bluuebunny/crossref_metadata_2025 huggingface dataset:
High prevalence of Leptospira spp. in sewer rats (Rattus norvegicus)
Authors: KRØJGAARD L. H. , VILLUMSEN S. , MARKUSSEN M. D. K. , JENSEN J. S. , LEIRS H. , HEIBERG A.-C.
Published: April 2009

Earlier studies on the ecology of leptospirosis in temperate regions focused mainly on free-ranging rats in rural areas. Here we report on the occurrence of Leptospira spp. in Rattus norvegicus living in sewers in a suburban area in Copenhagen, Denmark. In 2006–2007, about 30 rats were captured in sewers at each of six different locations. Rat kidneys were screened by PCR for pathogenic Leptospira spp. In one location no infected rats were found, whereas the prevalence in the remaining five locations ranged between 48% and 89%. Micro-agglutination tests showed that serogroup Pomona, Sejroe, and Icterohaemorrhagiae were the most common. Infection was related to age with the highest prevalence observed for adult rats but there was no difference in infection rate between sexes, suggesting primarily environmental transmission. Since most reported rat problems in urban areas are related to sewer rats, the surprisingly high level of infection calls for an increased public health concern.
Wouldn't It Be Nice If p, Therefore, p (for a moral p)
Authors: ENOCH DAVID
Published: April 2009

Instances of the argument-schema ‘Wouldn't it be nice if p, therefore, p’ are usually fallacious, but for a moral p they are not clearly as bad as they are elsewhere. I offer a diagnosis of this phenomenon, arguing that in some conditions – specified in terms of a logical property of the relevant normative operator – such arguments are actually valid (for a moral p).
The Wrong Kind of Solution to the Wrong Kind of Reason Problem
Authors: OLSON JONAS
Published: April 2009

The so-called Wrong Kind of Reason (WKR) problem for Scanlon's ‘buck-passing’ account of value has been much discussed recently. In a recent issue of Utilitas Gerald Lang provides a highly useful critique of extant proposed solutions to the WKR problem and suggests a novel solution of his own. In this note I offer a critique of Lang's solution and respond to some criticisms Lang directs at a Brentano-style approach suggested by Sven Danielsson and me.
Engaging with the State for the Common Good: Some Reflections on the Role of the Church
Authors: Smith Peter
Published: April 2009

The Canon Law of the Roman Catholic Church establishes the right of the Church to proclaim the Gospel and expound it, and to proclaim moral principles especially when this is required by fundamental rights or ‘for the salvation of souls’ (Canon 747). While this was taken for granted for centuries, society and culture have undergone rapid and extensive changes, especially over the last forty years. From what was once a Christian society and culture, we have moved to a multicultural and secular society, and have seen the rise of ‘ideological secularism’. The place of religion and religious values in the public forum is being questioned, and an aggressive secularism seeks to reduce religion and its practice to the private sphere. However, a healthy secularity should recognise both the autonomy of the state from control by the Church and also the right of the Church to proclaim its teaching and comment on social issues for the common good of humanity. This right is recognised in the 1948 Universal Declaration of Human Rights and the 1950 European Convention for the Protection of Human Rights and Fundamental Freedoms. From the Church's point of view, this right was recognised for all religions in the Second Vatican Council's ‘Declaration on Religious Liberty’. We must defend that right because the Church exists not for its own sake but for the sake of humanity.
A quantitative computational model for complete partial metric spaces via formal balls
Authors: ROMAGUERA SALVADOR , VALERO OSCAR
Published: April 2009

Given a partial metric space (X,p), we use (BX, ⊑dp) to denote the poset of formal balls of the associated quasi-metric space (X,dp). We obtain characterisations of complete partial metric spaces and sup-separable complete partial metric spaces in terms of domain-theoretic properties of (BX, ⊑dp). In particular, we prove that a partial metric space (X,p) is complete if and only if the poset (BX, ⊑dp) is a domain. Furthermore, for any complete partial metric space (X,p), we construct a Smyth complete quasi-metricqonBXthat extends the quasi-metricdpsuch that both the Scott topology and the partial order ⊑dpare induced byq. This is done using the partial quasi-metric concept recently introduced and discussed by H. P. Künzi, H. Pajoohesh and M. P. Schellekens (Künziet al. 2006). Our approach, which is inspired by methods due to A. Edalat and R. Heckmann (Edalat and Heckmann 1998), generalises to partial metric spaces the constructions given by R. Heckmann (Heckmann 1999) and J. J. M. M. Rutten (Rutten 1998) for metric spaces.
Challenges of Complexity in the 21st Century. An Interdisciplinary Introduction
Authors: Mainzer Klaus
Published: April 2009

