bluuebunny/crossref_metadata_2025 huggingface dataset:
Helminth parasite communities of allopatric populations of the frog Leptodactylus podicipinus from Pantanal, Brazil
Authors: Campião K.M. , da Silva R.J. , Ferreira V.L.
Published: October 2012

Several factors may influence the structure of parasite communities in amphibian hosts. In this study, we describe the helminth parasites of three allopatric populations of the frog Leptodactylus podicipinus and test whether host size and sex were determinants of the structure and composition of the helminth communities. One hundred and twenty-three anurans were collected from three different study sites within the Pantanal wetlands and surveyed for helminth parasites. We found 14 helminth taxa: 7 species of nematodes, 4 species of trematodes, 1 species of cestodes, 1 species of acanthocephalan and one unidentified cyst. Host sex and size did not cause significant differences in helminth abundance or richness. The structure of helminth communities from the three study sites varied in terms of species composition, abundance and diversity. Six out of 14 helminth taxa were found in the three localities. Among those, the nematodes Cosmocerca podicipinus and Rhabdias sp., the trematode Catadiscus propinquus and the helminth cyst showed significant differences in mean abundances. We suggest that such differences found among the three component communities are driven by biotic and abiotic factors operating locally. Moreover, these differences stress the importance of local conditions, such as hydrologic characteristics and landscape composition, on helminth community structure.
A Novel Analytical Framework for Dynamic Quaternion Ship Domains
Authors: Wang Ning
Published: October 2012

In this paper, a novel analytical framework for Dynamic Quaternion Ship Domain (DQSD) models has been initially proposed via the Quaternion Ship Domain (QSD) model structure. Unlike previous ship domains, the proposed DQSD model is able to capture essential subjectivity and objectivity of ship domains. To be specific, the significant characteristics are as follows:

(1)

The proposed DQSD model is integrated by three independent submodels of ship, human and circumstance, which are determined by ship manoeuvrability, navigator's states, and navigation circumstance, respectively.

(2)

The ship manoeuvrability derived from the MMG-type ship motion model is employed to establish the ship submodel which identifies the DQSD scale.

(3)

A novel navigator reliability model is proposed to realize the human submodel which defines the ship domain shape with navigator ability, physical and mental states being input variables.

(4)

In addition, visibility, wind force, wave and traffic congestion are incorporated into the circumstance submodel which is employed to zoom in or out of the DQSD-type ship domain.

Finally, the well-known Esso Osaka tanker model is used to conduct simulation studies on various typical stationary and dynamic situations, and comparative investigations with each other have been comprehensively analysed. Simulation results demonstrate that the DQSD model can capture critical dynamics of ship domains and undoubtedly be effective and superior to previous ship domains in terms of performance and accuracy.
Chronic Postconcussion Symptoms and Functional Outcomes in OEF/OIF Veterans with Self-Report of Blast Exposure
Authors: Verfaellie Mieke , Lafleche Ginette , Spiro Avron , Tun Carlos , Bousquet Kathryn
Published: October 2012

Postconcussion symptoms (PCS) and functional outcomes were evaluated in 91 OEF/OIF outpatient veterans with reported histories of blast-exposure, with the goal of evaluating (1) the association between these outcomes and a clinical diagnosis of mild traumatic brain injury (mTBI) with or without loss of consciousness (LOC); and (2) the influence of post-traumatic stress disorder (PTSD) and depression on PCS reporting and perceived functional limitations. Individuals who reported mTBI with LOC had greater PCS complaints than individuals who reported mTBI without LOC or individuals without mTBI. However, after adjusting for severity of PTSD and depression symptoms, this group difference disappeared. Functional limitations were particularly prominent in the psychosocial domain. Again, PTSD was significantly associated with functional outcomes, but the mTBI with LOC group had greater psychosocial limitations than the other two groups, even when PTSD and depression symptoms were taken into account. These findings highlight the role of mental health in both outcomes, but additionally point to the impact of mTBI with LOC on long-term psychosocial adjustment. (JINS, 2013, 19, 1–10)
Egocentric and Allocentric Spatial Representations in Williams Syndrome
Authors: Bernardino Inês , Mouga Susana , Castelo-Branco Miguel , van Asselen Marieke
Published: October 2012

Williams syndrome (WS) is a neurodevelopmental disorder characterized by severe visuospatial deficits, particularly affecting spatial navigation and wayfinding. Creating egocentric (viewer-dependent) and allocentric (viewer-independent) representations of space is essential for the development of these abilities. However, it remains unclear whether egocentric and allocentric representations are impaired in WS. In this study, we investigate egocentric and allocentric frames of reference in this disorder. A WS group (n = 18), as well as a chronological age-matched control group (n = 20), a non-verbal mental age-matched control group (n = 20) and a control group with intellectual disability (n = 17), was tested with a computerized and a 3D spatial judgment task. The results showed that WS participants are impaired when performing both egocentric and allocentric spatial judgments even when compared with mental age-matched control participants. This indicates that a substantial deficit affecting both spatial representations is present in WS. The egocentric impairment is in line with the dorsal visual pathway deficit previously reported in WS. Interestingly, the difficulties found in performing allocentric spatial judgments give important cues to better understand the ventral visual functioning in WS. (JINS, 2013, 19, 1–9)
Disassembling Glancing Angle Deposited Films for High-Throughput, Single-Post Growth Scaling Measurements
Authors: Siewert Joshua Morgan Arthur , LaForge Joshua Michael , Taschuk Michael Thomas , Brett Michael Julian
Published: October 2012

