were conducted to measure and compare the porosities, desorption characteristic curves, and saturated hydraulic conductivities of the decomposing organic layer of forest floors (duff). Samples were from six different canopy types, from both between and beside trees and from the upper and lower portions of the duff layer. Comparisons were made between the samples on the basis of three categories: canopy type, location, and layer. The hydrological properties were found to exhibit greater variation vertically within the duff layer than between canopy type and location.
Risk perceptions of arsenic in tap water and consumption of bottled water
Authors: Jakus Paul M. , Shaw W. Douglass , Nguyen To N. , Walker Mark
Published: May 2009

The demand for bottled water has increased rapidly over the past decade, but bottled water is extremely costly compared to tap water. The convenience of bottled water surely matters to consumers, but are others factors at work? This manuscript examines whether purchases of bottled water are associated with the perceived risk of tap water. All of the past studies on bottled water consumption have used simple scale measures of perceived risk that do not correspond to risk measures used by risk analysts. We elicit a probability‐based measure of risk and find that as perceived risks rise, expenditures for bottled water rise.
Observational evidence of a warm ocean current preceding a winter teleconnection pattern in the northwestern Pacific
Authors: Hirose Naoki , Nishimura Kazuya , Yamamoto Masaru
Published: May 2009

The role of the extratropical ocean in climate remains unclear due to the complexities in air‐sea interaction processes. We have found robust evidence for the Tsushima Warm Current (TWC) preceding the western Pacific (WP) teleconnection pattern by conducting an analysis over the past 30 years. The WP index in winter sharply succeeds the volume transport of the TWC in autumn, but rather smoothly connects with the El Niño indices, indicating a considerable role of the ocean current in the climate system. Correlation patterns of seasonal precipitation over the Japanese Islands are also consistent with this relationship. The significant lead‐lag correlations with the coherent structures of surface temperature indicate ocean‐to‐atmosphere feedback in which the interannual variation of the wind‐driven current, represented by the TWC transport, influences the regional climate conditions associated with the WP pattern in winter.
Atmospheric budget of primary biological aerosol particles from fungal spores
Authors: Heald Colette L. , Spracklen Dominick V.
Published: May 2009

The contribution of primary biological aerosol particles (PBAP) to the global budget of organic aerosol is poorly understood. Concentrations of mannitol, a biotracer for fungal spores, are used here to constrain the first global model (GEOS‐Chem) simulation of PBAP from fungi. Emissions are driven by leaf area index and atmospheric water vapor concentrations and are empirically optimized based on the geographical and seasonal variability of observed mannitol concentrations. Optimized global emissions total 28 Tg yr−1, with 25% of that total emitted as fine mode (PM2.5) aerosol. Fungal spores contribute 23% of total primary emissions of organic aerosol, or 7% of the fine‐mode source. Annual mean simulated surface concentrations of PBAP over vegetated regions range from 0.1–0.7 μgm−3 (PM2.5) and 0.4–3.0 μgm−3 (PM10), with the highest concentrations in the tropics, where PBAP may be the dominant source of organic aerosol. Further validation is required to reduce the substantial uncertainties on this budget.
Global distribution of whistler‐mode chorus waves observed on the THEMIS spacecraft
Authors: Li W. , Thorne R. M. , Angelopoulos V. , Bortnik J. , Cully C. M. , Ni B. , LeContel O. , Roux A. , Auster U. , Magnes W.
Published: May 2009

Whistler mode chorus waves are receiving increased scientific attention due to their important roles in both acceleration and loss processes of radiation belt electrons. A new global survey of whistler‐mode chorus waves is performed using magnetic field filter bank data from the THEMIS spacecraft with 5 probes in near‐equatorial orbits. Our results confirm earlier analyses of the strong dependence of wave amplitudes on geomagnetic activity, confinement of nightside emissions to low magnetic latitudes, and extension of dayside emissions to high latitudes. An important new finding is the strong occurrence rate of chorus on the dayside at L > 7, where moderate dayside chorus is present >10% of the time and can persist even during periods of low geomagnetic activity.
The future for blood‐stage vaccines against malaria
Authors: Richards Jack S , Beeson James G
Published: May 2009

