bluuebunny/crossref_metadata_2025 huggingface dataset:
Fumaric aciduria: an overview and the first Brazilian case report
Authors: Allegri Gabriella , Fernandes Marcia J. , Scalco Fernanda B. , Correia Patricia , Simoni Ruth E. , Llerena Juan C. , de Oliveira Maria L. Costa
Published: June 2010

Fumaric aciduria is a rare metabolic disease, with 40 cases reported so far. Fumarase deficiency leads mainly to brain abnormalities, developmental delay, and great accumulation of fumaric acid in urine. This work presents the first case of fumaric aciduria described in Brazil, which presented with some interesting clinical and biochemical findings such as colpocephaly, hepatic alterations, and marked metabolic acidosis since birth. Common findings were ventriculomegaly, hypotonia, and microcephaly. Biochemically, besides the high urinary fumaric acid excretion, atypical elevation of plasma citrulline, tyrosine and methionine levels were also observed. In order to show all features and variants of fumaric aciduria, literature data of 40 patients was reviewed and compared with the case reported here. Findings in all these patients demonstrate that this disorder does not yet have its phenotype completely defined; it is important that more patients be described.
Enhancement of Polyunsaturated Fatty Acid Production by Selenium Treatment in Polyunsaturated Fatty Acid‐Producing Fungus
Authors: Guan Xian‐Yue , Dai Chuan‐Chao , Xu Yu‐Fen
Published: June 2010

The effect of selenium (Se) treatment on the content of intracellular polyunsaturated fatty acids (PUFA) was investigated. Selenium treatment could effectively increase the yields of arachidonic acid (AA) and linoleic acid (LA). When AA‐producing Diasporangiumjonesianum recombinant strain D‐A1 was cultured in a medium containing 90 μg mL−1 Se, the growth of D.jonesianum recombinant strain D‐A1 was constrained, but the content of AA in the total fatty acids reached 9.3%, 1.7‐fold higher than the control. The content of LA was also increased from 25.9 to 37.7%. Under various culture conditions, Se treatment (90 μg mL−1) was generally beneficial to the yields of LA and AA. However, there was no significant increase in the contents of eicosapentaenoic acid (EPA) and γ‐linolenic acid. Therefore, the use of Se is advantageous for regulating the content of intracellular PUFA in D.jonesianum recombinant strain D‐A1, and could be good enhancer in the yields of AA and LA.
Intravenous immunoglobulin therapy for aspirin‐heparinoid‐resistant antiphospholipid syndrome
Authors: Shimada Shigeki , Yamada Hideto , Atsumi Tatsuya , Yamada Takashi , Sakuragi Noriaki , Minakami Hisanori
Published: June 2010

We encountered a woman who had a history of repeated fetal losses and positive tests for lupus anticoagulant, phosphatidylserine‐dependent antiprothrombin (aPS/PT) IgG, IgM and kininogen‐dependent antiphosphatidylethanolamine (aPE) IgG, IgM. Her previous pregnancy had ended in intrauterine fetal death at 24 weeks of gestation despite a therapy of low‐dose aspirin, prednisolone and danaparoid. During the present pregnancy, she was treated with repeated intravenous infusions of immunoglobulin (IVIg) together with low‐dose aspirin, prednisolone and heparin. When thrombocytopenia developed, she delivered a female baby weighing 2,152 g at 34 weeks of gestation by cesarean section. Titers of aPS/PT IgM and aPE IgM were reduced or maintained at low levels by repeated IVIg therapies. The IVIg therapy might be effective for aspirin‐heparinoid‐resistant antiphospholipid syndrome.
Assessment of left ventricular diastolic function by MR: why, how and when
Authors: Duarte Ricardo , Fernandez Gabriel
Published: June 2010

Cardiovascular magnetic resonance (CMR), a valuable non-invasive technique for the evaluation of the cardiovascular system, has already been accepted as the "gold standard" for the assessment of systolic function. The assessment of diastolic function is important not only for diagnosis purposes, but also in terms of prognosis. ECG-triggering phase-contrast (PC) CMR allows the routine assessment of diastolic function by measuring the transmitral and pulmonary venous flow with high accuracy and reproducibility, using morphological and quantitative parameters similar to those obtained by transthoracic echocardiography, which are so familiar to general cardiologists. Therefore, the increasing role of CMR in the assessment of the cardiovascular system requires a greater awareness and knowledge of this condition by radiologists. The aim of this study is to review the main mechanisms and common causes of left ventricle diastolic dysfunction, provide a practical approach for the assessment of LV diastolic function and illustrate the different degrees of diastolic dysfunction.
Illegale Drogen und Suchtproblematik als Herausforderung für Entwicklungsländer
Authors: Busse Anja
Published: June 2010

Einleitung

Drogenmissbrauch und Drogenabhängigkeit sind weltweite Probleme, die auch Entwicklungsländer stark betreffen. Die Umsetzung effektiver und evidenzbasierter Strategien der Suchtprävention und –behandlung ist gerade für Länder mit wenigen Ressourcen eine große Herausforderung.
Linnaeans outdoors: the transformative role of studying nature ‘on the move’ and outside
Authors: HODACS HANNA
Published: June 2010