The theory of nonlinear complex systems has become a proven problem-solving approach in the natural sciences from cosmic and quantum systems to cellular organisms and the brain. Even in modern engineering science self-organizing systems are developed to manage complex networks and processes. It is now recognized that many of our ecological, social, economic, and political problems are also of a global, complex, and nonlinear nature. Modern evolutionary economics can be modelled in the framework of complex systems and nonlinear dynamics. Historically, evolutionary economics was inspired by Schumpeterian concepts of business cycles and innovation dynamics. What are the laws of sociodynamics? What can we learn from nonlinear dynamics for complexity management in social, economic, financial and political systems? Is self-organization an acceptable strategy to handle the complexity in firms, institutions and organizations? The world-wide crisis of financial markets and economies is a challenge for complexity research. Misleading concepts of linear thinking and mild randomness (e.g. Gaussian distributions of Brownian motion) must be overcome by new approaches of nonlinear mathematics (e.g. non-Gaussian distribution), modelling the wild randomness of turbulence at the stock markets. Systemic crises need systemic answers. Nevertheless, human cognitive capabilities are often overwhelmed by the complexity of nonlinear systems they are forced to manage. Traditional mathematical decision theory assumed perfect rationality of economic agents (homo oeconomicus). Herbert Simon, Nobel Prize laureate of economics and one of the leading pioneers of systems science and cognitive science, introduced the principle of bounded rationality. Therefore, we need new insights into the factual microeconomic behaviour of economic agents by methods of humanities, cognitive and social sciences, which are sometimes called ‘experimental economics’. Social and economic dynamics are interdisciplinary challenges of modern complexity research.
The Brain, a Complex Self-organizing System
Authors: Singer Wolf
Published: April 2009

Our intuition assumes that there is a centre in our brain in which all relevant information converges and where all decisions are reached. To neurobiologists, the brain presents itself as a highly distributed system in which a very large number of processes occur simultaneously and in parallel without requiring coordination by a central convergence centre. The specific architecture resembles, in many respects, small world networks and raises the question of how the multiple operations occurring in parallel are bound together in order to give rise to coherent perception and action. Based on data obtained with massive parallel recordings, the hypothesis will be forwarded that temporal coherence serves as an important organizing principle and that this coherence is achieved by the synchronization of oscillatory activity in distinct frequency bands.
Managing Complexity in Socio-Economic Systems
Authors: Helbing Dirk
Published: April 2009

This contribution summarizes some typical features of complex systems such as non-linear interactions, chaotic dynamics, the ``butterfly effect’’, phase transitions, self-organized criticality, cascading effects, and power laws. These imply sometimes quite unexpected, counter-intuitive, or even paradoxical behaviors of socio-economic systems. A typical example is the faster-is-slower effect. Due to their tendency of self-organization, complex systems are often hard to control. Instead of trying to control their behavior, it would often be better to pursue the approach of guided self-organization, i.e. to use the driving forces of the system rather than to fight against them. This is illustrated by the example of hierarchical systems, which need to fulfill certain principles in order to be efficient and robust in an ever-changing environment. We also discuss the important role of fluctuations and heterogeneity for the adaptability, flexibility and robustness of complex systems. The presentation is enriched by a number of examples ranging from decision behavior up to production systems and disaster spreading.
Dancing with distress: helping people transform psychological problems with the Method of Levels two-step
Authors: Carey Timothy A.
Published: April 2009

The Method of Levels (MOL) shares many similarities with other therapeutic approaches and is perhaps most distinguishable by what it does not include rather than what it does use in sessions. MOL has two basic steps which are followed in an iterative procedure until the patient/client experiences a change or shift in their understanding and experience of a problem. This article explains the steps and uses examples and suggestions for practice to promote understanding.
Cognitive behavioural therapy with older adults: enthusiasm without the evidence?
Authors: Wilkinson Philip
Published: April 2009

Cognitive behavioural interventions specifically for older people have been described and researched for the last 30 years. However, despite a robust evidence base to support the use of CBT in the treatment of mental disorders in younger adults, trials with older people have generally been of poor methodological quality. Therefore, the potential of CBT to improve the outcome of late-life mental illness has not yet been adequately tested and demonstrated. The priorities, if this is to happen, are to develop standardized, reproducible CBT interventions and to evaluate these in large trials alongside medication or as part of case-management interventions.
Vergiftungen mit Pflanzen
Authors: Kupper Jacqueline , Reichert Cornelia
Published: April 2009

Die Einnahme von Pflanzen kann, wenn auch sehr selten, zu lebensbedrohlichen Vergiftungen führen. Stark giftige Pflanzen, bei denen tödliche Verläufe beschrieben sind, sind der blaue Eisenhut, die Eibe und die Herbstzeitlose. Zu tödlichen Intoxikationen mit Eisenhut und Eibe kommt es praktisch nur im Rahmen von Suiziden, während der Vergiftung mit den Blättern der Herbstzeitlose meist eine Verwechslung mit Blättern des Bärlauchs zugrunde liegt. Schwere Vergiftungen können auch durch Nachtschattengewächse, wie die Engelstrompete oder die Tollkirsche verursacht werden. Diese Pflanzen werden meist als Drogen konsumiert. Kindervergiftungen verlaufen in der Regel asymptomatisch oder leicht, da Kinder in der Regel nur kleinere Mengen Pflanzen einnehmen. Bei den meisten Pflanzenvergiftungen gibt es kein Antidot, und die Therapie ist rein symptomatisch.
Pilzvergiftungen – die Schattenseiten des Myzetismus
Authors: Flammer René , Schenk-Jäger Katharina M.
Published: April 2009