Malaria is a leading cause of mortality and morbidity globally, and effective vaccines are urgently needed. Malaria vaccine approaches can be broadly grouped as pre‐erythrocytic, blood stage and transmission blocking. This review focuses on blood‐stage vaccines, and considers the evidence supporting the development of blood‐stage vaccines, the advantages and challenges of this approach, potential targets, human vaccine studies and future directions. There is a strong rationale for the development of vaccines based on antigens of blood‐stage parasites. Symptomatic malaria is caused by blood‐stage parasitemia and acquired immunity in humans largely targets blood‐stage antigens. Several candidate vaccines have proved efficacious in animal models and at least one vaccine showed partial efficacy in a clinical trial. At present, all leading candidate blood‐stage antigens are merozoite proteins, located on the merozoite surface or within the apical organelles. Major challenges and priorities include overcoming antigenic diversity, identification of protective epitopes, understanding the nature and targets of protective immune responses, and defining antigen combinations that give the greatest efficacy. Additionally, objective criteria and approaches are needed to prioritize the large number of candidate antigens, and strong candidates need to be tested in clinical trials as quickly as possible.
Salmonella enterica serovar Typhi live vector vaccines finally come of age
Authors: Galen James E , Pasetti Marcela F , Tennant Sharon , Ruiz‐Olvera Patricia , Sztein Marcelo B , Levine Myron M
Published: May 2009

Attenuated Salmonella Typhi vaccine strains hold great promise as live vectors for presentation of foreign antigens from unrelated bacterial, viral and parasitic pathogens to the immune system. Although this approach has proved quite successful in experimental animal models for eliciting antigen‐specific mucosal, humoral and cellular responses, results have been disappointing for clinical trials carried out thus far. We hypothesize that the paucity of human responses to foreign antigens delivered by live vectors suggests that the strains and genetic approaches used to date have resulted in overattenuated vaccine strains with severely reduced immunogenicity. However, remarkable advances have now been made in the genetics of foreign antigen expression, understanding mechanisms of live vector immunity and refining immunization strategies. The time has now come for development of multivalent live vectors in which stable antigen expression and export is balanced with metabolic fitness to create highly immunogenic vaccines.
Inhibition of NADPH Oxidase is Neuroprotective after Ischemia—Reperfusion
Authors: Chen Hai , Song Yun Seon , Chan Pak H
Published: May 2009

Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase (NOX) is well known as a major source for superoxide radical generation in leukocytes. Superoxide radicals play a significant role in brain ischemia–reperfusion (I/R) injury. Recent data have also shown expression of NOX in the brain. However, the manner by which NOX is involved in pathologic processes after cerebral ischemia remains unknown. Therefore, we subjected mice deficient in the NOX subunit, gp91phox (gp91phox-/-), those treated with the NOX inhibitor, apocynin, and wild-type (WT) mice to 75 mins of focal ischemia followed by reperfusion. At 24 h of reperfusion, the gp91phox-/- and apocynin-treated mice showed 50% less brain infarction and 70% less cleaved spectrin compared with WT mice. The levels of 4-hydroxy-2-nonenal, malondialdehyde, and 8-hydroxy-2‘-deoxyguanosine increased significantly after I/R, indicating oxidative brain injury. NADPH oxidase inhibition reduced biomarker generation. Furthermore, NOX was involved in postischemic inflammation in the brains, as less intercellular adhesion molecule-1 upregulation and less neutrophil infiltration were found in the NOX-inhibited mice after I/R. Moreover, gp91phox expression increased after ischemia, and was further aggravated by genetic copper/zinc-superoxide dismutase (SOD1) ablation, but ameliorated in SOD1-overexpressing mice. This study suggests that NOX plays a role in oxidative stress and inflammation, thus contributing to ischemic brain injury.
In Vivo Near-Infrared Fluorescence Imaging of Matrix Metalloproteinase Activity after Cerebral Ischemia
Authors: Klohs Jan , Baeva Nevena , Steinbrink Jens , Bourayou Riad , Boettcher Chotima , Royl Georg , Megow Dirk , Dirnagl Ulrich , Priller Josef , Wunder Andreas
Published: May 2009