Travelling is an activity closely associated with Carolus Linnaeus (1707–1778) and his circle of students. This article discusses the transformative role of studying nature outdoors (turning novices into naturalists) in eighteenth-century Sweden, using the little-known journeys of Carl Bäck (1760–1776), Sven Anders Hedin (1750–1821) and Johan Lindwall (1743–1796) as examples. On these journeys, through different parts of Sweden in the 1770s, the outdoors was used, simultaneously, as both a classroom and a space for exploration. The article argues that this multifunctional use of the landscape (common within the Linnaean tradition) encouraged a democratization of the consumption of scientific knowledge and also, to some degree, of its production. More generally, the study also addresses issues of how and why science and scientists travel by discussing how botanical knowledge was reproduced and extended ‘on the move’, and what got senior and junior students moving.
Probiotics: beneficial factors of the defence system
Authors: Antoine Jean Michel
Published: June 2010

Probiotics, defined as living micro-organisms that provide a health benefit to the host when ingested in adequate amounts, have been used traditionally as food components to help the body to recover from diarrhoea. They are commonly ingested as part of fermented foods, mostly in fresh fermented dairy products. They can interact with the host through different components of the gut defence systems. There is mounting clinical evidence that some probiotics, but not all, help the defence of the host as demonstrated by either a shorter duration of infections or a decrease in the host's susceptibility to pathogens. Different components of the gut barrier can be involved in the strengthening of the body's defences: the gut microbiota, the gut epithelial barrier and the immune system. Many studies have been conducted in normal free-living subjects or in subjects during common infections like the common cold and show that some probiotic-containing foods can improve the functioning of or strengthen the body's defence. Specific probiotic foods can be included in the usual balanced diet of consumers to help them to better cope with the daily challenges of their environment.
Considerations for minimising the spread of infectious disease in Antarctic seabirds and seals
Authors: Grimaldi Wray , Jabour Julia , Woehler Eric J
Published: June 2010

Before 1998, concern was raised over the potential for human activities in Antarctica to introduce infectious disease organisms to native wildlife. A workshop was held that year to address this issue. In the last decade, there has been a dramatic increase in human traffic to the Antarctic and the number of commercial tourists visiting the Antarctic has steadily risen. Personnel of national science programmes, though relatively few in numbers, have the most intimate contact with wildlife and thus the greater potential to introduce organisms through their research activities. Many visitors are now able to arrive in the Antarctic from temperate regions within hours by aircraft, and from northern polar regions within 24 to 36 hours. Tourists, by their high numbers, also have the potential to transfer infectious disease agents among commonly visited sites. As of 2009, no outbreaks of infectious diseases in the Antarctic reported in the literature have been directly attributed to human activity, but the ameliorating climate may break down the barriers that have kept Antarctic wildlife relatively free of infectious diseases. Several agents of infectious diseases reported in Antarctic seabirds and seals are assessed for their likelihood to occur more frequently in terms of the characteristics of the agent, the behaviour of Antarctic wildlife, and the effects of an ameliorating climate (regional warming) in conjunction with continued increasing human activities.
Merely possible explanation
Authors: GUIGON GHISLAIN
Published: June 2010

Graham Oppy has argued that possible explanation entails explanation in order to object to Richard Gale and Alexander Pruss's new cosmological argument that it does not improve upon familiar cosmological arguments. Gale and Pruss, as well as Pruss individually, have granted Oppy's inference from possible explanation to explanation and argue that this inference provides a reason to believe that the strong principle of sufficient reason is true. In this article, I shall undermine Oppy's objection to the new cosmological argument by arguing that it is logically possible that some truths are merely possibly explained.
Continuous creation and secondary causation: the threat of occasionalism
Authors: MILLER TIMOTHY D.
Published: June 2010

One standard criticism of the doctrine of continuous creation is that it entails the occasionalist position that God alone is a true cause and that the events we commonly identify as causes are merely the occasions upon which God brings about effects. I begin by clearly stating Malebranche's argument from continuous creation to occasionalism. Next, I examine two strategies for resisting Malebranche's argument – strong and weak concurrentism – and argue that weak concurrentism is the more promising strategy. Finally, I argue that weak concurrentism requires a necessitarian approach to secondary causation.
Sceptical theism and divine lies
Authors: WIELENBERG ERIK J.
Published: June 2010

In this paper I develop a novel challenge for sceptical theists. I present a line of reasoning that appeals to sceptical theism to support scepticism about divine assertions. I claim that this reasoning is at least as plausible as one popular sceptical theistic strategy for responding to evidential arguments from evil. Thus, I seek to impale sceptical theists on the horns of a dilemma: concede that either (a) sceptical theism implies scepticism about divine assertions, or (b) the sceptical theistic strategy for responding to evidential arguments from evil fails. An implication of (a) is that sceptical theism is at odds with any religious tradition according to which there are certain claims that we can know to be true solely in virtue of the fact that God has told us that they are true. This result will render conceding (a) unattractive to many sceptical theists.
Characteristics of dissociable human learning systems
Authors: Shanks David R. , St. John Mark F.
Published: June 2010