With growing interest in nanostructured thin films produced by glancing angle deposition (GLAD), it becomes increasingly important to understand their overall growth mechanics and nanocolumn structure. We present a new method of isolating the individual nanocolumns of GLAD films, facilitating automated measurement of their broadening profiles. Data collected for α = 81° TiO2 vertical nanocolumns deposited across a range of substrate rotation rates demonstrates that these rates influence growth scaling parameters. Further, individual posts were found in each case that violate predicted Kardar-Parisi-Zhang growth scaling limits. The technique's current iteration is comparable to existing techniques in speed: though data were studied from 10,756 individual objects, the majority could not be confidently used in subsequent analysis. Further refinement may allow high-throughput automated film characterization and permit close examination of subtle growth trends, potentially enhancing control over GLAD film broadening and morphology.
Atom Probe Tomography Simulations and Density Functional Theory Calculations of Bonding Energies in Cu3Au
Authors: Boll Torben , Zhu Zhi-Yong , Al-Kassab Talaat , Schwingenschlögl Udo
Published: October 2012

In this article the Cu-Au binding energy in Cu3Au is determined by comparing experimental atom probe tomography (APT) results to simulations. The resulting bonding energy is supported by density functional theory calculations. The APT simulations are based on the Müller-Schottky equation, which is modified to include different atomic neighborhoods and their characteristic bonds. The local environment is considered up to the fifth next nearest neighbors. To compare the experimental with simulated APT data, the AtomVicinity algorithm, which provides statistical information about the positions of the neighboring atoms, is applied. The quality of this information is influenced by the field evaporation behavior of the different species, which is connected to the bonding energies.
Micro Energy-Dispersive X-Ray Fluoresence Mapping of Enamel and Dental Materials after Chemical Erosion
Authors: Soares Luís Eduardo Silva , de Oliveira Rodrigo , Nahórny Sídnei , Santo Ana Maria do Espírito , Martin Airton Abrahão
Published: October 2012

Energy-dispersive X-ray fluorescence was employed to test the hypothesis that beverage consumption or mouthwash utilization will change the chemical properties of dental materials and enamel mineral content. Bovine enamel samples (n= 45) each received two cavity preparations (n= 90), each pair filled with one of three dental materials (R: nanofilled composite resin; GIC: glass-ionomer cement; RMGIC: resin-modified GIC). Furthermore, they were treated with three different solutions (S: saliva; E: erosion/Pepsi Twist®; or EM: erosion+mouthwash/Colgate Plax®). It was found that mineral loss in enamel was greater in GICE samples than in RE > RMGICE > RMGICEM > REM > GICEM. An increased percentage of Zr was found in REM indicating organic matrix degradation. Dental materials tested (R, GIC, and RMGIC) were not able to protect adjacent enamel from acid erosion by the soft drink tested. The use of mouthwash promoted protection of enamel after erosion by the soft drink. To avoid chemical dissolution by mouthwashes, protection by resin composites with surface sealants is recommended.
Pulsatory andesite lava flow at Bagana Volcano
Authors: Wadge G. , Saunders S. , Itikarai I.
Published: October 2012

Using a time series of TerraSAR‐X spaceborne radar images we have measured the pulsatory motion of an andesite lava flow over a 14‐month period at Bagana Volcano, Papua New Guinea. Between October 2010 and December 2011, lava flowed continuously down the western flank of the volcano forming a 3 km‐long blocky lava flow with a channel, levees, overflows and branches. We captured four successive pulses of lava advancing down the channel system, the first such behavior of an andesite flow to be recorded using radar. Each pulse had a volume of the order of 107 m3 emplaced over many weeks. The average extrusion rate estimated from the radar data was 0.92 ± 0.35 m3 s−1, and varied between 0.3 and 1.8 m3 s−1, with higher rates occurring earlier in each pulse. This, together with observations of sulphur dioxide emissions, explosions and incandescence suggest a variable supply rate of magma through Bagana's conduit as the most likely source of the pulsatory behavior.
Crust and upper mantle structure beneath the Pacific Northwest from joint inversions of ambient noise and earthquake data
Authors: Wagner Lara S. , Fouch Matthew J. , James David E. , Hanson‐Hedgecock Sara
Published: October 2012

