bluuebunny/crossref_metadata_2025 huggingface dataset:
Procedural versus narrative cross-language priming and bilingual children's reading and sentence sequencing of same genre and opposite genre text in the other language
Authors: VITAL HEDVA , KARNIOL RACHEL
Published: November 2010

How bilingual children represent procedural versus narrative text is important for both pedagogical and theoretical reasons. To examine this issue, bilingual children and children learning English as a Second Language (ESL) read Hebrew sentences comprising either a procedural (i.e., “how to”) or a narrative text (i.e., description of “doing”) and reading times were measured. Half the children were primed with the same text, in English, in either the same genre or the opposite genre. Text sentences were then randomly sequenced and sentence sequencing mistakes and correct sentence sequencing times were assessed. Irrespective of genre, primed children read the Hebrew test text more quickly, and they read it as quickly as the English prime text. The priming effect was only evident on the last five sentences of each task. Primed children made fewer sentence sequencing mistakes than unprimed children, except when they were primed and tested with procedural text. With text reading times covaried, time for correct sequencing of the sentences showed only a main effect for genre. These data indicate that procedural genre material is harder to process than narrative genre material for bilingual children but that they are not aware of this greater difficulty. The data have important implications for our understanding of the way bilinguals construct mental models.
Rethinking emotion and material culture
Authors: Harris Oliver J.T. , Sørensen Tim Flohr
Published: November 2010

In this article, we wish to return to the suggestion made by Sarah Tarlow a decade ago about the importance of understanding emotions in archaeology as a central facet of human being and human actions. We suggest a further expansion of this that focuses exclusively on the relationship between material culture and emotions (as opposed to textually, verbally or iconographically informed approaches), and offer a vocabulary that may better equip archaeologists to incorporate emotions into their interpretations. We attempt to show the implications of such a vocabulary in a specific British Neolithic case study at the henge monument of Mount Pleasant.
Mission-Shaped or Paul-Shaped? Apostolic Challenges to theMission-Shaped Church
Authors: King Fergus J.
Published: November 2010

John M. Hull has raised a number of criticisms about the understanding of worship found inMission-Shaped Church: Church Planting and Fresh Expressions of Church in a Changing Context. In this article, some of these criticisms are explored further. Analysis of Paul’s proposed reforms to the Lord’s Supper in Corinth show that worship must address social concerns and not focus exclusively on a God-ward aspect. Paul does this by describing the Lord’s Supper as a paradigm for behaviour and world-view using the Greek symposium tradition. Paul’s response to the Corinthian situation raises questions about the suitability of the Homogeneous Unit Principle and its role in mission, as do aspects of the controversy with Peter documented in Galatians 2. His wider exploration of the sacramental dimension of ritual meals (1 Cor. 10–11) further shows that worship cannot be divorced from ethics and behaviour if it is to be truly effective and based on Pauline principles
Role of the plasmapause in dictating the ground accessibility of ELF/VLF chorus
Authors: Golden D. I. , Spasojevic M. , Foust F. R. , Lehtinen N. G. , Meredith N. P. , Inan U. S.
Published: November 2010

This study explores the manner in which the plasmapause is responsible for dictating which magnetospheric source regions of ELF/VLF chorus are able to propagate to and be received by midlatitude stations on the ground. First, we explore the effects of plasmapause extent on ground‐based observations of chorus via a 3 month study of ground‐based measurements of chorus at Palmer Station, Antarctica (L = 2.4, 50°S geomagnetic latitude), and data on the plasmapause extent from the IMAGE EUV instrument. It is found that chorus normalized occurrence peaks when the plasmapause is at L ∼ 2.6, somewhat higher than Palmer's L shell, and that this occurrence peak persists across a range of observed chorus frequencies. Next, reverse ray tracing is employed to evaluate the portion of the equatorial chorus source region, distributed in radial distance and wave normal, from which chorus is able to reach Palmer Station via propagation in a nonducted mode. The results of ray tracing are similar to those of observations, with a peak of expected occurrence when the plasmapause is at L ∼ 3. The exact location of the peak is frequency dependent. This supports the conclusion that the ability of chorus to propagate to low altitudes and the ground is a strong function of instantaneous plasmapause extent and that peak occurrence of chorus at a given ground station may occur when the L shell of the plasmapause is somewhat beyond that of the observing station. These results also suggest that chorus observed on the ground at midlatitude stations propagates predominantly in the nonducted mode.
Tree ring record of streamflow and drought in the upper Snake River
Authors: Wise Erika K.
Published: November 2010

Tree ring samples collected near the Snake River headwaters were augmented with preexisting tree ring chronologies to create a 415 year reconstruction of upper Snake River streamflow, extending the short instrumental record and providing the first description of multicentury water supply variability in this river. Results indicate that the region's early 21st century drought is severe even in the context of long‐term climatic variability and that the instrumental record is representative of low‐flow individual years. In terms of overall magnitude, droughts of the recent past are eclipsed by a sustained low‐flow period lasting for over 30 years in the early to mid‐1600s. A comparison of reconstructed Snake River flow with streamflow reconstructions of the Colorado, Sacramento, and Verde rivers suggests that changes in the predominance of zonal versus meridional atmospheric flow may have influenced drought patterns in the western United States through time.
mRNA turnover rate limits siRNA and microRNA efficacy
Authors: Larsson Erik , Sander Chris , Marks Debora
Published: November 2010