Die meisten Pilzvergiftungen manifestieren sich innerhalb von 12 Stunden mit Brechdurchfällen. Sie lassen sich grob in Ereignisse mit kurzer (< 4h) und langer Latenz (> 4h) einteilen. In der Regel muss bei langen Latenzzeiten (meistens 8 - 12 - 18h) ein Phalloides-Syndrom erwogen werden, besonders nach Verzehr unkontrollierter Wildpilze. Kürzere Latenzzeiten schließen jedoch eine Amatoxin-Vergiftung nicht aus. Denn üppige Mahlzeiten der auch an Chitin reichen Pilze, Mischgerichte und individuelle Faktoren verkürzen gelegentlich die Latenzzeit und verschleiern eine Amatoxinvergiftung. Deshalb ist jeder Brechdurchfall nach Pilzgenuss bis zum Gegenbeweis verdächtig auf eine Vergiftung durch amanitinhaltige Pilze. Wenn sich die Ursache der Beschwerden nicht innerhalb einer halben Stunde unter Beizug mykologischer Assistenz klären lässt, muss das Phalloides-Programm aktiviert werden. In der Zwischenzeit werden noch vorhandene Pilzfragmente im Abfall, in Mahlzeitenresten und Erbrochenem analysiert (Sporenanalyse) und der Urin auf Amanitine (ELISA) untersucht. Mit dem Grundsatz “Therapie vor Diagnose“ dürfte sich die Mortalität der Knollen­blätterpilzvergiftung von aktuell etwa 5% weiter senken lassen. Die aktuellen Therapieprogramme vermittelt das Schweizerische Toxikologische Informationszentrum (Tel. 145), ebenso die Adressen der speziell für Notfälle ausgebildeten Pilzfachleute, die auch unter www.vapko.ch aufgelistet sind. Von den 18 Vergiftungssyndromen stellen wir die in der Schweiz häufigsten und wichtigsten vor. In der Übersicht sind die anderen Syndrome mit aufgeführt. Realtiv häufig sind das Gastrointestinale Frühsyndrom mit Latenz < 4h und die Indigestion mit variabler Latenzzeit von 1–20h. Rauschzustände nach Genuss von Fliegen- und Pantherpilzen sind selten. Hingegen ist Psychodelie nach Genuss von Psilocyben häufig, wobei nur ausnahmsweise ärztliche Hilfe beansprucht wird. Bei Spätmanifestationen nach Tagen wie Nierenversagen oder Rhabdomyolyse empfiehlt sich die Frage nach mykophagen Gewohnheiten. Nur so wird man einem Orellanus- oder Equestre-Syndrom auf die Spur kommen. Pilze im Hausgarten verlocken Kinder oft zum Spielen und kleinen Kostproben. Wie soll man sich verängstigten Eltern gegenüber verhalten? Wie groß ist das toxikologische Potential der Pilze in den Gärten? Wir diskutieren die Optionen.
Analytik bei akuten Vergiftungen – was macht Sinn?
Authors: Rentsch Katharina M.
Published: April 2009

Da die Symptomatik bei akuten Vergiftungen oft zunächst uncharakteristisch und für eine sichere Diagnose untypisch ist, sind in vielen Fällen Laboruntersuchungen notwendig, um einerseits supportive Maßnahmen einleiten zu können. Andererseits kann damit die Diagnose einer Intoxikation erhärtet oder verworfen werden. Für die toxikologischen Untersuchungen werden sowohl Immunoassays als auch chromatographische Methoden eingesetzt. Allerdings können nicht alle Analyte mit diesen Verfahren nachgewiesen werden, so z.B. Ethanol und Metalle, z.B. Lithium. Als Probenmaterial wird Blut für die quantitative Bestimmung von definierten Verbindungen eingesetzt, ein toxikologisches Screening wird im Allgemeinen im Urin durchgeführt. In allen Situationen, die aufgrund der klinischen Symptomatik eine Intoxikation nicht ausschließen, sollte eine der Symptomatik angepasste toxikologische Screeninguntersuchung durchgeführt werden, sofern Therapieentscheide durch das Resultat beeinflusst werden. Eine spezifische quantitative Bestimmung der Noxe sollte bei Verdacht auf Intoxikationen mit Paracetamol, Lithium, Amanitin (Knollenblätterpilz), Colchizin, Alkohole und Glykole sowie Kohlenmonoxid und Zyanide durchgeführt werden.
Implications of anthropogenic river stage fluctuations on mass transport in a valley fill aquifer
Authors: Boutt David F. , Fleming Brandon J.
Published: April 2009

In humid regions a strong coupling between surface water features and groundwater systems may exist. In these environments the exchange of water and solute depends primarily on the hydraulic gradient between the reservoirs. We hypothesize that daily changes in river stage associated with anthropogenic water releases (such as those from a hydroelectric dam) cause anomalous mixing in the near‐stream environment by creating large hydraulic head gradients between the stream and adjacent aquifer. We present field observations of hydraulic gradient reversals in a shallow aquifer. Important physical processes observed in the field are explicitly reproduced in a physically based two‐dimensional numerical model of groundwater flow coupled to a simplistic surface water boundary condition. Mass transport simulations of a conservative solute introduced into the surface water are performed and examined relative to a stream condition without stage fluctuations. Simulations of 20 d for both fluctuating river stage and fixed high river stage show that more mass is introduced into the aquifer from the stream in the oscillating case even though the net water flux is zero. Enhanced transport by mechanical dispersion leads to mass being driven away from the hydraulic zone of influence of the river. The modification of local hydraulic gradients is likely to be important for understanding dissolved mass transport in near‐stream aquifer environments and can influence exchange zone processes under conditions of high‐frequency stream stage changes.
Simulation of low clouds from the CAM and the regional WRF with multiple nested resolutions
Authors: Lin Wuyin , Zhang Minghua , Wu Jingbo
Published: April 2009