We perform a joint inversion of phase velocities from both earthquake and ambient noise induced Rayleigh waves to determine shear wave velocity structure in the crust and upper mantle beneath the Pacific Northwest. We focus particularly on the areas affected by mid‐Miocene to present volcanic activity. The joint inversion, combined with the high density seismic network of the High Lava Plains seismic experiment and data from the EarthScope Transportable Array, provides outstanding resolution for this area. In Oregon, we find that the pattern of low velocities in the crust and uppermost mantle varies between the High Lava Plains physiographic province and the adjacent northwestern Basin and Range. These patterns may be due to the presence of the Brothers Fault Zone which separates the clockwise rotating northwest Basin and Range from the relatively undeformed areas further north. Further to the east, the Owyhee Plateau, Snake River Plain (SRP) and northeastern Basin and Range are characterized by high crustal velocities, though the depth extent of these fast wave speeds varies by province. Of particular interest is the mid‐crustal high velocity sill, previously only identified within the SRP. We show this anomaly extends significantly further south into Utah and Nevada. We suggest that one possible explanation is lateral crustal extrusion due to the emplacement of the high density mafic mid‐crustal sill structures within the SRP.
The Ionian Sea: The oldest in situ ocean fragment of the world?
Authors: Speranza Fabio , Minelli Liliana , Pignatelli Alessandro , Chiappini Massimo
Published: October 2012

It is well known that the Ionian Sea is characterized by thin (8–11 km) crystalline crust, thick (5–7 km) sedimentary cover, and low heat flow, typical for a Mesozoic (at least) basin. Yet seismic data have not yielded univocal interpretations, and a debate has developed on the oceanic versus “thinned continental” nature of the Ionian basin. Here we analyze the magnetic anomaly pattern of the Ionian Sea and compare it to synthetic fields produced by a geopotential field generator, considering realistic crust geometry. The Ionian basin is mostly characterized by slightly negative magnetic residuals and by a prominent positive (150 nT at sea level) “B” anomaly at the northwestern basin margin. We first test continental crust models, considering a homogeneous crystalline crust with K = 1 × 10−3, then a 5 km thick deep crustal layer of serpentinite (K = 1 × 10−1). The first model yields insignificant anomalies, while the second gives an anomaly pattern anticorrelated with the observed residuals. We subsequently test oceanic crust models, considering a 2 km thick 2A basaltic layer with K = 5 × 10−3, magnetic remanence of 5 A/m, and a unique magnetic polarity (no typical oceanic magnetic anomaly stripes are apparent in the observed data set). Magnetic remanence directions were derived from Pangean‐African paleopoles in the 290–190 Ma age window. Only reverse polarity models reproduce the B anomaly, and among them the 220–230 Ma models best approximate magnetic features observed on the abyssal plain and at the western basin boundary. The Ionian Sea turns out to be the oldest preserved oceanic floor known so far.
Influence of atmospheric intraseasonal oscillations on seasonal and interannual variability in the upper Indian Ocean
Authors: Duncan Benét , Han Weiqing
Published: October 2012

An ocean general circulation model, the Hybrid Coordinate Ocean Model (HYCOM), is used to examine the rectification of atmospheric intraseasonal oscillations (ISOs) on the mean and seasonal‐to‐interannual sea surface temperature (SST), mixed layer thickness (hm) and upper ocean heat content in the Indian Ocean. Existing studies have shown that ISOs rectify on seasonal and interannual equatorial surface currents and on cross‐equatorial transport, suggesting that they may also have important impacts on upper ocean variability. To evaluate these impacts, a hierarchy of HYCOM experiments isolates the ocean response to forcing by atmospheric ISO events. Other experiments isolate the ocean response to a range of intraseasonal forcing fields including shortwave radiation, precipitation, and winds. Results indicate that rectification of ISOs onto seasonal and interannual upper ocean variability does occur, and that it is important in some regions. The regions displaying maximum rectification vary between SST, hm, and upper ocean heat content, and from seasonal to interannual timescales. Strong seasonal SST rectification occurs in the Arabian Sea and in the Bay of Bengal. Because SSTs in the Arabian Sea are already warm (28°C), the ISO‐forced seasonal cycle peak of 0.6°C in May can affect convection there. Intraseasonal wind speed and stress have a much larger impact on seasonal and interannual SST, hm, and upper ocean heat content than either intraseasonal shortwave radiation or precipitation. The relative importance of entrainment and turbulent heat flux due to intraseasonal wind speed, and of upwelling, horizontal advection, and vertical mixing due to intraseasonal wind stress, varies with region.
Inferring ice formation processes from global‐scale black carbon profiles observed in the remote atmosphere and model simulations
Authors: Fan S.‐M. , Schwarz J. P. , Liu J. , Fahey D. W. , Ginoux P. , Horowitz L. W. , Levy H. , Ming Y. , Spackman J. R.
Published: October 2012

