bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient description logic reasoning in Prolog: The DLog system
Authors: LUKÁCSY GERGELY , SZEREDI PÉTER
Published: July 2009

Traditional algorithms for description logic (DL) instance retrieval are inefficient for large amounts of underlying data. As DL is becoming more and more popular in areas such as the Semantic Web and information integration, it is very important to have systems which can reason efficiently over large data sets. In this paper we present an approach to transform DL axioms, formalised in the$\mathcal{SHIQ}$DL language, into a Prolog program under the unique name assumption. This transformation is performed with no knowledge about particular individuals: they are accessed dynamically during the normal Prolog execution of the generated program. This technique, together with the top-down Prolog execution, implies that only those pieces of data are accessed that are indeed important for answering the query. This makes it possible to store the individuals in a database instead of memory, which results in better scalability and helps in using DL ontologies directly on top of existing information sources. The transformation process consists of two steps: (1) the DL axioms are converted to first-order clauses of a restricted form, and (2) a Prolog program is generated from these clauses. Step (2), which is the focus of the present paper, actually works on more general clauses than those obtainable by applying step (1) to a$\mathcal{SHIQ}$knowledge base. We first present a base transformation, the output of which can be either executed using a simple interpreter or further extended to executable Prolog code. We then discuss several optimisation techniques, applicable to the output of the base transformation. Some of these techniques are specific to our approach, while others are general enough to be interesting for DL reasoner implementors not using Prolog. We give an overview ofDLog, a DL reasoner in Prolog, which is an implementation of the techniques outlined above. We evaluate the performance of DLog and compare it to some widely used DL reasoners, such as RacerPro, Pellet and KAON2.
Financial innovation and climate change: the case of renewable energy certificates and the role of the GATS
Authors: DELIMATSIS PANAGIOTIS
Published: July 2009

Energy has come to the forefront of the public debate in the past decade for two main reasons: the first relates to the lack of a secure, continuous, and unconditional energy supply in the importing countries, mostly developed and transition economies, which are still dependent on non-renewable carbon-based fossil fuels. The second reason is that uncontrolled production, distribution, and use of conventional energy may lead to environmental degradation and global warming. Renewable energy certificates (RECs) are instruments that allow countries to promote energy generation from renewables and form part of domestic policies aimed at climate change mitigation and adaptation. Since RECs can be traded in secondary markets, this paper discusses issues raised by the nature of and the trade in RECs which can be of concern for the General Agreement on Trade in Services (GATS) and the multilateral regulation of trade in financial services, notably in the case where World Trade Organisation (WTO) Members undertook sweeping commitments in financial services which equally apply to trade in RECs.
DEMETER observations of transmitter‐induced precipitation of inner radiation belt electrons
Authors: Graf K. L. , Inan U. S. , Piddyachiy D. , Kulkarni P. , Parrot M. , Sauvaud J. A.
Published: July 2009

Near loss cone energetic electron flux increases induced by ground‐based very low frequency (VLF) transmissions are observed directly via satellite‐based detection. In 2 years of experiments ranging from 27 March 2006 through 2 April 2008 with the 21.4‐kHz transmitter NPM in Lualualei, Hawaii, and the French satellite DEMETER (detection of electromagnetic emissions transmitted from earthquake regions), only a few cases of detection of individual pulses of transmitter‐induced precipitation of inner radiation belt electrons have been realized. Analysis of the specific cases of detection allow comparison of precipitating flux with predictions based on ray‐tracing analyses of wave propagation and test particle modeling of the wave‐particle interaction. Results indicate that the precipitated flux of >100 keV electrons induced by the NPM transmitter peaks at L ≃ 1.9 and, in the rare cases of detection, may be at higher energies than the ∼100 keV peak predicted by the model. The low detection rate is attributed to the orientation of the DEMETER particle detector, which is mostly overwhelmed by the trapped population at the location of detection.
Regional representativity of AERONET observation sites during the biomass burning season in South America determined by correlation studies with MODIS Aerosol Optical Depth
Authors: Hoelzemann Judith J. , Longo Karla M. , Fonseca Rafael M. , do Rosário Nilton M. E. , Elbern Hendrik , Freitas Saulo R. , Pires Carlos
Published: July 2009