The microRNA pathway participates in basic cellular processes and its discovery has enabled the development of si/shRNAs as powerful investigational tools and potential therapeutics. Based on a simple kinetic model of the mRNA life cycle, we hypothesized that mRNAs with high turnover rates may be more resistant to RNAi‐mediated silencing. The results of a simple reporter experiment strongly supported this hypothesis. We followed this with a genome‐wide scale analysis of a rich corpus of experiments, including RT–qPCR validation data for thousands of siRNAs, siRNA/microRNA overexpression data and mRNA stability data. We find that short‐lived transcripts are less affected by microRNA overexpression, suggesting that microRNA target prediction would be improved if mRNA turnover rates were considered. Similarly, short‐lived transcripts are more difficult to silence using siRNAs, and our results may explain why certain transcripts are inherently recalcitrant to perturbation by small RNAs.
Crossing Disciplinary Boundaries to Understand Human Drivers of Environmental Threats
Authors: Rosa Eugene , Dietz Thomas
Published: November 2010

A wide range of ecological studies affirms the cumulative damage to ecosystem capital and services around the globe. They also point to the overwhelming role that anthropogenic or human drivers play in global ecological damage. The MAHB is intended to combine what we know about human drivers of environmental threats with what the social sciences know about changing human behavior and institutions. A variety of social sciences have taken up the first task of identifying the key human activities—at both the local, cumulative level and at the systemic level—most responsible for global environmental change. Considerable progress has been made in our understanding of land use and land cover change, of vulnerability, resilience, and adaptation, of the governance of common pool resources, and of demographic and economic factors. Each of these advances is the result of integrating ecological principals and findings into disciplined social science research. This presentation highlights one of these integrating approaches, the STIRPAT approach, that adds social and political variables and statistical sophistication from the social sciences to the widely adopted IPAT formula.
The Role of the Gut Microbiota in Ulcerative Colitis
Authors: Young Vincent , Chang Eugene , Meyer Folker , Sogin Mitchell , Schmidt Thomas , Tiedje James
Published: November 2010

The overall goal of our Demonstration Project is to address the hypothesis that the gut microbiota plays a critical role in the pathogenesis of inflammatory bowel disease (IBD). To circumvent the confounding effects of mucosal inflammation and medications that independently bias microbial selection, we have set out to study a unique clinical model of ulcerative colitis (pouchitis) where the development and status of the gut microbiota can be assessed prospectively and relative to the outcome of disease. Pouchitis is an inflammatory condition of a surgically-created pseudorectum that is unique to ulcerative colitis and rarely occurs when this procedure is performed for treatment of other non-IBD diseases. Since the incidence of developing pouchitis within one year is over 50%, the likelihood of detecting antecedent changes in microbiota is high. Our multi-center study involves an integrated team of researchers with expertise in clinical manifestations of pouchitis (Univ. Chicago), cultivation of diverse microorganisms (MSU), molecular microbial ecology (MSU/UMich/MBL), and metagenomics (ANL). Our goal is to enroll up to 50 patients with pouchitis who will be followed clinically and endoscopically (sampling from the unprepped pouch) for a period of 18 months each. Though the use of high-throughput, cost-effective technologies, which members of this team have played a key role in developing, we intend to demonstrate a critical role for the gut microbiome in the development of the dysregulated mucosal immune response that is the hallmark of IBD. In order to identify associations between the structure and dynamics of the gut microbial community and specific clinical endpoints, we will scan for markers in the fecal microbial community that are associated with specific, quantifiable measures of disease activity or progression. Collectively, these studies will provide insights into how enteric microbiota cause or contribute to the etiopathogenesis of human ulcerative colitis. This knowledge will lead the way to novel ways to monitor patients with IBD and to guide the development of novel preventative and therapeutic interventions.In accordance with the guidelines of the Human Microbiome Project (HMP), data generated by this study (NCBI Project ID 463154) will be subject to a 12 month publication moratorium from the date of data submission to dbGaP and SRA.
Linking stoichiometric homeostasis with ecosystem structure, functioning, and stability
Authors: Yu Qiang , Chen Quansheng , Elser James , Cease Arianne , He Nianpeng , Wu Honghui , Zhang Guangming , Wu Jianguo , Bai Yongfei , Han Xingguo
Published: November 2010

Ecosystem structure, functioning, and stability have been a focus of ecological and environmental sciences during the past two decades. The mechanisms underlying their relationship, however, are not well understood. Based on comprehensive studies in Inner Mongolia grassland, here we show that species-level stoichiometric homeostasis was consistently positively correlated with dominance and stability on both 2-year and 27-year temporal scales and across a 1200-km spatial transect. At the community level, stoichiometric homeostasis was also positively correlated with ecosystem function and stability in most cases. Thus, homeostatic species tend to have high and stable biomass; and ecosystems dominated by more homeostatic species have higher productivity and greater stability. By modulating organism responses to key environmental drivers, stoichiometric homeostasis appears to be a major mechanism responsible for the structure, functioning, and stability of grassland ecosystems.
A bestiary of non-linear functions for growth analysis
Authors: Paine C. E. Timothy , Marthews Toby , Vogt Deborah , Purves Drew , Rees Mark , Hector Andy , Turnbull Lindsay
Published: November 2010