Black carbon (BC) aerosol absorbs solar radiation and can act as cloud condensation nucleus and ice formation nucleus. The current generation of climate models have difficulty in accurately predicting global‐scale BC concentrations. Previously, an ensemble of such models was compared to measurements, revealing model biases in the tropical troposphere and in the polar troposphere. Here global aerosol distributions are simulated using different parameterizations of wet removal, and model results are compared to BC profiles observed in the remote atmosphere to explore the possible sources of these biases. The model‐data comparison suggests a slow removal of BC aerosol during transport to the Arctic in winter and spring, because ice crystal growth causes evaporation of liquid cloud via the Bergeron process and, hence, release of BC aerosol back to ambient air. By contrast, more efficient model wet removal is needed in the cold upper troposphere over the tropical Pacific. Parcel model simulations with detailed droplet and ice nucleation and growth processes suggest that ice formation in this region may be suppressed due to a lack of ice nuclei (mainly insoluble dust particles) in the remote atmosphere, allowing liquid and mixed‐phase clouds to persist under freezing temperatures, and forming liquid precipitation capable of removing aerosol incorporated in cloud water. Falling ice crystals can scavenge droplets in lower clouds, which also results in efficient removal of cloud condensation nuclei. The combination of models with global‐scale BC measurements in this study has provided new, latitude‐dependent information on ice formation processes in the atmosphere, and highlights the importance of a consistent treatment of aerosol and moist physics in climate models.
Life cycle of midlatitude deep convective systems in a Lagrangian framework
Authors: Feng Zhe , Dong Xiquan , Xi Baike , McFarlane Sally A. , Kennedy Aaron , Lin Bing , Minnis Patrick
Published: October 2012

Deep convective systems (DCSs) consist of intense convective cores (CC), large stratiform rain (SR) regions, and extensive nonprecipitating anvil clouds (AC). This study focuses on the evolution of these three components and the factors that affect system lifetime and AC production. An automated satellite tracking method is used in conjunction with a recently developed multisensor hybrid classification to analyze the evolution of DCS structure in a Lagrangian framework over the central United States. Composite analysis from 4221 tracked DCSs during two warm seasons (May–August, 2010–2011) shows that maximum system size correlates with lifetime, and longer‐lived DCSs have more extensive SR and AC. For short to medium systems (lifetimes <6 h), the lifetime is mainly attributed to the intensity of the initial convection. Systems that last longer than 6 h are associated with up to 50% higher midtropospheric relative humidity and up to 40% stronger middle to upper tropospheric wind shear. Such environments allow continuous growth of detrained hydrometeors by deposition, supporting further development of the SR and AC region, as indicated by the increased staggered timing between stratiform clouds and peak convective intensity, thus prolonging the system lifetime beyond 6 h. Regression analysis shows that the areal coverage of thick AC is strongly correlated with the size of CC, updraft strength, and SR area. Ambient upper tropospheric wind speed and wind shear also play an important role for convective AC production, where for systems with large AC (radius >120 km) they are 24% and 20% higher, respectively, than those with small AC (radius = 20 km).
Simulating the thermochemical magmatic and tectonic evolution of Venus's mantle and lithosphere: Two‐dimensional models
Authors: Armann Marina , Tackley Paul J.
Published: October 2012

Numerical convection models of the thermochemical evolution of Venus are compared to present‐day topography and geoid and recent resurfacing history. The models include melting, magmatism, decaying heat‐producing elements, core cooling, realistic temperature‐dependent viscosity and either stagnant lid or episodic lithospheric overturn. In stagnant lid convection the dominant mode of heat loss is magmatic heat pipe, which requires massive magmatism and produces very thick crust, inconsistent with observations. Partitioning of heat‐producing elements into the crust helps but does not help enough. Episodic lid overturn interspersed by periods of quiescence effectively loses Venus's heat while giving lower rates of volcanism and a thinner crust. Calculations predict 5–8 overturn events over Venus's history, each lasting ∼150 Myr, initiating in one place and then spreading globally. During quiescent periods convection keeps the lithosphere thin. Magmatism keeps the mantle temperature ∼constant over Venus's history. Crustal recycling occurs by entrainment in stagnant lid convection, and by lid overturn in episodic mode. Venus‐like amplitudes of topography and geoid can be produced in either stagnant or episodic modes, with a viscosity profile that is Earth‐like but shifted to higher values. The basalt density inversion below the olivine‐perovskite transition causes compositional stratification around 730 km; breakdown of this layering increases episodicity but far less than episodic lid overturn. The classical stagnant lid mode with interior temperature ∼rheological temperature scale lower than TCMBis not reached because mantle temperature is controlled by magmatism while the core cools slowly from a superheated start. Core heat flow decreases with time, possibly shutting off the dynamo, particularly in episodic cases.
Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network
Authors: Pérez-Gutiérrez Rocío-Anaís , López-Ramírez Varinia , Islas África , Alcaraz Luis David , Hernández-González Ismael , Olivera Beatriz Carely Luna , Santillán Moisés , Eguiarte Luis E , Souza Valeria , Travisano Michael , Olmedo-Alvarez Gabriela
Published: October 2012