Matrix metalloproteinases (MMPs) have been implicated in the pathophysiology of cerebral ischemia. In this study, we explored whether MMP activity can be visualized by noninvasive near-infrared fluorescence (NIRF) imaging using an MMP-activatable probe in a mouse model of stroke. C57BI6 mice were subjected to transient middle cerebral artery occlusion (MCAO) or sham operation. Noninvasive NIRF imaging was performed 24 h after probe injection, and target-to-background ratios (TBRs) between the two hemispheres were determined. TBRs were significantly higher in MCAO mice injected with the MMP-activatable probe than in sham-operated mice and in MCAO mice that were injected with the nonactivatable probe as controls. Treatment with an MMP inhibitor resulted in significantly lower TBRs and lesion volumes compared to injection of vehicle. To test the contribution of MMP-9 to the fluorescence signal, MMP9-deficient (MMP9−/-) mice and wild-type controls were subjected to MCAO of different durations to attain comparable lesion volumes. TBRs were significantly lower in MMP9−/- mice, suggesting a substantial contribution of MMP-9 activity to the signal. Our study shows that MMP activity after cerebral ischemia can be imaged noninvasively with NIRF using an MMP-activatable probe, which might be a useful tool to study MMP activity in the pathophysiology of the disease.
DDBJ Activities: Contribution to the Research in Information Biology
Authors: Mashima Jun , Kosuge Takehide , Okido Toshihisa , Kodama Yuichi , Ikeo Kazuho , Sugawara Hideaki , Tateno Yoshio , Gojobori Takashi
Published: May 2009

DDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; "http://www.insdc.org/":http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also collecting and releasing gene expression data at CIBEX (Center for Information Biology gene EXpression database; "http://cibex.nig.ac.jp/":http://cibex.nig.ac.jp/). Furthermore, DDBJ contributed to international annotation jamborees such as FANTOM (mouse), H-Inv (human), RAP (rice) and E. coli K12. DDBJ provides many services to the research in information biology or bioinformatics. They include Web-API for Biology (WABI) "http://www.xml.nig.ac.jp/":http://www.xml.nig.ac.jp/ and All-round Retrieval of Sequence and Annotation (ARSA) "http://arsa.ddbj.nig.ac.jp/":http://arsa.ddbj.nig.ac.jp/. These activities are presented with the perspective of DDBJ in the coming years.
Present and future of proteomics data curation at the PRIDE database
Authors: Vizcaino Juan Antonio , Hermjakob Henning , Martens Lennart
Published: May 2009

Significant progress has been made in improving the accessibility and utility of the large amounts of generated high-throughput proteomics data by the introduction of publicly available proteomics repositories. One such repository is PRIDE (the ‘PRoteomics IDEntifications’ database, "http://www.ebi.ac.uk/pride":http://www.ebi.ac.uk/pride). PRIDE stores mass spectrometry related data, including peptide and protein identifications, mass spectra and valuable additional metadata.At present, data curation in PRIDE is limited to data submission support. The format in which all submissions need to take place is PRIDE XML. Mass spectrometry derived data is very heterogeneous in terms of experimental approaches, instrumentation, data formats, etc. This is why conversion of all this different data to PRIDE XML is far from being trivial and can be very time consuming, since tailored submission pipelines must be often constructed. However, the situation has now ameliorated since some new tools like PRIDE converter ("http://code.google.com/p/pride-converter":http://code.google.com/p/pride-converter). are now available for submitters to convert their data to PRIDE XML.In the near future, data curation in PRIDE will be significantly extended. High-quality data will be included in a new repository called PRIDE-plus. First of all, it will be necessary to create a set of minimal requirement rules to decide which datasets can be included in PRIDE-plus. Then, the design and implementation of new curation tools to perform data quality assessment will be essential. It will also be necessary to do research into the automation of these new curation and annotation tasks.