A number of ways of taxonomizing human learning have been proposed. We examine the evidence for one such proposal, namely, that there exist independent explicit and implicit learning systems. This combines two further distinctions, (1) between learning that takes place with versus without concurrent awareness, and (2) between learning that involves the encoding of instances (or fragments) versus the induction of abstract rules or hypotheses. Implicit learning is assumed to involve unconscious rule learning. We examine the evidence for implicit learning derived from subliminal learning, conditioning, artificial grammar learning, instrumental learning, and reaction times in sequence learning. We conclude that unconscious learning has not been satisfactorily established in any of these areas. The assumption that learning in some of these tasks (e.g., artificial grammar learning) is predominantly based on rule abstraction is questionable. When subjects cannot report the “implicitly learned” rules that govern stimulus selection, this is often because their knowledge consists of instances or fragments of the training stimuli rather than rules. In contrast to the distinction between conscious and unconscious learning, the distinction between instance and rule learning is a sound and meaningful way of taxonomizing human learning. We discuss various computational models of these two forms of learning.
Neural correlates of consciousness are not pictorial representations
Authors: Rees Geraint , Frith Chris
Published: June 2010

O'Regan & Noë (O&N) are pessimistic about the prospects for discovering the neural correlates of consciousness. They argue that there can be no one-to-one correspondence between awareness and patterns of neural activity in the brain, so a project attempting to identify the neural correlates of consciousness is doomed to failure. We believe that this degree of pessimism may be overstated; recent empirical data show some convergence in describing consistent patterns of neural activity associated with visual consciousness.
Screening for Chagas' disease in HIV-positive immigrants from endemic areas
Authors: RODRÍGUEZ-GUARDADO A. , ALVAREZ V. ASENSI , RODRÍGUEZ PEREZ M. , ALVAREZ P. MEJUTO , FLORES-CHAVEZ M. , GONZÁLEZ P. ALONSO , SÁNCHEZ J. A. CARTÓN
Published: June 2010

Chagas' disease is an opportunistic infection in the setting of HIV/AIDS. The arrival of HIV-positive immigrants from endemic areas to non-endemic countries makes possible the detection of Chagas' disease in this group of patients. We describe the results of a screening programme conducted in the HIV-positive immigrant population arriving from endemic areas who attended the Tropical Medicine Unit of Hospital Universitario Central of Asturias during 2008. We determined anti-T. cruzi antibodies in all HIV patients arriving from endemic areas who were followed up. The ID-Chagas antibody test was used as a screening assay. The positive cases were confirmed with ELISA, IFAT and PCR. We analysed 19 HIV-positive immigrants, of which two (10·5%) had a positive antibody test for Chagas' disease confirmed. PCR was positive in both cases. There was no difference between the co-infected and the non-co-infected patients with respect to race, place of birth and residence, CD4+ cell count, and HIV viral load count. Direct microscopic examination of blood was negative in both positive cases. The positive patients were a man from Bolivia and woman from Paraguay. The overlap of HIV and T. cruzi infection occurs not only in endemic areas but also in non-endemic areas of North America and Europe where the diagnosis may be even more difficult due to low diagnostic suspicion. The implementation of screening programmes in this population group is needed for the early diagnostic of Chagas' disease.
Model predictions and evaluation of possible control strategies for the 2009 A/H1N1v influenza pandemic in Italy
Authors: AJELLI M. , MERLER S. , PUGLIESE A. , RIZZO C.
Published: June 2010

We describe the real-time modelling analysis conducted in Italy during the early phases of the 2009 A/H1N1v influenza pandemic in order to estimate the impact of the pandemic and of the related mitigation measures implemented. Results are presented along with a comparison with epidemiological surveillance data which subsequently became available. Simulated epidemics were fitted to the estimated number of influenza-like syndromes collected within the Italian sentinel surveillance systems and showed good agreement with the timing of the observed epidemic. On the basis of the model predictions, we estimated the underreporting factor of the influenza surveillance system to be in the range 3·3–3·7 depending on the scenario considered. Model prediction suggested that the epidemic would peak in early November. These predictions have proved to be a valuable support for public health policy-makers in planning interventions for mitigating the spread of the pandemic.
Molecular epidemiology of hepatitis E virus in humans, pigs and wild boars in Sweden
Authors: WIDÉN F. , SUNDQVIST L. , MATYI-TOTH A. , METREVELI G. , BELÁK S. , HALLGREN G. , NORDER H.
Published: June 2010

Hepatitis E infections in humans are usually acquired in endemic countries in Asia or Africa. In Sweden 17 cases infected in Europe, between 1993 and 2009, were identified. All had clinical hepatitis E with unknown source of infection. Hepatitis E virus (HEV) was identified in faecal samples from 63 piglets in 12 pig farms in Sweden. HEV was also identified in blood from 13 out of 159 investigated Swedish wild boars from nine counties. Partial HEV genomes from humans, pigs and wild boars were sequenced and compared by phylogeny. The results showed close relatedness between HEV strains from piglets from the same farm and from wild boars from the same county. HEV strains from humans showed relatedness with strains from pigs and wild boars from the same county. This study showed that HEV strains form geographical clusters in the phylogenetic tree. The methods used in this study may thus be used for tracing the origin of an infecting strain. Furthermore, this study indicated that there are endemic sources of human HEV infections in Sweden.
An optimal alternative to Conflation
Authors: Crowhurst Megan J.
Published: June 2010