Understanding the principles that govern community assemblages is a central goal of ecology. There is limited experimental evidence in natural settings showing that microbial assembly in communities are influenced by antagonistic interactions. We, therefore, analyzed antagonism among bacterial isolates from a taxonomically related bacterial guild obtained from five sites in sediments from a fresh water system. We hypothesized that if antagonistic interactions acted as a shaping force of the community assembly, then the frequency of resistance to antagonism among bacterial isolates originating from a given site would be higher than the resistance to conspecifics originating from a different assemblage. Antagonism assays were conducted between 78 thermoresistant isolates, of which 72 were Bacillus spp. Sensitive, resistant and antagonistic isolates co-occurred at each site, but the within-site frequency of resistance observed was higher than that observed when assessed across-sites. We found that antagonism results from bacteriocin-like substances aimed at the exclusion of conspecifics. More than 6000 interactions were scored and described by a directed network with hierarchical structure that exhibited properties that resembled a food chain, where the different Bacillus taxonomic groups occupied specific positions. For some tested interacting pairs, the unidirectional interaction could be explained by competition that inhibited growth or completely excluded one of the pair members. This is the first report on the prevalence and specificity of Bacillus interactions in a natural setting and provides evidence for the influence of bacterial antagonist interactions in the assemblage of a taxonomically related guild in local communities.
Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium
Authors: Carini Paul , Steindler Laura , Beszteri Sara , Giovannoni Stephen J
Published: October 2012

Chemoheterotrophic marine bacteria of the SAR11 clade are Earth’s most abundant organisms. Following the first cultivation of a SAR11 bacterium, ‘Candidatus Pelagibacter ubique’ strain HTCC1062 (Ca. P. ubique) in 2002, unusual nutritional requirements were identified for reduced sulfur compounds and glycine or serine. These requirements were linked to genome streamlining resulting from selection for efficient resource utilization in nutrient-limited ocean habitats. Here we report the first successful cultivation of Ca. P. ubique on a defined artificial seawater medium (AMS1), and an additional requirement for pyruvate or pyruvate precursors. Optimal growth was observed with the collective addition of inorganic macro- and micronutrients, vitamins, methionine, glycine and pyruvate. Methionine served as the sole sulfur source but methionine and glycine were not sufficient to support growth. Optimal cell yields were obtained when the stoichiometry between glycine and pyruvate was 1:4, and incomplete cell division was observed in cultures starved for pyruvate. Glucose and oxaloacetate could fully replace pyruvate, but not acetate, taurine or a variety of tricarboxylic acid cycle intermediates. Moreover, both glycine betaine and serine could substitute for glycine. Interestingly, glycolate partially restored growth in the absence of glycine. We propose that this is the result of the use of glycolate, a product of phytoplankton metabolism, as both a carbon source for respiration and as a precursor to glycine. These findings are important because they provide support for the hypothesis that some micro-organisms are challenging to cultivate because of unusual nutrient requirements caused by streamlining selection and gene loss. Our findings also illustrate unusual metabolic rearrangements that adapt these cells to extreme oligotrophy, and underscore the challenge of reconstructing metabolism from genome sequences in organisms that have non-canonical metabolic pathways.
Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes
Authors: Yanagawa Katsunori , Morono Yuki , de Beer Dirk , Haeckel Matthias , Sunamura Michinari , Futagami Taiki , Hoshino Tatsuhiko , Terada Takeshi , Nakamura Ko-ichi , Urabe Tetsuro , Rehder Gregor , Boetius Antje , Inagaki Fumio
Published: October 2012

Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13–30 cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 3–9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community.
Comparable light stimulation of organic nutrient uptake by SAR11 and Prochlorococcus in the North Atlantic subtropical gyre
Authors: Gómez-Pereira Paola R , Hartmann Manuela , Grob Carolina , Tarran Glen A , Martin Adrian P , Fuchs Bernhard M , Scanlan David J , Zubkov Mikhail V
Published: October 2012

Subtropical oceanic gyres are the most extensive biomes on Earth where SAR11 and Prochlorococcus bacterioplankton numerically dominate the surface waters depleted in inorganic macronutrients as well as in dissolved organic matter. In such nutrient poor conditions bacterioplankton could become photoheterotrophic, that is, potentially enhance uptake of scarce organic molecules using the available solar radiation to energise appropriate transport systems. Here, we assessed the photoheterotrophy of the key microbial taxa in the North Atlantic oligotrophic gyre and adjacent regions using 33P-ATP, 3H-ATP and 35S-methionine tracers. Light-stimulated uptake of these substrates was assessed in two dominant bacterioplankton groups discriminated by flow cytometric sorting of tracer-labelled cells and identified using catalysed reporter deposition fluorescence in situ hybridisation. One group of cells, encompassing 48% of all bacterioplankton, were identified as members of the SAR11 clade, whereas the other group (24% of all bacterioplankton) was Prochlorococcus. When exposed to light, SAR11 cells took 31% more ATP and 32% more methionine, whereas the Prochlorococcus cells took 33% more ATP and 34% more methionine. Other bacterioplankton did not demonstrate light stimulation. Thus, the SAR11 and Prochlorococcus groups, with distinctly different light-harvesting mechanisms, used light equally to enhance, by approximately one-third, the uptake of different types of organic molecules. Our findings indicate the significance of light-driven uptake of essential organic nutrients by the dominant bacterioplankton groups in the surface waters of one of the less productive, vast regions of the world’s oceans—the oligotrophic North Atlantic subtropical gyre.
The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale
Authors: Hazard Christina , Gosling Paul , van der Gast Christopher J , Mitchell Derek T , Doohan Fiona M , Bending Gary D
Published: October 2012