Current climate models have shown systematic simulation biases of low clouds that have cast great uncertainties on the climate sensitivity of these models. Among them is the deficient amount of low clouds over the storm tracks. This study uses the NCAR Community Atmospheric Model (CAM) and the Weather Research and Forecasting model (WRF) to study the cause of the failure of the global model in simulating low clouds associated with a frontal passage over the North Atlantic. The global model is shown to simulate the large‐scale circulation that can support the boundary layer instabilities responsible for the observed clouds, but because the global model does not resolve the unstable modes, the instability cannot be realized. The resolution requirement of cloud simulations is discussed. This study also demonstrates the feasibility of cloud parameterization by nesting high resolution models into coarse resolution models to tap into the dynamical properties of the large‐scale flows.
Diversity of channeling flow in heterogeneous aperture distribution inferred from integrated experimental‐numerical analysis on flow through shear fracture in granite
Authors: Watanabe Noriaki , Hirano Nobuo , Tsuchiya Noriyoshi
Published: April 2009

Shear (Mode II) fractures with shear displacements of 1 and 5 mm were generated by direct shear on granite under normal stresses of 1, 20, and 60 MPa. Fracture surface mapping showed that the surface roughnesses of the shear fractures decreased with increasing shear displacement and normal stress and were smaller than those of tensile fractures reported in our previous study. Fluid flow experiments on the shear fractures provided fracture permeabilities at a wide range of confining pressures of 10–100 MPa. Nonmonotonic permeability was usually observed to decrease with increasing confining pressure. However, the permeability changes were different between the shear fractures generated at the normal stress of ≤20 and 60 MPa. In addition, obvious permeability changes with shear displacement were observed for 60 MPa, whereas no significant difference was observed for ≤20 MPa. Comparing the shear fractures with the tensile fractures having shear displacements revealed clear differences, even for equivalent shear displacements. Numerical models that were constructed using the data of the fracture surface mapping by matching their permeabilities with the experimentally evaluated fracture permeabilities revealed the development of preferential flow paths, i.e., channeling flows, for the shear fractures, providing a diversity of channeling flow in heterogeneous aperture distributions of rock fractures in the Earth's crust.
Fallout and distribution of volcanic ash over Argentina following the May 2008 explosive eruption of Chaitén, Chile
Authors: Watt Sebastian F. L. , Pyle David M. , Mather Tamsin A. , Martin Robert S. , Matthews Naomi E.
Published: April 2009

The major explosive eruption of Chaitén volcano, Chile, in May 2008 provided a rare opportunity to track the long‐range dispersal and deposition of fine volcanic ash. The eruption followed ∼10,000 years of quiescence, was the largest explosive eruption globally since Hudson, Chile, in 1991, and was the first explosive rhyolitic eruption since Novarupta, Alaska, in 1912. Field examination of distal ashfall indicates that ∼1.6 × 1011 kg of ash (dense rock equivalent volume of ∼0.07 km3) was deposited over ∼2 × 105 km2 of Argentina during the first week of eruption. The minimum eruption magnitude, estimated from the mass of the tephra deposit, is 4.2. Several discrete ashfall units are identifiable from their distribution and grain size characteristics, with more energetic phases showing a bimodal size distribution and evidence of cloud aggregation processes. Ash chemistry was uniform throughout the early stages of eruption and is consistent with magma storage prior to eruption at depths of 3–6 km. Deposition of ash over a continental region allowed the tracking of eruption development and demonstrates the potential complexity of tephra dispersal from a single eruption, which in this case comprised several phases over a week‐long period of intense activity.
A central California coastal ocean modeling study: 2. Adjoint sensitivities to local and remote forcing mechanisms
Authors: Veneziani M. , Edwards C. A. , Moore A. M.
Published: April 2009

The sensitivity of particular features within the California Current System to remote and local forcing is numerically investigated using the adjoint model version of the Regional Ocean Modeling System. We define three integral measures of nearshore surface temperature, cross‐shore transport, and sea surface height as metrics that characterize important aspects of the coastal circulation. We determine the metrics' relative sensitivity to different components of the surface external forcing and model initial condition fields. Calculations are performed for 14‐d intervals over the 5‐year period from 2000 to 2004. Sensitivities are ranked in terms of their relative importance in the annual average, and their seasonal cycle is examined. Contributions from different portions of the domain are identified to determine the importance of local versus remote forcing. Local forcing, particularly wind stress and, at times, heat flux, are the dominant forcing contributors to temperature and transport sensitivities, although model initial conditions can contribute quantitatively on the same order as surface fluxes. The sea surface height metric reveals important nonlocal effects, particularly along the open boundary of this regional simulation.
Estimation and mapping of wintertime increase in water ice content of the Martian surface soil based on seasonal Thermal Emission Spectrometer thermal inertia variations
Authors: Kuzmin R. O. , Zabalueva E. V. , Christensen P. R.
Published: April 2009