Plant growth is an essential ecological process, integrating across scales from physiology to community dynamics. Predicting the growth of plants is essential to understand a wide range of ecological issues, including competition, plant-herbivore interactions and ecosystem functioning.A challenge in modeling plant growth is that growth rates almost universally decrease with increasing size, for a variety of reasons. Traditional analyses of growth are hampered by the need to remain within the structures of linear models, which handle this slowing poorly. We demonstrate the implementation of a variety of non-linear models that are more appropriate for modeling plant growth than are the traditional, linear, models.Ecological inference is frequently based on growth rates, rather than model parameters. Traditional calculations of absolute and relative growth rates assume that they are invariant with respect to time or biomass, which is almost never valid. We advocate and demonstrate the calculation of function-derived growth rates, which highlight the time- and biomass-varying nature of growth. We further show how uncertainty in estimated parameter values can be propagated to express uncertainty in absolute and relative growth rates.The use of non-linear models and function-derived growth rates can facilitate testing novel hypotheses in population and community ecology. Even so, we acknowledge that fitting non-linear models can be tricky. To foster the spread of these methods, we make many recommendations for ecologists to follow when their hypotheses lead them into the subject of plant growth.
The impact of forest logging and fragmentation on the species richness and density of Malagasy rainforest carnivores
Authors: Gerber Brian , Karpanty Sarah , Randrianantenaina Johny
Published: November 2010

Despite significant efforts to understand and conserve Madagascar’s unique biodiversity, relatively little is known about the island’s carnivore populations. We sampled four rainforest sites to explore the effects of forest logging and fragmentation on carnivore species richness and the density of the two largest endemic carnivores, the Fossa (Cryptoprocta ferox) and Malagasy Civet (Fossa fossana). Our rainforest sites were selected across a gradient of increasing anthropogenic disturbance from primary to selectively-logged to fragmented forest < 2.5 km from primary forest, to fragmented forest > 20 km from primary forest. We deployed a minimum of 26 passive infrared camera stations at each forest site to non-invasively sample carnivores. By identifying C. ferox and F. fossana individuals based on unique pelage patterns, we were able to apply capture-recapture analyses using the Huggins model in Program MARK and Program DENSITY. We used a buffer of full mean-maximum-distance-moved (MMDM) and a spatially-explicit capture-recapture (SECR) method to estimate density. A total of 5,579 camera-trap nights yielded detections of five endemic carnivores (C. ferox, F. fossana, ring-tailed mongoose Galidia elegans, broad-striped mongoose Galidictus fasciata, small-toothed civet Eupleres goudotii). We found variation in carnivore species richness among the four sites. All endemic carnivores were present in the primary and selectively-logged rainforest, while overall endemic species richness was greatly reduced in the fragmented forests. Density also varied significantly among the rainforest sites. F. fossana density (individuals/km-2 ± SE) decreased significantly between the primary rainforest (SECR 3.19 ±0.55, MMDM 2.47 ±0.13) and selectively-logged rainforest (SECR 1.38 ± 0.223, MMDM 1.22 ± 0.055). F. fossana was absent from both fragmented sites. C. ferox density also decreased significantly between the primary rainforest (SECR 0.12 ± 0.05, MMDM 0.14 ± 0.001) and the selectively-logged rainforest (SECR 0.09 ±0.04, MMDM 0.09 ±0.002). C. ferox was absent from the fragmented rainforest > 20 km from primary forest, yet we did detect a single individual at the fragmented rainforest < 2.5 km from the primary forest. Our results suggest that forest logging and fragmentation negatively impact C. ferox and F. fossana populations in Malagasy rainforests. Unlike F. fossana, C. ferox appears to be able to occupy rainforest fragments near primary forest. Our study provides the first assessment of carnivore population parameters in the eastern rainforests of Madagascar and will be of importance to Malagasy governmental and non-governmental agencies seeking to more accurately assess the status of these species and to best set management goals.
Mutational analysis of residues in the regulatory CBS domains of Moorella thermoacetica pyrophosphatase corresponding to disease-related residues of human proteins
Authors: Jämsen Joonas , Tuominen Heidi , Baykov Alexander A. , Lahti Reijo
Published: November 2010