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis (‘everything is everywhere, but, the environment selects’) was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.
Optimisation of biphenyl acetic acid inhibitors of diacylglycerol acetyl transferase 1 – the discovery of AZD2353
Authors: Waring Michael J. , Birch Alan M. , Birtles Susan , Buckett Linda K. , Butlin Roger J. , Campbell Leonie , Gutierrez Pablo Morentin , Kemmitt Paul D. , Leach Andrew G. , MacFaul Philip A. , O'Donnell Charles , Turnbull Andrew V.
Published: October 2012

Focus on ligand efficiency, ligand lipophilicity efficiency, and conformational restriction led to the discovery of AZD2353.
Investigations on the oxygen dependence of a 2-oxoglutarate histone demethylase
Authors: Sánchez-Fernández Elena M. , Tarhonskaya Hanna , Al-Qahtani Khalid , Hopkinson Richard J. , McCullagh James S. O. , Schofield Christopher J. , Flashman Emily
Published: October 2012

Histone Nϵ-methyl lysine demethylases are important in epigenetic regulation. KDM4E (histone lysine demethylase 4E) is a representative member of the large Fe(II)/2-oxoglutarate- dependent family of human histone demethylases. In the present study we report kinetic studies on the reaction of KDM4E with O2. Steady-state assays showed that KDM4E has a graded response to O2 over a physiologically relevant range of O2 concentrations. Pre-steady state assays implied that KDM4E reacts slowly with O2 and that there are variations in the reaction kinetics which are dependent on the methylation status of the substrate. The results demonstrate the potential for histone demethylase activity to be regulated by oxygen availability.
Acute regulation of 5′-AMP-activated protein kinase by long-chain fatty acid, glucose and insulin in rat primary adipocytes
Authors: Hebbachi Abdel , Saggerson David
Published: October 2012

Palmitate increased AMPK (5′-AMP-activated protein kinase) activity, glucose utilization and 2-DOG (2-deoxyglucose) transport in rat adipocytes. All three effects were blocked by the AMPK inhibitor Compound C, leading to the conclusion that in response to an increase in long-chain NEFA (non-esterified fatty acid) concentration AMPK mediated an enhancement of adipocyte glucose transport, thereby providing increased glycerol 3-phosphate for FA (fatty acid) esterification to TAG (triacylglycerol). Activation of AMPK in response to palmitate was not due to an increase in the adipocyte AMP:ATP ratio. Glucose decreased AMPK activity and effects of palmitate and glucose on AMPK activity were antagonistic. While insulin had no effect on basal AMPK activity insulin did decrease AMPK activity in the presence of palmitate and also decreased the percentage effectiveness of palmitate to increase the transport of 2-DOG. It is suggested that activation of adipocyte AMPK by NEFA, as well as decreasing the activity of hormone-sensitive lipase, could modulate adipose tissue dynamics by increasing FA esterification and, under certain circumstances, FA synthesis.
From large-scale to small-scale dynamos in a spherical shell
Authors: Richardson K. J. , Hollerbach R. , Proctor M. R. E.
Published: October 2012

Kinematic dynamo action in a spherical shell is studied with a small-scale cellular prescribed velocity field. Three velocity fields are considered, all of which are axisymmetric and have a large-scale separation between the shell size and the dominant scale of the motion. The first flow is steady and strongly helical, so that a mean field dynamo might be expected. We find that indeed large-scale dynamo action is obtained at onset, but that the dynamo is of small-scale type at large magnetic Reynolds number Rm, where advection processes dominate and the magnetic field is generated on the scale of the cells in the flow. We study the transition between these two dynamo processes and find a gradual transition as Rm is increased, where the energy is slowly passed from the large scales to the small scales as the two dynamo processes morph into one another. The second flow, a time-dependent version of the first, produces almost identical results, but the transition appears to occur at smaller Rm than in the steady case and there is some evidence of fast dynamo action as Rm becomes large. The third flow, a nonhelical variant of the first flow, is also studied, and small-scale dynamo action was found at onset in this case, with a much larger critical value of Rm for growth of the magnetic field.
Symmetry-adapted perturbation theory based on unrestricted Kohn-Sham orbitals for high-spin open-shell van der Waals complexes
Authors: Hapka Michał , Żuchowski Piotr S. , Szczęśniak Małgorzata M. , Chałasiński Grzegorz
Published: October 2012