Results of the Mars Global Surveyor Thermal Emission Spectrometer (TES) thermal inertia seasonal variations analysis show significant increase of the thermal inertia during autumn‐winter periods in the middle latitudes. This observed increase occurred with regular repetition during each of the three Mars years of the TES observations. Two climatic factors (atmospheric dust loading and water ice (frost) formation in the soil) might lead to the real and/or apparent seasonal increase in thermal inertia. We compare maps of summertime and wintertime thermal inertia at similarly low atmospheric dust opacity within the latitude belt ±50°, outside of the seasonal CO2 ice cover. On the basis of the results of such comparison we developed a new method for estimating and mapping the wintertime increase of the water ice within the surface soil layer corresponding to the daily thermal skin depth of 2–10 cm. We use both the nomograms of relation between the thermal inertia for dry and icy soil compiled for different water ice content and an analytical approach. Comparison of the mapped wintertime TES thermal inertia values with computed values of the parameter for icy soil at different ice amounts shows that the wintertime thermal inertia values in the latitude ranges 40°–50°N and 40°–50°S are consistent with the presence of the water ice amount in the soil from 4 up to 17 vol % (locally), whereas at lower latitudes the ice amount is mainly less than 1 vol %. Mapping results show that the zone with a soil water ice amount of >3 vol % is much more in the northern hemisphere than in the southern one.
Mass balance of the Prince of Wales Icefield, Ellesmere Island, Nunavut, Canada
Authors: Mair Douglas , Burgess David , Sharp Martin , Dowdeswell Julian A. , Benham Toby , Marshall Shawn , Cawkwell Fiona
Published: April 2009

This paper estimates the mass balance of the Prince of Wales Icefield, Ellesmere Island, Canada, averaged over four decades, from measurements of surface mass balance (SMB) and iceberg calving. Shallow ice core net accumulation measurements and annual mass balance stake measurements are used in conjunction with a digital elevation model and knowledge of the location of the dominant moisture source for precipitation over the ice cap to interpolate and extrapolate spatial patterns of SMB across the Prince of Wales Icefield. The contribution of iceberg calving to the mass balance is calculated from estimates of (1) the annual volume of ice discharged at the major tidewater glacier termini and (2) the annual volume loss or gain due to terminus fluctuations. Two different approaches to determining the SMB conclude that the SMB of the ice field is approximately in balance (average equals −0.1 ± 0.4 km3 w.e. a−1, where w.e. means water equivalent) largely because of its proximity to the main year‐round moisture source that is the Smith Sound portion of the North Open Water polynya. Iceberg calving is a highly significant component of mass loss (−1.9 ± 0.2 km3 w.e. a−1) and is sufficient to make the overall mass balance of the ice field averaged over the period 1963–2003 clearly negative (−2 ± 0.45 km3 w.e. a−1, equivalent to a mean‐specific mass balance across the ice field of −0.1 m w.e. a−1). The Prince of Wales Icefield contributes ∼0.005 mm a−1 to global eustatic sea level rise.
Chaotic dynamics of super‐diffusion revisited
Authors: Cushman John H. , Park Moongyu , O'Malley Daniel
Published: April 2009

Super‐diffusive mixing in geophysics occurs in atmospheric turbulence, near surface currents in the oceans, and fracture flow in the subsurface to name a few examples. Models of super‐diffusion have been around since L. F. Richardson's pioneering work in the 1920's. Here we construct a family of super‐diffusive stochastic processes Xα(t), 0 < α, with independent, nonstationary increments, but a priori defined mean‐square displacement given by tα+1. The case α = 2 corresponds to Richardson super‐diffusion. The family of processes is a nonstationary extension of Brownian motion and hence completely characterized by its first two moments. The Fokker‐Planck equation for Xα(t) is classical diffusive with time dependent diffusion coefficient given by tα/2. In contrast to what is found in fractional Brownian motion, where the fractal dimension depends on the Hurst exponent, here the fractal dimension and hence complexity of the process is the same for all exponents α as that of classical Brownian motion. An analytical expression is developed for the finite‐size Lyapunov exponent and numerical examples presented.
Subduction of North Pacific central mode water associated with subsurface mesoscale eddy
Authors: Oka Eitarou , Toyama Katsuya , Suga Toshio
Published: April 2009

During a shipboard high‐density hydrographic survey carried out in the western North Pacific in fall 2008, we observed an anticyclonic eddy with a thickness of 150 dbar and a diameter of 40 km near 500 dbar depth at 27.5°N, 145°E. This subsurface mesoscale eddy contains the North Pacific central mode water (CMW), which has anomalously low potential vorticity and high dissolved oxygen compared to the climatological CMW properties in the same region. Profiling float measurements detect similar CMW patches near and south of the Kuroshio Extension as well as southward CMW migration within the CMW formation region north of the Kuroshio Extension. These observed facts suggest that CMW is subducted into the permanent pycnocline not only through large‐scale eastward advection near the northern edge of the subtropical gyre but also through southward cross‐frontal advection associated with the formation and migration of subsurface mesoscale eddies.
Long‐lived auroral structures and atmospheric losses through auroral flux tubes on Mars
Authors: Dubinin E. , Fraenz M. , Woch J. , Barabash S. , Lundin R.
Published: April 2009