mtCBS-PPase [CBS (cystathionine β-synthase) domain-containing pyrophosphatase from Moorella thermoacetica] contains a pair of CBS domains that strongly bind adenine nucleotides, thereby regulating enzyme activity. Eight residues associated with the CBS domains of mtCBS-PPase were screened to explore possible associations with regulation of enzyme activity. The majority of the substitutions (V99A, R168A, Y169A, Y169F, Y188A and H189A) enhanced the catalytic activity of mtCBS-PPase, two substitutions (R170A and R187G) decreased activity, and one substitution (K100G) had no effect. AMP-binding affinity was markedly decreased in the V99A, R168A and Y169A mutant proteins, and elevated in the R187G and H189A mutant proteins. Remarkably, the R168A and Y169A substitutions changed the effect of AMP from inhibition to activation. The stoichiometry of AMP binding increased from one to two AMP molecules per CBS domain pair in the Y169F, R170A, R187G and Y188A variants. The ADP-binding affinity decreased in three and increased in four mutant proteins. These findings identify residues determining the strength and selectivity of nucleotide binding, as well as the direction (inhibition or activation) of the subsequent effect. The data suggest that mutations in human CBS domain-containing proteins can be translated into a bacterial context. Furthermore, our data support the hypothesis that the CBS domains act as an ‘internal inhibitor’ of mtCBS-PPase.
Regulation of pendrin by pH: dependence on glycosylation
Authors: Azroyan Anie , Laghmani Kamel , Crambert Gilles , Mordasini David , Doucet Alain , Edwards Aurélie
Published: November 2010

Mutations in the anion exchanger pendrin are responsible for Pendred syndrome, an autosomal recessive disease characterized by deafness and goitre. Pendrin is highly expressed in kidney collecting ducts, where it acts as a chloride/bicarbonate exchanger and thereby contributes to the regulation of acid–base homoeostasis and blood pressure. The present study aimed to characterize the intrinsic properties of pendrin. Mouse pendrin was transfected in HEK (human embryonic kidney) 293 and OKP (opossum kidney proximal tubule) cells and its activity was determined by monitoring changes in the intracellular pH induced by variations of transmembrane anion gradients. Combining measurements of pendrin activity with mathematical modelling we found that its affinity for Cl−, HCO3− and OH− varies with intracellular pH, with increased activity at low intracellular pH. Maximal pendrin activity was also stimulated at low extracellular pH, suggesting the presence of both intracellular and extracellular proton regulatory sites. We identified five putative pendrin glycosylation sites, only two of which are used. Mutagenesis-induced disruption of pendrin glycosylation did not alter its cell-surface expression or polarized targeting to the apical membrane and basal activity, but fully abrogated its sensitivity to extracellular pH. The hither to unknown regulation of pendrin by external pH may constitute a key mechanism in controlling ionic exchanges across the collecting duct and inner ear.
Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism
Authors: Chang Yuanyuan , Wu Jian , Tong Xia-Jing , Zhou Jin-Qiu , Ding Jianping
Published: November 2010

Saccharomyces cerevesiae Rph1 is a histone demethylase orthologous to human JMJD2A (Jumonji-domain-containing protein 2A) that can specifically demethylate tri- and di-methylated Lys36 of histone H3. c-Rph1, the catalytic core of Rph1, is responsible for the demethylase activity, which is essential for the transcription elongation of some actively transcribed genes. In the present work, we report the crystal structures of c-Rph1 in apo form and in complex with Ni2+ and α-KG [2-oxoglutarate (α-ketoglutarate)]. The structure of c-Rph1 is composed of a JmjN (Jumonji N) domain, a long β-hairpin, a mixed structural motif and a JmjC domain. The α-KG cofactor forms hydrogen-bonding interactions with the side chains of conserved residues, and the Ni2+ ion at the active site is chelated by conserved residues and the cofactor. Structural comparison of Rph1 with JMJD2A indicates that the substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long β-hairpin and the mixed structural motif; and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. In vitro biochemical results show that mutations of the key residues at the catalytic centre and in the substrate-binding cleft abolish the demethylase activity. In vivo growth phenotype analyses also demonstrate that these residues are essential for its functional roles in transcription elongation. Taken together, our structural and biological data provide insights into the molecular basis of the histone demethylase activity and the substrate specificity of Rph1.
Differentiation of AFS cells derived from the EGFP gene transgenic porcine fetuses
Authors: Zheng Yue‐Mao , Dang Yong‐Hui , Xu Yong‐Ping , Sai Wu‐Jia‐Fu , An Zhi‐Xing
Published: November 2010

We have obtained the EGFP (enhanced green fluorescence protein) gene transgenic porcine fetuses before. The aims of this study were (i) to determine whether stem cells could be isolated from amniotic fluid of the transgenic porcine fetuses, and (ii) to determine if these stem cells could express EGFP and differentiate in vitro. The results demonstrated that stem cells could be isolated from amniotic fluid of the EGFP gene transgenic porcine fetuses and could express EGFP and differentiate in vitro. Undifferentiated AFSs (amniotic fluid‐derived stem cells) expressed POU5F1, THY1 and SOX2, while the following differentiation cells expressed markers for chondrogenic (COL2A1), osteogenic (osteocalcin and osteonectin) and neurogenic cells such as astrocyte (GFAP), oligodendrocyte (GALC) and neuron (NF, ENO2 and MAP).
Providing Access to Medical Products at Prices Patients can Afford is a Priority for the European Parliament
Authors: Martin David
Published: November 2010