Two open-shell formulations of the symmetry-adapted perturbation theory are presented. They are based on the spin-unrestricted Kohn-Sham (SAPT(UKS)) and unrestricted Hartree-Fock (SAPT(UHF)) descriptions of the monomers, respectively. The key reason behind development of SAPT(UKS) is that it is more compatible with density functional theory (DFT) compared to the previous formulation of open-shell SAPT based on spin-restricted Kohn-Sham method of Żuchowski et al. [J. Chem. Phys. 129, 084101 (2008)10.1063/1.2968556]. The performance of SAPT(UKS) and SAPT(UHF) is tested for the following open-shell van der Waals complexes: He⋯NH, H2O⋯HO2, He⋯OH, Ar⋯OH, Ar⋯NO. The results show an excellent agreement between SAPT(UKS) and SAPT(ROKS). Furthermore, for the first time SAPT based on DFT is shown to be suitable for the treatment of interactions involving Π-state radicals (He⋯OH, Ar⋯OH, Ar⋯NO). In the interactions of transition metal dimers ($^3\Sigma _u^+$Σu+3)Au2 and ($^{13}\Sigma _g^+$Σg+13)Cr2 we show that SAPT is incompatible with the use of effective core potentials. The interaction energies of both systems expressed instead as supermolecular UHF interaction plus dispersion from SAPT(UKS) result in reasonably accurate potential curves.
Depressed scattering across grain boundaries in single crystal graphene
Authors: Chen Jiao , Jin Zhi , Ma Peng , Wang Hong , Wang Haomin , Shi Jingyuan , Peng Songang , Liu Xinyu , Ye Tianchun
Published: October 2012

We investigated the electrical and quantum properties of single-crystal graphene (SCG) synthesized by chemical vapor deposition (CVD). Quantum Hall effect and Shubnikov de Hass oscillation, a distinguishing feature of a 2-dimensional electronic material system, were observed during the low temperature transport measurements. Decreased scattering from grain boundaries in SCG was proven through extracting information from weak localization theory. Our results facilitate understanding the electrical properties of SCG grown by CVD and its applications in high speed transistor and quantum devices.
Response to “Comment on ‘Elastic incoherent neutron scattering operating by varying instrumental energy resolution: Principle, simulations, and experiments of the resolution elastic neutron scattering (RENS)’” [Rev. Sci. Instrum. 83, 107101 (2012)]
Authors: Magazù Salvatore , Migliardo Federica , Benedetto Antonio
Published: October 2012

Recently [S. Magazù et al., Rev. Sci. Instrum. 82, 105115 (2011)10.1063/1.3641870] we have proposed a new method for characterizing, by neutron scattering, the dynamical properties of complex material systems, such as, the ones of interest in the biophysical field. This approach called Resolution Elastic Neutron Scattering, in short RENS, is based on the detection of the elastically scattered neutron intensity as a function of the instrumental energy resolution. By experimental, theoretical, and numerical findings, we have pointed out that an inflection point occurs in the elastic intensity when the system relaxation time approaches the instrumental energy resolution time. This approach, differently from quasi-elastic neutron scattering (QENS), gives the chance to evaluate the system relaxation times without using pre-defined models that can be wrong and/or misleading. Here, we reply to a Comment on the above-mentioned main paper in which Wuttke proposes a different approach to evaluate the above-mentioned inflection point; on this regard, it should be noticed that the existence of the inflection point, which is the main topic of our work, is not questioned and that the approach proposed by Wuttke in the Comment, although valid for a class of dynamical processes, is not applicable when different and distinct processes occur simultaneously at different time scale.
Brandaris 128 ultra-high-speed imaging facility: 10 years of operation, updates, and enhanced features
Authors: Gelderblom Erik C. , Vos Hendrik J. , Mastik Frits , Faez Telli , Luan Ying , Kokhuis Tom J. A. , van der Steen Antonius F. W. , Lohse Detlef , de Jong Nico , Versluis Michel
Published: October 2012

The Brandaris 128 ultra-high-speed imaging facility has been updated over the last 10 years through modifications made to the camera's hardware and software. At its introduction the camera was able to record 6 sequences of 128 images (500 × 292 pixels) at a maximum frame rate of 25 Mfps. The segmented mode of the camera was revised to allow for subdivision of the 128 image sensors into arbitrary segments (1–128) with an inter-segment time of 17 μs. Furthermore, a region of interest can be selected to increase the number of recordings within a single run of the camera from 6 up to 125. By extending the imaging system with a laser-induced fluorescence setup, time-resolved ultra-high-speed fluorescence imaging of microscopic objects has been enabled. Minor updates to the system are also reported here.
Hybrid Alfvén resonant mode generation in the magnetosphere-ionosphere coupling system
Authors: Hiraki Yasutaka , Watanabe Tomo-Hiko
Published: October 2012

Feedback unstable Alfvén waves involving global field-line oscillations and the ionospheric Alfvén resonator (IAR) were comprehensively studied to clarify their properties of frequency dispersion, growth rate, and eigenfunctions. It is discovered that a new mode called here the hybrid Alfvén resonant (HAR) mode can be destabilized in the magnetosphere-ionosphere coupling system with a realistic Alfvén velocity profile. The HAR mode found in a high frequency range over 0.3 Hz is caused by coupling of IAR modes with strong dispersion and magnetospheric cavity resonances. The harmonic relation of HAR eigenfrequencies is characterized by a constant frequency shift from those of IAR modes. The three modes are robustly found even if effects of two-fluid process and ionospheric collision are taken into account and thus are anticipated to be detected by magnetic field observations in a frequency range of 0.3–1 Hz in auroral and polar-cap regions.
Accurate potential energy curves for HeH+ isotopologues
Authors: Tung Wei-Cheng , Pavanello Michele , Adamowicz Ludwik
Published: October 2012