An issue which engaged the attention of phonologists following the publication of Halle & Vergnaud's ground-breaking Essay on stress (1987a) was the proper treatment of stress systems in which iterative foot structure is apparently required to locate the main prominence, yet expected secondary stresses are absent in the output. The solution proposed by Halle & Vergnaud was that unwanted secondary stresses are removed by a special repair mechanism, Conflation, accompanied by the automatic erasure of headless feet. The pattern which initially motivated the rule was found to exist in a very few languages: Cairene Arabic (Mitchell 1956, 1960, 1962; Langendoen 1968; McCarthy 1979; Stevens & Salib 1987), Seminole/Creek (Haas 1977; Jackson 1987; Tyhurst 1987) and possibly Palestinian Arabic (Brame 1973; Kenstowicz & Abdul-Karim 1980; Hayes 1995; inter al.).
Storm‐enhanced plasma density features investigated during the Bastille Day Superstorm
Authors: Horvath Ildiko , Lovell Brian C.
Published: June 2010

Field‐aligned passes track true profiles. Such Defense Meteorological Satellite Program passes permitted investigating storm‐enhanced plasma density (SED) feature development during the Bastille Day Superstorm in a comprehensive way. We tracked equatorial ionization anomaly (EIA) and SED features and their underlying forward fountain circulation and downward SED plume plasma flows, respectively. Northward subauroral polarization stream E fields detaching plasma and producing SED plumes were also detected. We assessed the effects of South Atlantic Magnetic Anomaly and summer‐to‐winter interhemispheric plasma flows on the EIA and found a southward dipping gradient in drift/flow when no storm/evening‐related fountain strengthening occurred. We investigated the relative importance of different plasma sources in SED development. An extremely large plasma enhancement seen over Florida at 2200 UT on 15 July 2000 was a SED feature that was tracked by many GPS total electron content (TEC) maps as a 200 TEC unit (TECU) enhancement. We tracked its equally large conjugate pair over Trelew (Argentine Patagonia) and unraveled their development. Their underlying SED plume supplied most of the plasma. Appearing between these two SED features, a small and highly asymmetrical EIA offered on each side a low baseline upon which the downward streaming SED plume plasma piled up. Contradicting a currently accepted explanation, there was no enhanced fountain action detected to contribute 150 TECU to the 200 TECU. Later (∼2400 UT), there was enhanced fountain action, but SED plume contribution still dominated. Proven by observational evidence, SED development is a complex process of SED plume plasma flows and equatorward wind effects that cannot be described by one single explanation.
Refinements to a prognostic scheme of skin sea surface temperature
Authors: Takaya Yuhei , Bidlot Jean‐Raymond , Beljaars Anton C. M. , Janssen Peter A. E. M.
Published: June 2010

Refinements to a prognostic scheme of skin sea surface temperature (SST) are proposed and tested. The refinements consist of two modifications of a Monin‐Obukhov similarity function for stable conditions and mixing enhancement by the Langmuir circulation. The modified scheme is tested with the European Centre for Medium‐Range Weather Forecasts model. The modified scheme shows better agreement of the diurnal SST amplitude with estimates from satellite observations. The scheme is also validated with moored buoy observations of the Arabian Sea Mixed Layer Dynamics Experiment. The off‐line model with the modified scheme reproduces the observed diurnal SST variability well. Additionally, it is found that the parameterization of the effect of the Langmuir circulation enhances ocean mixing and reduces the diurnal variability of SST under wavy conditions.
Climatology of convective density currents in the southern foothills of the Atlas Mountains
Authors: Emmel C. , Knippertz P. , Schulz O.
Published: June 2010

Density currents fed by evaporationally cooled air are an important dust storm–generating feature and can constitute a source of moisture in arid regions. Recently, the existence of such systems has been demonstrated for the area between the High Atlas Mountains and the Sahara desert in southern Morocco on the basis of case studies. Here, a climatological analysis is presented that uses data from the dense climate station network of the IMPETUS project (An Integrated Approach to the Efficient Management of Scarce Water Resources in West Africa) for the 5 year period 2002–2006. Objective criteria mainly based upon abrupt changes in wind and dew point temperature are defined to identify possible density current situations. The preselected events are then subjectively evaluated with the help of satellite imagery and surface observations to exclude causes for air mass changes other than moist convective cold pool formation. On average, 11 ± 4 density currents per year are detected with the main season lasting from April to September. Density currents occur mainly in the afternoon and evening due to the diurnal cycle of moist convection. Mean changes at the leading edge are increases in 2 m dew point temperature and wind speed by 5.4°C and 8.2 m s−1, respectively, and a decrease in 2 m air temperature of 2.3°C. The High Atlas and Jebel Saghro are found to be the most important source regions, while only a few systems originate over the Saharan lowlands. Labilization of the atmosphere due to upper‐level troughs over northwest Africa and an enhanced moisture content favor density current formation. In addition, detailed case studies representative of different density current types are presented.
Relationship between soil moisture and vegetation in the Kairouan plain region of Tunisia using low spatial resolution satellite data
Authors: Zribi M. , Paris Anguela T. , Duchemin B. , Lili Z. , Wagner W. , Hasenauer S. , Chehbouni A.
Published: June 2010