India, popularly described as ‘the pharmacy of the developing world’ both because of it huge market in generic medicines and its developing research-based pharmaceutical industry, has since 2007 been in negotiations to agree on the provisions of a bilateral Free Trade Agreement (FTA) with the European Union (EU). David Martin, with fellow MEPs and a network of public health groups, is calling on the EU Commission to ensure that demands on India to take on higher intellectual property (IP) standards within the terms of the FTA should not undermine the supply of low-cost generic medicines to the poor and suffering of the developing world or set a precedent for the future of IP protection globally.
Response of a Government Hospital to Prescription Cost Savings through its Hospital Formulary in Thailand
Authors: Burapadaja Siriporn , Chinawong Dujrudee
Published: November 2010

It is in doubt about whether response of government hospitals to prescription cost savings can be evaluated through hospital formularies. The objective was to determine a measure reflecting such response and methods to increase it. An observation on products in a government hospital formulary included their numbers; prices; classes; category, essential medicine (EM) or non-EM; EM sub-lists, List A (basic) to List E; type, generic or brand; and hospital availability, single or dual. The numbers and prices of products were associated with the topics observed. A dominant character of EMs was to increase the numbers, but that of generics was to decrease the prices of products. Single availability expanded the prices of generic and brand products but dual availability narrowed them. For generic products, the numbers decreased but the prices increased from basic to upper EM sub-lists. A hospital formulary could reflect trend of prescription and cost, therefore it is clear that response to prescription cost savings could be determined through it. Proportion of products that are both EM and generic has been considered as measures indicating such response. Including more EMs and generics and delisting unnecessary brands in the basic EM sub-list and major classes could enhance the response.
Water binding sites in 2-para- and 2-ortho-fluorophenylethanol: A high-resolution UV experiment and ab initio calculations
Authors: Karaminkov R. , Chervenkov S. , Neusser H. J.
Published: November 2010

The singly hydrated complexes of the flexible prototype molecules 2-para-fluorophenylethanol and 2-ortho-fluorophenylethanol have been investigated by combination of high-resolution resonance-enhanced two-photon ionization spectroscopy in a cold supersonic beam and quantum chemistry ab initio calculations. We have identified the conformational structures of the above complexes, which correspond to water binding to the most stable gauche monomer’s conformers in both cases. No structural changes of the host molecules upon the attachment of a single water molecule have been found. For the 2-ortho-fluorophenylethanol-water complex we have observed an additional structure with one of the higher-in-energy gauche conformers of the monomer. This corroborates the assumption that the complexation with water stabilizes the higher-energy conformer of the monomer, precluding it from relaxation to the lowest-energy geometry.
Efficiency enhancement of a dielectric barrier plasma discharge by dielectric barrier optimization
Authors: Meiners Annette , Leck Michael , Abel Bernd
Published: November 2010

The characteristic feature of a dielectric barrier discharge (DBD) is the dielectric barrier placed between the electrodes. In the present work, the influence of the dielectric barrier to the properties of a DBD in air was investigated. Spectroscopic characterization of the DBD and electrical measurements were carried out. It was shown that the efficiency of a DBD can be considerably improved by optimizing the dielectric barrier. The dielectric material should possess an appropriate relative permittivity and thickness. For thin dielectric barriers, a high secondary emission coefficient becomes important. Additionally, the use of only one dielectric barrier is advantageous.
Capillary wave motion excited by high frequency surface acoustic waves
Authors: Tan Ming K. , Friend James R. , Matar Omar K. , Yeo Leslie Y.
Published: November 2010

This paper presents a numerical and experimental study of capillary wave motion excited by high frequency surface acoustic waves (SAWs). The objective of this study is to provide insight into the dynamic behavior of the fluid free surface and its dependence on the excitation amplitude. A two-dimensional numerical model that couples the motion of the piezoelectric substrate to a thin liquid layer atop the substrate is constructed. A perturbation method, in the limit of small-amplitude acoustic waves, is used to decompose the equations governing fluid motion to resolve the widely differing time scales associated with the high frequency excitation. While this model focuses on the free surface dynamics in the low-amplitude flow regime, the experimental study focuses on the high-amplitude flow regime. Transformation of time series data from both experiments and simulations into the frequency domain reveals that, in the low-amplitude regime, a fundamental resonant frequency and a superharmonic frequency are found in the frequency spectra. The former is found to be identical to that of the applied SAW, and the free surface displacement magnitude is comparable to that of the substrate displacement. Our numerical results also confirm previous speculation that the separation distance between two displacement antinodal points on the free surface is δSt≈λSAW/2 for a film and δSt≈λf/2 for a drop, where λSAW and λf denote the SAW wavelength and the acoustic wavelength in the fluid, respectively. Finally, in the high-amplitude regime, strong nonlinearities shift the acoustic energy to a lower frequency than that of the SAW; this low-frequency broadband response, quite contrary to the subharmonic half-frequency capillary wave excitation predicted by the classical linear or weakly nonlinear Faraday theories, is supported by a scaling analysis of the momentum equations.
On the evolution of film roughness during magnetron sputtering deposition
Authors: Turkin A. A. , Pei Y. T. , Shaha K. P. , Chen C. Q. , Vainshtein D. I. , De Hosson J. Th. M.
Published: November 2010