New accurate ground-state potential energy curves (PEC) for the 4HeH+, 4HeD+, 3HeH+, and 3HeD+ isotopologues are calculated with 600 explicitly correlated Gaussian (ECG) functions with shifted centers in the range between R = 0.35 a0 and 145 a0. The calculations include the adiabatic corrections (AC). The absolute accuracy of all Born-Oppenheimer (BO) PEC points is better than 0.0018 cm−1 and it is better than 0.0005 cm−1 for the ACs. With respect to the very recent BO PEC calculations performed by Pachucki with 20 000 generalized Heitler-London explicitly correlated functions [K. Pachucki, Phys. Rev. A 85, 042511 (2012)]10.1103/PhysRevA.85.042511, the present energy calculated at R = 1.46 a0 (a point near the BO equilibrium distance) lies above by only 0.0012 cm−1. Using Pachucki's BO energy at the equilibrium distance of R = 1.463 283 a0, and the adiabatic corrections calculated in this work for the 4HeH+, 4HeD+, 3HeH+, and 3HeD+ isotopologues, the following values are obtained for their PEC depths: 16 448.99893 cm−1, 16 456.86246 cm−1, 16 451.50635 cm−1, and 16 459.36988 cm−1, respectively. We also calculate the rovibrational (rovib) frequencies for the four isotopologues using the BO PEC of Pachucki augmented with the present ACs. The improvements over the BO+AC PEC of Bishop and Cheung (BC) [J. Mol. Spectrosc. 75, 462 (1979)]10.1016/0022-2852(79)90090-0 are 1.522 cm−1 at R = 4.5 a0 and 0.322 cm−1 at R = ∞. To partially account for the nonadiabatic effects in the rovib calculations an effective reduced-mass approach is used. With that, the present 4HeH+ rovibrational transitions are considerably improved over the BC transitions as compared with the experimental values. Now the rovibrational transitions near the dissociation limit are as well reproduced by the present calculations as the lower transitions. For example, for the 4HeD+ transitions corresponding to the ν = 13-9 hot bands the results are off from the experimental values by less than 0.023 cm−1. This confirms high accuracy of the present PECs at larger internuclear separations.
Device simulation of intermediate band solar cells: Effects of doping and concentration
Authors: Yoshida Katsuhisa , Okada Yoshitaka , Sano Nobuyuki
Published: October 2012

We present a numerical study on the fundamental operation principle of an intermediate band solar cell (IBSC) by using the self-consistent drift-diffusion method; the effects of doping in the IB region and incident light concentration on the operation characteristics are investigated. We find that under light illumination the electrostatic potential profile of IBSC strongly and intricately depends on both the electron density in IB and the carrier generation/recombination rates through IB. Introduction of doping in the IB region produces larger short-circuit current than that of IBSCs without doping under low light concentrations. Under high light concentrations, on the other hand, the doping dependence of the short-circuit current diminishes due to the photofilling effects. Although recombination processes through IB degrade the open-circuit voltage and fill factor compared to single junction solar cells under low light concentrations, they are greatly improved under high light concentrations by the photofilling effects. As a result, IBSCs could exceed in efficiency the single junction solar cells.
Temperature dependent band offsets in PbSe/PbEuSe quantum well heterostructures
Authors: Simma M. , Bauer G. , Springholz G.
Published: October 2012

The band offsets of PbSe/Pb1−xEuxSe multi-quantum wells grown by molecular beam epitaxy are determined as a function of temperature and europium content using temperature-modulated differential transmission spectroscopy. The confined quantum well states in the valence and conduction bands are analyzed using a k·p model with envelope function approximation. From the fit of the experimental data, the normalized conduction band offset is determined as 0.45±0.15 of the band gap difference, independently of Eu content up to 14% and temperature from 20 to 300 K.
Investigation of an improved relativistic backward wave oscillator in efficiency and power capacity
Authors: Song W. , Chen C. H. , Sun J. , Zhang X. W. , Shao H. , Song Z. M. , Huo S. F. , Shi Y. C. , Li X. Z.
Published: October 2012

Investigation of relativistic backward wave oscillator with high efficiency and power capacity is presented in this paper. To obtain high power and high efficiency, a TM021 mode resonant reflector is used to reduce the pulse shortening and increase power capacity to about 1.7 times. Meanwhile, an extraction cavity at the end of slow wave structure is employed to improve the efficiency from less than 30% to over 40%, through the beam-wave interaction intensification and better energy conversion from modulated electron beam to the electromagnetic field. Consistent with the numerical results, microwave with a power of 3.2 GW, a frequency of 9.75 GHz, and a pulse width of 27 ns was obtained in the high power microwave generation experiment, where the electron beam energy was configured to be ∼910 kV and its current to be ∼8.6 kA. The efficiency of the RBWO exceeds 40% at a voltage range of 870 kV–1000 kV.