The ASPERA‐3 observations of electron and ion fluxes over the regions dominated by crustal magnetic fields show the existence of long‐lived and active aurora‐type magnetic flux tubes with a width of 20–150 km. The activity manifests itself by large electron energy fluxes (≥10−4 W/m2) and strong distortions in the upper (350–400 km) ionosphere. In some events the peaked electron energy distributions typical for Earth aurora are so pronounced that they are present in velocity distribution functions. A significant depletion of such auroral flux tubes is accompanied by the appearance of oxygen beams and a heating of the ions of ionospheric origin. Auroral activity was observed on several subsequent orbits of the Mars Express spacecraft during more than two weeks implying a stable existence of aurora on Mars. Atmospheric loss driven by energy deposition in the auroral flux tubes is estimated as ∼1023 s−1.
GOAssay: from Gene Ontology to Assays IDentifiers - Towards Automatic Functional Annotation of PubChem BioAssays
Authors: Guha Rajarshi , Gobeill Julien , Ruch Patrick
Published: April 2009

OBJECTIVES: We report on a experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer (GOCat). METHODS and MATERIALS: The assays are processed to filter out non functional information, then the textual content is sent to the categorizer, which provide a ranked list of GO descriptors based on a GOA-learned association model. RESULTS: The GO descriptors are regarded as irrelevant for only 18% of the assays. CONCLUSION: Semantic enrichment of PubChem assays with functional genomics categories seems effective at least to navigate PubChem assays. AVAILABILITIES: the database is hosted by the University of Indiana at "http://goassay.rguha.net/index.html":http://goassay.rguha.net/index.html; the GO categorizer interface and service is available at the University of Geneva "http://eagl.unige.ch/EAGLi/":http://eagl.unige.ch/EAGLi/.
Grid technology for collaborative ontology development
Authors: Aitken Stuart , Dang Kemian , Bard Jonathan
Published: April 2009

In contrast with the centrally-organised curation of the Gene Ontology, many biological ontologies are developed by loosely-organised groups who develop their ontology remotely. These groups tend to be formed from scientists and bio-informaticians from research groups with a common interest, who want to create a resource that will be useful to the community, rather than being formally mandated. Until recently, technological support for bio-ontology development relied on stand-alone editors running on users’ desk- tops for creating new ontology versions (e.g. OBO-Edit, COBrA and Protégé) and on private email, email lists and perhaps Wikis for the distribution of ontology files and discussions. Clearly, much better use could be made of the storage, versioning and visualisation techniques being developed by the database and e- Science communities. BioSphere is an online ontology editor supporting multiple users and is underpinned by a server that stores versions (in OWL-XML) and provides a discussion portal.
Plant Metabolic Pathways in MetaCyc and SolCyc
Authors: Pujar Anuradha , Caspi Ron , Menda Naama , Tecle Isaak , Karp Peter , Mueller Lukas
Published: April 2009

MetaCyc is a metabolic encyclopedia of experimentally validated biochemical pathways curated from scientific literature, that spans all organisms, with an emphasis on plants and microbes. The Pathway tools is a complex curation software suite that enables curation of reactions, construction of pathways and annotation with one or more representative enzymes, that include information such as substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements, genes if cloned and links to external databases. In addition curators are able to provide concise, review-level summaries and extensive literature citations. The present database release includes more than 1200 pathways from more than 1549 organisms, 7312 reactions, 5127 enzymes, 4748 genes, 7234 chemical compounds, curated from 17916 citations. The MetaCyc database is the reference database on which the pathways are predicted from annotated genomes by PathoLogic called Pathway/genome Databases (PGDB's). The Biocyc Database ("biocyc.org":http://biocyc.org) has a collection over 300 PGDB's. Each BioCyc Database describes the genome and predicted metabolic pathways of a single organism, which are then taken up by interested groups for curation. SolCyc is one such PGDB, developed for the clade oriented Solanceae Genomics Network (SGN) database. It has predicted metabolic pathway databases of significant species belonging to Solanaceae and includes Lycocyc(tomato), Solacyc (eggplant), Nicotianacyc (tobacco),Petuniacyc (Petunia), Capcyc (Capsicum) , Potatocyc (potato). An interactive webinterface has been developed for the seamless flow of information from the SGN phenotype and locus database with SolCyc. This facilitates researchers with the capacity to search for underlying metabolic pathway information of genes and phenotypes that has been curated into the SolCyc database.
Broadening Pfam Protein Sequence Annotations
Authors: Mistry Jaina , Cogghill Penny , Eddy Sean , Finn Rob , Tate John , Bateman Alex
Published: April 2009