The effect of long-range screening on the surface morphology of thin films grown with pulsed-dc (p-dc) magnetron sputtering is studied. The surface evolution is described by a stochastic diffusion equation that includes the nonlocal shadowing effects in three spatial dimensions. The diffusional relaxation and the angular distribution of the incident particle flux strongly influence the transition to the shadowing growth regime. In the magnetron sputtering deposition the shadowing effect is essential because of the configuration of the magnetron system (finite size of sputtered targets, rotating sample holder, etc.). A realistic angular distribution of depositing particles is constructed by taking into account the cylindrical magnetron geometry. Simulation results are compared with the experimental data of surface roughness evolution during 100 and 350 kHz p-dc deposition, respectively.
Enhanced power conversion efficiency of p-i-n type organic solar cells by employing a p-layer of palladium phthalocyanine
Authors: Kim Inho , Haverinen Hanna M. , Li Jian , Jabbour Ghassan E.
Published: November 2010

We demonstrate an enhancement in the power conversion efficiency (PCE) of p-i-n type organic solar cells consisting of zinc phthalocyanine (ZnPc) and fullerene (C60) using a p-layer of palladium phthalocyanine (PdPc). Solar cells employing three different device structures such as ZnPc/ZnPc:C60/C60, PdPc/PdPc:C60/C60, and PdPc/ZnPc:C60/C60 with varying thickness of mixed interlayers were fabricated by thermal evaporation. The mixed i-layers were deposited by co-evaporation of MPc (M=Zn,Pd) and C60 by 1:1 ratio. PCE of 3.7% was obtained for optimized cells consisting of PdPc/ZnPc:C60/C60, while cells with device structure of ZnPc/ZnPc:C60/C60 showed PCE of 3.2%.
Effect of embedding Fe3O4 nanoparticles in silica spheres on the optical transmission properties of three-dimensional magnetic photonic crystals
Authors: Fang Mei , Volotinen Tarja T. , Kulkarni S. K. , Belova Lyubov , Rao K. V.
Published: November 2010

Magnetic and optical properties of three-dimensional fcc-structured magnetic photonic crystals (MPCs), consisting of SiO2 spheres, in the size range 260–680 nm, embedded with 0–6.4 wt % Fe3O4 nanoparticles have been investigated. In the wide spatial angle transmission spectra for these crystals at normal incidence of light in the UV-visible range, five photonic band gaps (PBGs) due to Bragg diffraction from different crystal planes have been observed. The Bragg wavelengths (λB) of PBGs in both the nonmagnetic and MPCs of the same structure are found to depend linearly on the sphere size. From the slope of this linear function the calculated effective refractive index is found to increase with the concentration of the magnetite nanoparticles in the MPCs, and is consistent with the result calculated from the average dielectric constant. We also find λB of PBGs are dependent on the angle of the incidence of the light. Furthermore, for small angles this angular dependency is more strongly dependent on the polarization of incident light for MPCs than for the non-MPCs. Thus, magnetic nanocomposite PCs can be designed to incorporate additional functionality in the development of potential magneto-optical devices.
Improved Kelvin probe force microscopy for imaging individual DNA molecules on insulating surfaces
Authors: Leung Carl , Maradan Dario , Kramer Armin , Howorka Stefan , Mesquida Patrick , Hoogenboom Bart W.
Published: November 2010

Electrostatic forces and potentials are keys in determining the interactions between biomolecules. We have recently imaged the topography and electrostatic surface potential of nucleic acid molecules on silicon surfaces using Kelvin probe force microscopy (KPFM). Here, we demonstrate KPFM imaging on insulating surfaces like mica, which provides access to configurations of DNA that are projections of its structure in solution. In particular, we apply dual-frequency mode to minimize the tip-sample distance at which the Kelvin probe signal is acquired and use the fundamental resonance of the cantilever to determine surface potential and its first overtone to detect the topography.
First-order reversal curve analysis of graded anisotropy FePtCu films
Authors: Bonanni Valentina , Fang Yeyu , Dumas Randy K. , Zha Chaolin , Bonetti Stefano , Nogués Josep , Åkerman Johan
Published: November 2010

The reversal mechanisms of graded anisotropy FePtCu films have been investigated by alternating gradient magnetometer (AGM) and magneto-optical Kerr effect (MOKE) measurements with first-order reversal curve (FORC) techniques. The AGM-FORC analysis, which clearly shows the presence of soft and hard components, is unable to resolve how these phases are distributed throughout the film thickness. MOKE-FORC measurements, which preferentially probe the surface of the film, reveal that the soft components are indeed located toward the top surface. Combining AGM-FORC with the inherent surface sensitivity of MOKE-FORC analysis allows for a comprehensive analysis of heterogeneous systems such as graded materials.
The Structural Accessibility Layer (SAL): Revealing how Urban Structure Constrains Travel Choice
Authors: Silva Cecilia , Pinho Paulo
Published: November 2010