This paper presents an analysis of ground‐based Aerosol Optical Depth (AOD) observations by the Aerosol Robotic Network (AERONET) in South America from 2001 to 2007 in comparison with the satellite AOD product of Moderate Resolution Imaging Spectroradiometer (MODIS), aboard TERRA and AQUA satellites. Data of 12 observation sites were used with primary interest in AERONET sites located in or downwind of areas with high biomass burning activity and with measurements available for the full time range. Fires cause the predominant carbonaceous aerosol emission signal during the dry season in South America and are therefore a special focus of this study. Interannual and seasonal behavior of the observed AOD at different sites were investigated, showing clear differences between purely fire and urban influenced sites. An intercomparison of AERONET and MODIS AOD annual correlations revealed that neither an interannual long‐term trend may be observed nor that correlations differ significantly owing to different overpass times of TERRA and AQUA. Individual anisotropic representativity areas for each AERONET site were derived by correlating daily AOD of each site for all years with available individual MODIS AOD pixels gridded to 1° × 1°. Results showed that for many sites a good AOD correlation (R2 > 0.5) persists for large, often strongly anisotropic, areas. The climatological areas of common regional aerosol regimes often extend over several hundreds of kilometers, sometimes far across national boundaries. As a practical application, these strongly inhomogeneous and anisotropic areas of influence are being implemented in the tropospheric aerosol data assimilation system of the Coupled Chemistry‐Aerosol‐Tracer Transport Model coupled to the Brazilian Regional Atmospheric Modeling System (CCATT‐BRAMS) at the Brazilian National Institute for Space Research (INPE). This new information promises an improved exploitation of local site sampling and, thus, chemical weather forecast.
Surface and subsurface seawater temperature reconstruction using Mg/Ca microanalysis of planktonic foraminifera Globigerinoides ruber, Globigerinoides sacculifer, and Pulleniatina obliquiloculata
Authors: Sadekov Aleksey , Eggins Stephen M. , De Deckker Patrick , Ninnemann Ulysses , Kuhnt Wolfgang , Bassinot Franck
Published: July 2009

Laser–ablation inductively coupled plasma–mass spectrometry microanalyses of Mg/Ca across individual final chambers of three planktonic foraminifera species, Globigerinoides ruber, G. sacculifer, and Pulleniatina obliquiloculata, reveal significant interspecies differences in test Mg concentrations. Whereas these three species have similar Mg/Ca values at low sea surface temperatures (∼22°C), they diverge markedly at high sea surface temperatures (∼29°C). Explanations for these differences in species Mg/Ca values based on detailed comparison of species intratest Mg/Ca distributions suggest that compositional variability within tests cannot account for the observed deviation of species Mg/Ca values in warm‐water equatorial regions. Multiple regression modeling and δ18O analysis of Globigerinoides sacculifer tests indicate that interspecies differences in Mg/Ca values result from different depth habitats. The average Mg/Ca values of G. ruber final chambers reflect the temperature of the surface mixed layer (0–25 m), whereas those of G. sacculifer and Pulleniatina obliquiloculata correlate best with subsurface temperatures at 50–75 m and 100–125 m water depths, respectively. Mg/Ca calibration to the temperatures at these depths reveals a similar temperature control on Mg test composition in all species. Combining our results with Mg/Ca values from published culturing experiments, we derive a generalized equation for the effect of temperature and seawater salinity on foraminiferal Mg/Ca. We also show that the Mg/Ca composition of specific calcite layers within foraminiferal tests, including the low‐Mg/Ca layers of Globigerinoides ruber and G. sacculifer and the cortex layer of Pulleniatina obliquiloculata, correlates with seawater temperature and can be used as an additional proxy for seawater temperature.
Earthquake hazards program reauthorization
Authors: Showstack Randy
Published: July 2009

With the U.S. National Earthquake Hazards Reduction Program (NEHRP) coming up for reauthorization and with funding for the program expiring at the end of fiscal year (FY) 2009, a subcommittee of the House of Representatives Committee on Science and Technology held an 11 June hearing to examine the program and question whether it should be focused solely on earthquakes or be broadened to include other hazards as well.

Subcommittee chair David Wu (D‐Oreg.) told Eos that in drafting reauthorization legislation, he is leaning toward a multihazard approach for NEHRP. ‘As we discuss the successes in earthquake mitigation and priorities moving forward, we must note that research for other hazards has yet to produce the same advances. This lag may exist because wind, fire, and tsunami mitigation do not have the same federal [research and development] structure that has produced our many advances on the seismic front,” he noted at the hearing.
Carbon storage initiatives at energy department
Authors: Showstack Randy
Published: July 2009

The U.S. Department of Energy (DOE) recently announced several initiatives related to carbon capture. On 12 June, DOE secretary Steven Chu announced an agreement with the FutureGen Alliance that advances construction of the country's first commercial‐scale, fully integrated carbon capture and sequestration project in Mattoon, Ill. After estimating costs and doing other assessments, DOE and the alliance will decide in 2010 whether to move forward or discontinue the project. “Developing this technology is critically important for reducing greenhouse gas emissions in the U.S. and around the world,” said Chu. The total anticipated financial contribution for the project is $1.1 billion from DOE and $400–600 million from the alliance.
Subsidence in Coastal Louisiana: Understanding Subsidence: Implications for Coastal Restoration and Protection Planning; New Orleans, Louisiana, 13 January 2009
Authors: Yuill Brendan , Reed Denise J.
Published: July 2009