The present paper proposes an empirical approach for the modeling of vegetation development, using moisture measurements only. The study is based simply on the use of two databases: one containing soil moisture products derived from ERS scatterometer data over the period 1991–2006 and the other containing normalized difference vegetation indices (NDVI) derived from advanced very high resolution radiometer over the period 1991–2000. The study is applied over the Kairouan plain, the central semiarid region of Tunisia (North Africa). Soil moisture products were first validated on the basis of comparisons with Global Soil Wetness Project, Phase 2 Data, outputs and rainfall events. The soil moisture distribution during the rainy period between October and May is described and is found to be correlated with the vegetation dynamics estimated using the NDVI products. Finally, a semiempirical model is proposed, based on satellite moisture and NDVI products, which allows the NDVI value to be estimated for a period of 1 month during the rainy season as a function of the moisture profile estimations obtained during the previous months. This approach could prove very useful and provide a simple tool for the modeling of vegetation dynamics during rainy seasons in semiarid regions.
Determining leaf area index and leafy tree roughness using terrestrial laser scanning
Authors: Antonarakis A. S. , Richards K. S. , Brasington J. , Muller E.
Published: June 2010

Vegetation roughness, and more specifically forest roughness, is a necessary component in better defining flood dynamics both in the sense of changes in river catchment characteristics and the dynamics of forest changes and management. Extracting roughness parameters from riparian forests can be a complicated process involving different components for different required scales and flow depths. For flow depths that enter a forest canopy, roughness at both the woody branch and foliage level is necessary. This study attempts to extract roughness for this leafy component using a relatively new remote sensing technique in the form of terrestrial laser scanning. Terrestrial laser scanning is used in this study due to its ability to obtain millions of points within relatively small forest stands. This form of lidar can be used to determine the gaps present in foliaged canopies in order to determine the leaf area index. The leaf area index can then be directly input into resistance equations to determine the flow resistance at different flow depths. Leaf area indices created using ground scanning are compared in this study to indices calculated using simple regression equations. The dominant riparian forests investigated in this study are planted and natural poplar forests over a lowland section of the Garonne River in Southern France. Final foliage roughness values were added to woody branch roughness from a previous study, resulting in total planted riparian forest roughness values of around Manning's n = 0.170–0.195 and around n = 0.245–330 for in‐canopy flow of 6 and 8 m, respectively, and around n = 0.590 and around n = 0.750 for a natural forest stand at the same flow depths.
Jupiter's magnetospheric change by Io's volcanoes
Authors: Yoneda M. , Nozawa H. , Misawa H. , Kagitani M. , Okano S.
Published: June 2010

Monitoring observations of Jupiter's sodium nebula and [SII] 673.1 nm emission from the Io plasma torus were made for 20 days in 2003. During these observations, the brightness of the sodium nebula showed a small enhancement which seemed to be caused by Io's volcanic outburst. During this enhancement, [SII] 673.1 nm brightness and the ion temperature (scale height) along Jupiter's magnetic fields did not show any significant change, but magnetic flux tube content of S+ ion was calculated from the [SII] 673.1 nm brightness and the scale height, and an increase of the ion flux tube content was clearly identified. Thus, increase of supplied plasma from Io seems to be reflected in both plasma density and ion temperature. We conclude that Io's volcanic enhancement with a duration time of a few days can change Jupiter's inner magnetospheric environment in aspects of both ion density and temperature.
Video Games in Psychotherapy
Authors: Ceranoglu T. Atilla
Published: June 2010

Video games have found their way into the clinical care of youth in most medical fields, and academic interest in their use is increasing steadily. The popularity of video games among youth may qualify them as a useful tool in psychotherapy for children and adolescents. Limited literature on use of video games in mental health care suggests that they can help young patients become more cooperative and enthusiastic about psychotherapy. Recent experience suggests that video games may facilitate therapeutic relationships, complement the psychological assessment of youth by evaluating cognitive skills, and elaborate and clarify conflicts during the therapy process. Concerns about video game content, perceived effects on youth, and lack of familiarity with this medium may form a barrier in their use in therapy offices. Further research on the benefits of video game use in psychotherapy, including patient characteristics that may moderate outcomes, is needed. Finally, future collaborations between clinicians and video game developers may produce specific games to be used in psychotherapy.
The Cognitive Atlas: Employing Interaction Design Processes to Facilitate Collaborative Ontology Creation
Authors: Miller Eric , Seppa Christian , Kittur Aniket , Sabb Fred , Poldrack Russell
Published: June 2010