Urban mobility problems, such as congestion, have been threatening the quality of life, competitiveness, and sustainable development of urban areas. The need for an integrated approach to land use and transport in mobility management has been widely recognised. Accessibility measures are believed to provide a useful framework to support this integrated approach. Some of these measures can also reveal the mobility potential created by urban structures. This paper introduces the concept of structural accessibility and a new planning tool—the Structural Accessibility Layer (SAL). This tool measures structural accessibility by comparing accessibility levels between different transport modes to a range of activities in a given territory. An application to Greater Oporto is developed in order to discuss the potential of SAL for planning practice. Results were assessed by a number of local experts discussing its applicability, robustness, and usefulness. This research produced sound evidence of the added value of the SAL in planning practice. Indeed, the SAL was found to deliver a good representation of location conditions for mobility providing interesting insights for policy design and for planning practice.
The Economic Integration of New Sectors in Rural Areas: A Case Study of the Shetland Economy
Authors: Roberts Deborah , Newlands David
Published: November 2010

A temporal structural path analysis of the Shetland Islands from 1971 to 2003 is used to describe the process by which two new sectors associated with the discovery of North Sea oil became integrated into the wider Shetland economy. The results confirm that it can take considerable time for incoming sectors to become integrated within an economy and that integration may increase when a sector is in decline. It is argued that structural path analysis provides complementary insights into the process of economic integration which are complementary to those gained from more standard multiplier techniques, and that both are useful to rural development analysts charged with maximising the benefits of incoming sectors and/or minimising the adverse effects of a sector in decline.
Investigating the Knowledge interface between Stakeholder Engagement and Plan-Making
Authors: Legacy Crystal
Published: November 2010

The ‘ideal deliberative procedure’ provides structure to the process of stakeholder deliberation, yet creates a tension with the formal processes of strategic plan-making. This paper examines process design by drawing upon communicative planning theory, and the rational comprehensive model and deliberative democracy literature. In the context of metropolitan strategic spatial plan-making, the aim of this paper is to examine how the knowledge interface between the process of stakeholder engagement and the process of plan-making enables or inhibits implementation of the plan. A retrospective study examining the development of two metropolitan strategic spatial plans: Greater Perth's the Network City plan and Greater Vancouver's the Livable Region Strategic Plan is provided. It is revealed that the engagement of the planners, the public and the politicians occurs within formal stakeholder engagement ‘events’ positioned at different stages of the plan-making process. This paper reveals that the deliberation among the professional planners and the politicians at the process design stage steers the plan-making process in a manner that retains its legitimacy and creates a more implementable plan.
The Nose Tells it to the Eyes: Crossmodal Associations between Olfaction and Vision
Authors: Seigneuric Alix , Durand Karine , Jiang Tao , Baudouin Jean-Yves , Schaal Benoist
Published: November 2010

Crossmodal linkage between the olfactory and visual senses is still largely underexplored. In this study, we investigated crossmodal olfactory – visual associations by testing whether and how visual processing of objects is affected by the presence of olfactory cues. To this end, we explored the influence of prior learned associations between an odour (eg odour of orange) and a visual stimulus naturally associated with that odour (picture of orange) on the movements of the eyes over a complex scene. Participants were asked to freely explore a photograph containing an odour-related visual cue embedded among other objects while being exposed to the corresponding odour (subjects were unaware of the presence of the odour). Eye movements were recorded to analyse the order and distribution of fixations on each object of the scene. Our data show that the odour-related visual cue was explored faster and for a shorter time in the presence of the congruent odour. These findings suggest that odours can affect visual processing by attracting attention to the possible odour source and by facilitating its identification.
Estuarine geomorphology and low salinity requirement for fertilisation influence spawning site location in the diadromous fish, Galaxias maculatus
Authors: Hicks Andy , Barbee Nicole C. , Swearer Stephen E. , Downes Barbara J.
Published: November 2010

In habitats such as estuaries, which are characterised by large and fluctuating gradients in abiotic variables, finding appropriate habitat for successful spawning and egg development can be critical to a species’ survival. We explored how salinity requirements for successful fertilisation may govern the distribution of estuarine spawning habitat for the diadromous fish, Galaxias maculatus, which spawns in inundated vegetation on estuary banks during spring tides. Artificial fertilisation experiments confirmed that successful fertilisation only occurs at low salinities (<20). Thus, we predicted that egg distributions would depend upon the extent of low-salinity surface waters in an estuary. Using estuary geomorphology classification schemes, which classify estuaries by physical and chemical characteristics such as their salinity dynamics, we hypothesised that stratified estuaries would provide a greater extent of low salinity surface water than well-mixed estuaries. This prediction was supported by surveys of egg distributions in five estuaries in Victoria, Australia. Eggs were distributed over a greater proportion of ‘stratified’ v. ‘mixed’ estuary types. We suggest that combining knowledge of the spawning requirements of a species and physical properties of the habitat, such as those encapsulated in estuary geomorphic classification schemes, can greatly facilitate efforts to identify critical habitats and thus aid in species management and conservation.
Toward a whole-landscape approach for sustainable land use in the tropics
Authors: DeFries R. , Rosenzweig C.
Published: November 2010