Pfam is a database of conserved protein families or domains commonly used for genome annotation and sequence classification. It comprises two parts: (1) Pfam-A families, which are fully annotated and consist of a representative seed alignment, HMMs, and a full alignment comprising all sequences that score above the curated threshold; (2) Pfam-B families, which are automatically generated clusters of domains not matched by Pfam-A but that often indicate conserved sequence regions. Pfam release 23.0 predicts at least one Pfam-A domain on 74% of the sequences in UniProtKB, and predicts either a Pfam-A or Pfam-B domain on 93% of the sequences in UniProtKB.With the ever increasing rate of deposition of new proteins of all qualities into the underlying repositories, it is essential that Pfam continues to grow in order to maintain its coverage. We have used a number of strategies to improve the annotation provided by Pfam, and these include both building new families and expanding existing ones. Pfam has also greatly benefited from contributions from its user community. New family and functional annotation submissions from an S. pombe curator have ensured that Pfam has a high coverage - 83% - of the S. pombe proteome. Many of the early Pfam-A models have not been altered since they were first deposited. As the diversity of the sequence databases grows, the diversity within a Pfam seed alignment can become too narrow for representing the breadth of sequences that should belong to that family. The result is that some of the early Pfam-A HMMs fail to detect remote homologues. To address this problem we have rebuilt a large proportion of Pfam-A families, which has increased the Pfam-A coverage by 1-2%. Another strategy we have used has been that of targeted building, where a particular system or complex is examined in detail to ensure families exist for all components and annotation is consistent. In terms of building new Pfam-A families, the two major starting points are Pfam-B clusters and novel structures. From these we have built ~1000 families between releases 22.0 and 23.0, and a further 800 families since release 23.0.Between Pfam releases 22.0 and 23.0 we have changed the the way in which Pfam-B families are generated. Previously, Pfam-B families were created from PRODOM clusters that were based on a much smaller sequence database than the one upon which Pfam was built. We now use the ADDA algorithm that generates clusters from the same underlying sequence database as Pfam is based on, thus resulting in a more comprehensive Pfam-B contribution. This has increased the sequence coverage contributed by Pfam-B substantially from 3.9% to 11.8%. In a further drive to improve coverage, Pfam is currently evaluating a new release of the HMMER software (HMMER3) used to construct and search the Pfam HMMs. Early results show that HMMER3 is ~100 fold faster and has increased specificity and sensitivity compared with HMMER2.
Modeling of colloidal transport in capillaries
Authors: Stober G. , Steinbock L. J. , Keyser U. F.
Published: April 2009

We dynamically model the full ionic current signature of micron-sized colloids passing through microcapillaries in silico for the first time. Our novel computer simulation allows free adjustment of all relevant experimental parameters such as the geometry of the used orifice, noise sources, external applied pressure or voltage, and the charge of the particles passing through the channel. We demonstrate that our algorithm correctly describes the experimentally observed signals in our recently introduced microcapillary based Coulter counters. Finally, we quantitatively investigate the influence of DNA-functionalized particles on the signal amplitude as a function of salt concentration and particle size.
Development of high-density helicon plasma sources and their applications
Authors: Shinohara Shunjiro , Hada Tohru , Motomura Taisei , Tanaka Kenji , Tanikawa Takao , Toki Kyoichiro , Tanaka Yoshikazu , Shamrai Konstantin P.
Published: April 2009

We report on the development of unique, high-density helicon plasma sources and describe their applications. Characterization of one of the largest helicon plasma sources yet constructed is made. Scalings of the particle production efficiency are derived from various plasma production devices in open literature and our own data from long and short cylinder devices, i.e., high and low values of the aspect ratio A (the ratio of the axial length to the diameter), considering the power balance in the framework of a simple diffusion model. A high plasma production efficiency is demonstrated, and we clarify the structures of the excited waves in the low A region down to 0.075 (the large device diameter of 73.8 cm with the axial length as short as 5.5 cm). We describe the application to plasma propulsion using a new concept that employs no electrodes. A very small diameter (2.5 cm) helicon plasma with 1013 cm−3 density is produced, and the preliminary results of electromagnetic plasma acceleration are briefly described.
Conducting atomic force microscopy studies of nanoscale cobalt silicide Schottky barriers on Si(111) and Si(100)
Authors: Tedesco J. L. , Rowe J. E. , Nemanich R. J.
Published: April 2009

Cobalt silicide (CoSi2) islands have been formed by the deposition of thin films (∼0.1–0.3 nm) of cobalt on clean Si(111) and Si(100) substrates in ultrahigh vacuum (UHV) followed by annealing to ∼880 °C. Conducting atomic force microscopy has been performed on these islands to characterize and measure their current-voltage (I-V) characteristics. Current-voltage curves were analyzed using standard thermionic emission theory to obtain the Schottky barrier heights and ideality factors between the silicide islands and the silicon substrates. Current-voltage measurements were performed ex situ for one set of samples (termed “passivated surfaces”) where the silicon surface surrounding the islands was passivated with a native oxide. Other samples (termed “clean surfaces”) remained in UHV, while I-V curves were recorded. By comparing the barrier heights and ideality factors for islands on passivated surfaces and clean surfaces, the effects of the nonpassivated surfaces on conduction have been studied. The barrier heights measured from CoSi2 islands on clean surfaces are found to be ∼0.2–0.3 eV below barrier heights measured from similar islands on passivated surfaces. The main cause of the reduced Schottky barrier in the clean surface samples is attributed to Fermi level pinning by nonpassivated surface states of the clean silicon surface. However, the measured barrier heights of the islands are equivalent on both clean Si(111) and Si(100) surfaces, suggesting that the nonpassivated surface is influenced by cobalt impurities. Furthermore, the barrier heights of islands on the clean surfaces are lower than what can be explained by Fermi level pinning alone, suggesting the presence of additional reductions in the Schottky barrier heights. These variations are greater than what can be attributed to experimental error, and the additional barrier height lowering is primarily attributed to spreading resistance effects. Schottky barrier inhomogeneity is also identified as a possible cause of the additional barrier height lowering and nonideality in the Schottky contacts. Current-voltage measurements of the clean surface samples were also obtained at several temperatures. The barrier heights were found to decrease, and the ideality factors were found to increase with decreasing temperature. The dependence of the barrier height is attributed to the temperature variation of the Fermi level.
Excitation resolved color conversion of CdSe/ZnS core/shell quantum dot solids for hybrid white light emitting diodes
Authors: Nizamoglu Sedat , Demir Hilmi Volkan
Published: April 2009