The Cognitive Atlas is a collaborative knowledge-building project that aims to develop an ontology that characterizes the current conceptual framework among researchers in cognitive science and neuroscience. The project objectives from the beginning focused on usability, simplicity, and utility for end users. Support for Semantic Web technologies was also a priority in order to support interoperability with other neuroscience projects and knowledge bases. Current off-the-shelf semantic web or semantic wiki technologies, however, do not often lend themselves to simple user interaction designs for non-technical researchers and practitioners; the abstract nature and complexity of these systems acts as point of friction for user interaction, inhibiting usability and utility. Instead, we take an alternate interaction design approach driven by user centered design processes rather than a base set of semantic technologies. This paper reviews the initial two rounds of design and development of the Cognitive Atlas system, including interactive design decisions and their implementation as guided by current industry practices for the development of complex interactive systems.
Theory and micromagnetics of pinning mechanism at cylindrical defects in perpendicular magnetic films
Authors: Punz D. , Lee J. , Fuger M. , Fidler J. , Schrefl T. , Suess D.
Published: June 2010

A theoretical model is developed to describe the pinning energy and the pinning field as a function of pore density, pore diameter and material parameters of a magnetic film. It is shown that the pinning energy and pinning field increases monotonically with increasing pore diameter. A magnetic storage concept is introduced which combines percolated media and graded media which allows to write on magnetic films with ultra high anisotropies.
The effect of plasma flow on line-tied magnetohydrodynamic modes
Authors: Arcudi Francesco , Delzanno Gian Luca , Finn John M.
Published: June 2010

The linear stability of a linear pinch to kink modes with line-tying boundary conditions and equilibrium axial flow is studied. Numerical results in visco-resistive magnetohydrodynamics show that for long plasmas, in which the line-tying stabilization effect is weak, plasma flow is stabilizing. For shorter plasmas, near the length at which line-tying stabilizes the mode for zero flow, the flow can be destabilizing. A simple model using reduced ideal magnetohydrodynamics with a step-function current density and an even simpler one-dimensional sound wave model with equilibrium flow elucidate these effects. It is concluded that: (1) The stabilization in long plasmas is due to convective stabilization; (2) the destabilization for short plasmas can be explained using a picture involving the coupling of two stable waves, one propagating in the forward direction and one in the backward direction; and (3) strong magnetic shear suppresses the flow destabilization for short plasmas.
Magnetic anisotropy and metal-insulator transition in SrRuO3 thin films at different growth temperatures
Authors: Wang X. W. , Wang X. , Zhang Y. Q. , Zhu Y. L. , Wang Z. J. , Zhang Z. D.
Published: June 2010

Magnetic and transport properties of SrRuO3 film grown on SrTiO3 at different substrate temperatures have been investigated. Metallic behavior over the temperature range from 5 to 300 K is observed in the film grown at 750 °C. With a decrease in the growth temperature, a metal-insulator transition occurs for films grown at 700 and 650 °C, with transition temperatures of 15 K and 250 K, respectively, and a complete insulator behavior shows up in the film grown at 600 °C. Correspondingly, out-of–plane (OOP) magnetic anisotropy is gradually weakened, leading to complete magnetic isotropy in the film grown at 600 °C. The OOP lattice constant increases from 0.395 nm, for the film grown at 750 °C, up to 0.403 nm for the film grown at 600 °C. The correlation between the magnetic properties, transport properties, and the lattice constants indicates that the magnetic anisotropy and the metal-insulator transition (or insulator behavior) are caused mainly by strain in the SRO films, with correspondingly larger strain in films grown at lower temperatures.
Study of stress distribution in a cleaved Si shallow trench isolation structure using confocal micro-Raman system
Authors: Tada Tetsuya , Poborchii Vladimir , Kanayama Toshihiko
Published: June 2010

We measured local stress distributions in a cleaved Si shallow trench isolation (STI) structure. We used a high-spatial-resolution confocal UV micro-Raman system with an excitation wavelength of 364 nm. The polarization dependence of Raman spectra enabled us to quantitatively estimate the stress direction and intensity on the (1¯10) cross-section. We observed stress relaxation due to the cleavage resulted in an abrupt change in the intensity and polarity of stress around the cross-sectional surface. Finite element method simulations reproduced well the measurement results and confirmed that this change was due to out-of-plane elastic deformation of the cleaved surface. This accurate comparison of the measurement data and the simulation is based on the feature that the UV Raman measurement selectively detects the surface regions, making this method particularly useful in stress distribution analyses.
Effects of Li content on the structural, optical, and electrical properties of LiZnMgO films
Authors: Tsai Chia-Lung , Wang Mu-Shan , Chen Ya-Hui , Chang Hsing-Cheng , Liu Chia-Jyi , Lee Ching-Ting , Shih Yu-Tai , Huang Hsueh-Jung , Lin Yow-Jon
Published: June 2010

This study investigates the effect of Li content on the structural, optical, and electrical properties of sol-gel LiZnMgO films by x-ray diffraction, scanning electron microscopy, photoluminescence, and conductivity measurements. A dependence of crystallite size and conduction type upon Li content has been found. The abnormal shift of the (002) diffraction peak position determined from x-ray diffraction measurements and conduction type determined by Hall effect measurements are closely related to the defects/different defect types. It is shown that n-type conversion of LiZnMgO films is a result of the increase in the donor density based on the change in stoichiometry.
Distributed feedback transistor laser
Authors: Dixon F. , Feng M. , Holonyak N.
Published: June 2010