Increasing food production and mitigating climate change are two primary but seemingly contradictory objectives for tropical landscapes. This special feature examines synergies and trade-offs among these objectives. Four themes emerge from the papers: the important roles of both forest and agriculture sectors for climate mitigation in tropical countries; the minor contribution from deforestation-related agricultural expansion to overall food production at global and continental scales; the opportunities for synergies between improved food production and reductions in greenhouse gas emissions through diversion of agricultural expansion to already-cleared lands, improved soil, crop, and livestock management, and agroforestry; and the need for targeted policy and management interventions to make these synergistic opportunities a reality. We conclude that agricultural intensification is a key factor to meet dual objectives of food production and climate mitigation, but there is no single panacea for balancing these objectives in all tropical landscapes. Place-specific strategies for sustainable land use emerge from assessments of current land use, demographics, and other biophysical and socioeconomic characteristics, using a whole-landscape, multisector perspective.
Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing
Authors: Shearer A. Eliot , DeLuca Adam P. , Hildebrand Michael S. , Taylor Kyle R. , Gurrola José , Scherer Steve , Scheetz Todd E. , Smith Richard J. H.
Published: November 2010

The extreme genetic heterogeneity of nonsyndromic hearing loss (NSHL) makes genetic diagnosis expensive and time consuming using available methods. To assess the feasibility of target-enrichment and massively parallel sequencing technologies to interrogate all exons of all genes implicated in NSHL, we tested nine patients diagnosed with hearing loss. Solid-phase (NimbleGen) or solution-based (SureSelect) sequence capture, followed by 454 or Illumina sequencing, respectively, were compared. Sequencing reads were mapped using GSMAPPER, BFAST, and BOWTIE, and pathogenic variants were identified using a custom-variant calling and annotation pipeline (ASAP) that incorporates publicly available in silico pathogenicity prediction tools (SIFT, BLOSUM, Polyphen2, and Align-GVGD). Samples included one negative control, three positive controls (one biological replicate), and six unknowns (10 samples total), in which we genotyped 605 single nucleotide polymorphisms (SNPs) by Sanger sequencing to measure sensitivity and specificity for SureSelect-Illumina and NimbleGen-454 methods at saturating sequence coverage. Causative mutations were identified in the positive controls but not in the negative control. In five of six idiopathic hearing loss patients we identified the pathogenic mutation. Massively parallel sequencing technologies provide sensitivity, specificity, and reproducibility at levels sufficient to perform genetic diagnosis of hearing loss.
Arsenic tolerance in
Arabidopsis
is mediated by two ABCC-type phytochelatin transporters
Authors: Song Won-Yong , Park Jiyoung , Mendoza-Cózatl David G. , Suter-Grotemeyer Marianne , Shim Donghwan , Hörtensteiner Stefan , Geisler Markus , Weder Barbara , Rea Philip A. , Rentsch Doris , Schroeder Julian I. , Lee Youngsook , Martinoia Enrico
Published: November 2010

Arsenic is an extremely toxic metalloid causing serious health problems. In Southeast Asia, aquifers providing drinking and agricultural water for tens of millions of people are contaminated with arsenic. To reduce nutritional arsenic intake through the consumption of contaminated plants, identification of the mechanisms for arsenic accumulation and detoxification in plants is a prerequisite. Phytochelatins (PCs) are glutathione-derived peptides that chelate heavy metals and metalloids such as arsenic, thereby functioning as the first step in their detoxification. Plant vacuoles act as final detoxification stores for heavy metals and arsenic. The essential PC–metal(loid) transporters that sequester toxic metal(loid)s in plant vacuoles have long been sought but remain unidentified in plants. Here we show that in the absence of two ABCC-type transporters, AtABCC1 and AtABCC2,
Arabidopsis thaliana
is extremely sensitive to arsenic and arsenic-based herbicides. Heterologous expression of these ABCC transporters in phytochelatin-producing
Saccharomyces cerevisiae
enhanced arsenic tolerance and accumulation. Furthermore, membrane vesicles isolated from these yeasts exhibited a pronounced arsenite [As(III)]–PC
2
transport activity. Vacuoles isolated from
atabcc1 atabcc2
double knockout plants exhibited a very low residual As(III)–PC
2
transport activity, and interestingly, less PC was produced in mutant plants when exposed to arsenic. Overexpression of
AtPCS1
and
AtABCC1
resulted in plants exhibiting increased arsenic tolerance. Our findings demonstrate that AtABCC1 and AtABCC2 are the long-sought and major vacuolar PC transporters. Modulation of vacuolar PC transporters in other plants may allow engineering of plants suited either for phytoremediation or reduced accumulation of arsenic in edible organs.
The cell biology of polycystic kidney disease
Authors: Chapin Hannah C. , Caplan Michael J.
Published: November 2010

Polycystic kidney disease is a common genetic disorder in which fluid-filled cysts displace normal renal tubules. Here we focus on autosomal dominant polycystic kidney disease, which is attributable to mutations in the PKD1 and PKD2 genes and which is characterized by perturbations of renal epithelial cell growth control, fluid transport, and morphogenesis. The mechanisms that connect the underlying genetic defects to disease pathogenesis are poorly understood, but their exploration is shedding new light on interesting cell biological processes and suggesting novel therapeutic targets.