In this paper, for their use as nanoluminophors on color-conversion white light emitting diodes (LEDs), we present spectrally resolved relative quantum efficiency and relative color (photon) conversion efficiency of CdSe/ZnS core/shell nanocrystal (NC) emitters in the solid-state film. We observe that both the averaged relative quantum efficiency and the averaged relative photon conversion efficiency of these NC solids increase with the increasing photon pump energy. Therefore, the excitation LED platform emitting at shorter wavelengths facilitates such NC luminophor solids to be more efficiently pumped optically. Furthermore, we investigate the spectral time-resolved spectroscopy of NCs in solution and in film with 0.4–2.4 nmol integrated number of NCs in the spectral range of 610–660 nm. We observe that the average lifetime of NCs increases toward longer wavelengths as the number of in-film NCs increases. With the increased amount of NCs, the average lifetime increases even further and the emission of NCs is shifted further toward red. This is attributed to the enhanced nonradiative energy transfer between these NCs due to the inhomogeneous size distribution. Thus, in principle, for fine tuning of the collective color of NCs for color-conversion LEDs, it is important to control the energy transfer by changing the integrated number of NCs.
Continuum analysis of the nucleus growth of reverse domains in large ferroelectric crystals
Authors: Neumeister Peter , Balke Herbert , Lupascu Doru C.
Published: April 2009

Polarization reversal in ferroelectrics arises due to domain nucleation and domain wall motion. The nucleation of reverse domains at crystal boundaries is the fundamental initiation process observed in single crystals. The classical continuum approach by Landauer determines an insurmountable energy barrier to extrinsic domain nucleation. We rediscuss the continuum approach. Predetermined surface states are found to be a misleading concept. Alternate energy contributions, for example, due to a dead layer or due to charge injection as well as reduced domain wall energy and anisotropy of domain wall energy, have to be included into a convincing picture of domain nucleation.
Micromagnetics of single and double point contact spin torque oscillators
Authors: Hrkac G. , Schrefl T. , Dean J. , Goncharov A. , Bance S. , Allwood D. , Suess D. , Fidler J.
Published: April 2009

In micromagnetic simulations of spin waves in thin film geometries special boundary conditions have to be applied at the boundary of the computational domain in order to avoid the reflection of spin waves. In this paper we proposed to use an artificially rough surface that will suppress spin wave reflections in order to treat spin torque oscillators with point contact geometry numerically. It is shown that the surface roughness model disperses the reflected spin waves and improves the signal to background noise ratio. The model is tested in comparison to conventional approaches such as extended layer systems, variable damping constant, and focal point methods for double point contacts. The surface roughness model gives solutions that are stable in time, in qualitative agreement with experiments and capable to reproduce phenomena such as phase locking in double point contacts.
Krajewski diagrams and the standard model
Authors: Stephan Christoph A.
Published: April 2009

This paper provides a complete list of Krajewski diagrams representing the standard model of particle physics. We will give the possible representations of the algebra and the anomaly free lifts which provide the representation of the standard model gauge group on the fermionic Hilbert space. The algebra representations following from the Krajewski diagrams are not complete in the sense that the corresponding spectral triples do not necessarily obey to the axiom of Poincaré duality. This defect may be repaired by adding new particles to the model, i.e., by building models beyond the standard model. The aim of this list of finite spectral triples (up to Poincaré duality) is therefore to provide a basis for model building beyond the standard model.
The dispersion of single-domain BaFe12O19 particles in water
Authors: Lisjak Darja , Drofenik Miha
Published: April 2009

We have studied the dispersion of single-domain BaFe12O19 particles in water and calculated the interparticle interaction energies due to the van der Waals and magnetic dipole-dipole forces. The magnitudes of the attraction energies varied significantly with the particles’ sizes and the separation distances between the particles. The contribution of the van der Waals potential was important only for the closest separation distances (up to 3 nm). The thermal energy exceeded the magnetic dipole-dipole attraction between the particles with radii larger than 20 nm at separation distances of several 100 nm. The electrosteric stabilization of the BaFe12O19 particles was possible only for particles with radii up to 15 nm and thicknesses up to 6 nm. The studied BaFe12O19 powder was a combination of several fractions, with respect to the particles’ sizes. The particles were treated with a surfactant, dodecylbenzylsulfonic acid, using a combination of milling and high-power ultrasound. The zeta-potential of the surfaces of these particles increased in comparison to the raw particles. We analyzed the dispersed particles using thermogravimetry, mass spectrometry, and transmission electron microscopy, and we determined the parameters for the stabilization of the BaFe12O19 powder.