Single longitudinal mode operation of an InGaP/GaAs/InGaAs quantum well heterojunction bipolar transistor laser is reported. A third order distributed feedback surface grating is fabricated in the top emitter AlGaAs confining layers using soft photocurable nanoimprint lithography. The device produces continuous wave laser operation with a peak wavelength λ=959.75 nm and threshold current IB=13 mA operating at −70 °C. For devices with cleaved ends a sidemode suppression ratio >25 dB has been achieved.
A statistical mechanical theory for a two-dimensional model of water
Authors: Urbic Tomaz , Dill Ken A.
Published: June 2010

We develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of the Truskett and Dill (TD) treatment of the “Mercedes-Benz” (MB) model. The present model gives better predictions than TD for hydrogen-bond populations in liquid water by distinguishing strong cooperative hydrogen bonds from weaker ones. We explore properties versus temperature T and pressure p. We find that the volumetric and thermal properties follow the same trends with T as real water and are in good general agreement with Monte Carlo simulations of MB water, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds for increasing temperature. The model reproduces that pressure squeezes out water’s heat capacity and leads to a negative thermal expansion coefficient at low temperatures. In terms of water structuring, the variance in hydrogen-bonding angles increases with both T and p, while the variance in water density increases with T but decreases with p. Hydrogen bonding is an energy storage mechanism that leads to water’s large heat capacity (for its size) and to the fragility in its cagelike structures, which are easily melted by temperature and pressure to a more van der Waals-like liquid state.
Structure and chemistry of the (111)Sc2O3/(0001) GaN epitaxial interface
Authors: Weng X. , Tian W. , Schlom D. G. , Dickey E. C.
Published: June 2010

The structure and chemistry of the (111)Sc2O3/(0001) GaN epitaxial interface grown by molecular-beam epitaxy have been investigated. High-resolution transmission electron microscopy reveals an abrupt Sc2O3/GaN interface with a hexagonal misfit dislocation network. These dislocations have Burgers vectors of (a/3)⟨112¯0⟩GaN and line directions parallel to ⟨11¯00⟩GaN, with an average spacing of ∼3.8 nm. Scanning transmission electron microscopy and electron energy loss spectrometry reveal the intermixing of Sc, O, and N over a region with a width of ∼1.5 nm at the interface.
A robust cell cycle control mechanism limits E2F-induced proliferation of terminally differentiated cells in vivo
Authors: Buttitta Laura A. , Katzaroff Alexia J. , Edgar Bruce A.
Published: June 2010

Terminally differentiated cells in Drosophila melanogaster wings and eyes are largely resistant to proliferation upon deregulation of either E2F or cyclin E (CycE), but exogenous expression of both factors together can bypass cell cycle exit. In this study, we show this is the result of cooperation of cell cycle control mechanisms that limit E2F-CycE positive feedback and prevent cycling after terminal differentiation. Aberrant CycE activity after differentiation leads to the degradation of E2F activator complexes, which increases the proportion of CycE-resistant E2F repressor complexes, resulting in stable E2F target gene repression. If E2F-dependent repression is lost after differentiation, high anaphase-promoting complex/cyclosome (APC/C) activity degrades key E2F targets to limit cell cycle reentry. Providing both CycE and E2F activities bypasses exit by simultaneously inhibiting the APC/C and inducing a group of E2F target genes essential for cell cycle reentry after differentiation. These mechanisms are essential for proper development, as evading them leads to tissue outgrowths composed of dividing but terminally differentiated cells.
MAPK signaling to the early secretory pathway revealed by kinase/phosphatase functional screening
Authors: Farhan Hesso , Wendeler Markus W. , Mitrovic Sandra , Fava Eugenio , Silberberg Yael , Sharan Roded , Zerial Marino , Hauri Hans-Peter
Published: June 2010

To what extent the secretory pathway is regulated by cellular signaling is unknown. In this study, we used RNA interference to explore the function of human kinases and phosphatases in controlling the organization of and trafficking within the secretory pathway. We identified 122 kinases/phosphatases that affect endoplasmic reticulum (ER) export, ER exit sites (ERESs), and/or the Golgi apparatus. Numerous kinases/phosphatases regulate the number of ERESs and ER to Golgi protein trafficking. Among the pathways identified, the Raf–MEK (MAPK/ERK [extracellular signal-regulated kinase] kinase)–ERK cascade, including its regulatory proteins CNK1 (connector enhancer of the kinase suppressor of Ras-1) and neurofibromin, controls the number of ERESs via ERK2, which targets Sec16, a key regulator of ERESs and COPII (coat protein II) vesicle biogenesis. Our analysis reveals an unanticipated complexity of kinase/phosphatase-mediated regulation of the secretory pathway, uncovering a link between growth factor signaling and ER export.
Simulation modelling as a tool for examining the consequences of spatial structure and connectivity on local and regional population dynamics
Authors: Kerr Lisa A. , Cadrin Steven X. , Secor Dave H.
Published: June 2010

Kerr, L. A., Cadrin, S. X., and Secor, D. H. 2010. Simulation modelling as a tool for examining the consequences of spatial structure and connectivity on local and regional population dynamics. – ICES Journal of Marine Science, 67: 1631–1639. An understanding of the mechanisms underlying population persistence makes fisheries management more effective. A model framework is described, which can test hypotheses about spatial structure and connectivity within and between populations and their influence on the productivity (spawning-stock biomass, SSB), stability (variation in SSB), resilience (time to rebuild SSB after environmental disturbance), and sustainability (maximum sustainable fishing mortality and yield) of systems. The general model consists of linked age-structured submodels that incorporate the unique demographics and dynamics of population components, along with the degree and type of connectivity between them. The flexibility of this framework is illustrated with three case studies examining (i) spatial structure within a population of white perch, (ii) different types and degrees of connectivity between populations of Atlantic herring, and (iii) spatial heterogeneity and connectivity within a stock of Atlantic cod. System variance is reduced by abundant, stable population components, and the asynchronous responses of those components. Components with high productivity contributed disproportionately to the resilience of systems. Increased synchrony of component responses to environmental forcing decreased the stability of the overall system. Simulation modelling is a useful approach to evaluate the consequences of spatial structure and connectivity, and can be used to understand better the productivity and dynamics of local and regional populations.
Retrospective growth analysis of Atlantic salmon Salmo salar and implications for abundance trends
Authors: Hogan F. , Friedland K. D.
Published: June 2010

Scale archives of Atlantic salmon Salmo salar from Maine, U.S.A., were examined to determine whether ocean conditions affected the long‐term trends in S. salar populations in the southern tier of the species' range in North America. To date, scale analyses of southern tier populations have been limited to hatchery fish; previous studies suggest that post‐smolt growth does not influence recruitment, with the exception that winter growth may play a role in stock maturation rate. A time series of scales from the Machias and Narraguagus Rivers spanning the years 1946 to 1999 was analysed. Image analysis was used to measure intercirculi spacing, which provided proxy variables of growth rate. Post‐smolt growth increment has increased since the early 1990s, as returns have decreased, suggesting that survival factors act on post‐smolts independent of growth. The data support the hypothesis of a decoupling between freshwater size and early marine growth. Growth during the second sea winter was independent of post‐smolt growth, suggesting that individuals are capable of significant compensatory growth. Southern tier North American stocks exhibit a similar pattern of independence between growth and survival as observed for northern tier North American stocks. These data support the inference that the recruitment of the North American and European subspecies is governed by fundamentally different mechanisms.
Gene expression profiling and network analysis of peripheral blood monocytes in a chronic model of allergic asthma
Authors: Dorsam Glenn P. , Hoselton Scott A. , Sandy Ashley R. , Samarasinghe Amali E. , Vomhof‐DeKrey Emilie E. , Dorsam Sheri T. , Schuh Jane M.
Published: June 2010

The Aspergillus fumigatus mouse model of asthma mimics the characteristics of human fungal asthma, including local and systemic inflammation. Monocyte/macrophage lineage cells direct innate immune responses and guide adaptive responses. To identify gene expression changes in peripheral blood monocytes in the context of fungal allergy, mice were exposed to systemic and intranasal inoculations of fungal antigen (sensitized), and naïve and sensitized animals were challenged intratracheally with live A. fumigatus conidia. Microarray analysis of blood monocytes from allergic versus non‐allergic mice showed ≥ twofold modulation of 45 genes. Ingenuity pathway analysis revealed a network of these genes involved in antigen presentation, inflammation, and immune cell trafficking. These data show that allergen sensitization and challenge affects gene expression in peripheral monocytes.
Interleukin‐8 induction due to diffusely adherent Escherichia coli possessing Afa/Dr genes depends on flagella and epithelial Toll‐like receptor 5
Authors: Arikawa Kentaro , Nishikawa Yoshikazu
Published: June 2010

DAEC is considered potentially diarrheagenic. For diffuse adhesion, the role of the Afa, which was originally identified as a uropathogenic factor, is now understood. However, the role of DAEC in diarrheal disease remains controversial because DAEC is often isolated not only from patients but also from healthy individuals. Previously, we suggested that Afa/Dr DAEC, which can induce high levels of IL‐8 secretion in cultures of human carcinoma epithelial cells (HEp‐2, Caco‐2), is enterovirulent. In the present study, we examined whether IL‐8 secretion induced by certain Afa/Dr DAEC strains was primarily due to flagella via TLR5. All IL‐8 high‐inducing strains were highly motile in swarming tests. Partially purified flagella induced IL‐8 in a dose‐dependent manner. However, IL‐8 induction was inhibited by small‐interfering RNA against TLR5 or by treating flagella with disialoganglioside‐GD1a, a TLR5 blocker. TLR5 is reportedly located on the basolateral side of intestinal epithelia; flagella should not have reached TLR5 from the apical side beyond tight junctions. Reduction in the number of intracellular organisms by wortmannin, a PI3K inhibitor, did not reduce IL‐8 secretion. Afa/Dr DAEC seemed to loosen the tight junctions because it quickly reduced transepithelial electrical resistance after infection. Decreased resistance led to increased IL‐8 production. In conclusion, diffuse adhesion itself is insufficient to induce high levels of IL‐8, and simultaneous stimulation by flagella via TLR5 is likely required for additional induction. Clinically, high motility may be a candidate criterion for predicting the ability of Afa/Dr DAEC strains to induce higher levels of IL‐8 secretion.