The high rates of subsidence in coastal Louisiana are a well‐documented component of regional land loss, ecosystem function deterioration, and coastal engineering failures. For agencies tasked with managing the effects of subsidence, the wide variability of these rates and their sharp spatial gradients pose significant challenges. Further, there is a lack of scientific consensus on what processes are most responsible for the observed subsidence, which creates uncertainty surrounding spatial patterns of subsidence, as well as a lack of consensus on what areas are most susceptible to it–not trivial questions for the resource management community.
Water Politics and Development Cooperation: Local Power Plays and Global Governance
Authors: Gupta Joyeeta
Published: July 2009

With 2015 looming and the eight millennium development goals—ranging from reducing poverty to creating a global partnership on environmental issues—adopted by world leaders at the U.N. General Assembly meeting in 2000 looking more and more like an unachievable dream, I reached for this book in the hope that there would be clear messages on water politics and development cooperation. I was disappointed. Although the book has clear messages, they are embedded in the different chapters; the editors have not clearly distilled the messages or put them in context and in relation to each other. Having said that, each chapter in the five parts of the book is well structured and provides a clear analysis of the issues studied and of some key messages.
Retrieving the composition and concentration of aerosols over the Indo‐Gangetic basin using CALIOP and AERONET data
Authors: Ganguly Dilip , Ginoux P. , Ramaswamy V. , Winker D. M. , Holben B. N. , Tripathi S. N.
Published: July 2009

Most GCMs (General Circulation Models) fail to reproduce the AOD (aerosol optical depth) peak over the Indo‐Gangetic basin (IGB) as noticed through satellite observations. Insufficient data on aerosol composition makes it difficult to improve GCM results over this source region. In this work, we retrieve the composition and concentration of aerosols over the IGB region, to a first order approximation, by combining the spectral measurements of AOD, single scattering albedo and size distribution available from AERONET (Aerosol Robotic Network) and the extinction profile of aerosols from CALIOP (Cloud‐Aerosol Lidar with Orthogonal Polarization). Comparison of our results with AM2 (Atmospheric GCM) simulations reveal that AM2 is largely underestimating organics and black carbon concentrations over this region during all months. Sulfate is also underestimated during most months but, there is an overestimation from May to September. There is a compelling need for improving the aerosol inventories and dust sources over the region in order to make realistic assessment of the impacts of aerosols on the south Asian monsoon.
Evolution of kurtosis for wind waves
Authors: Annenkov S. Y. , Shrira V. I.
Published: July 2009

Long‐term evolution of random wind waves is studied by direct numerical simulation within the framework of the Zakharov equation. The emphasis is on kurtosis as a single characteristics of field departure from Gaussianity. For generic wave fields generated by a steady or changing wind, kurtosis is found to be almost entirely due to bound harmonics. This observation enables one to predict the departure of evolving wave fields from Gaussianity, capitalizing on the already existing capability of wave spectra forecasting. Kurtosis rapidly adjusts to a sharp increase of wind and slowly decreases after a drop of wind. Typically kurtosis is in the range 0.1–0.3, which implies a tangible increase of freak wave probability compared to the Rayleigh distribution. Evolution of narrow‐banded fields is qualitatively different from the generic case of wind waves: statistics is essentially non‐Gaussian, which confirms that in this special case the standard kinetic equation paradigm is inapplicable.
Asymmetry in zonal phase propagation of ENSO sea surface temperature anomalies
Authors: McPhaden Michael J. , Zhang Xuebin
Published: July 2009

It is often emphasized in the literature that the phase propagation of El Niño sea surface temperature (SST) anomalies along the equator changed from westward to eastward after a mid‐ to late‐1970s climate regime shift in the Pacific. Theories have been developed to explain this change of phase propagation in terms of changes in background state on which El Niño events develop. Those theories also suggest that the direction of La Niña anomaly phase propagation should have changed from westward to eastward as well. However, the direction of La Niña SST anomaly phase propagation did not change after the mid‐ to late‐1970s. Instead, La Niña SSTs continued to exhibit westward phase propagation along the equator, a feature overlooked in both observational analyses and theories. This paper highlights the asymmetry in zonal phase propagation between El Niño and La Niña sea surface temperature anomalies since 1980 and discusses the implications of that asymmetry for understanding El Niño/Southern Oscillation (ENSO) dynamics.
Dominant source regions of the Earth's “hum” are coastal
Authors: Bromirski Peter D. , Gerstoft Peter
Published: July 2009

Hum beam power observations using the USArray EarthScope transportable array, combined with infragravity wave observations, show that the dominant source area of the Earth's hum over the 120–400 s period band during winter months is the Pacific coast of North America, with the western coast of Europe a secondary source region. Correlation of hum with model ocean wave heights indicates that the Pacific coast of Central America is an important hum source region when impacted by austral storm waves. Hum is excited by relatively local infragravity wave forcing as ocean swell propagates along coasts, with no indication of significant deep‐ocean hum generation.
Architectural differentiation reflects bacterial community structure in stream biofilms
Authors: Besemer Katharina , Hödl Iris , Singer Gabriel , Battin Tom J
Published: July 2009

Laboratory studies have documented the extensive architectural differentiation of biofilms into complex structures, including filamentous streamers generated by turbulent flow. Still, it remains elusive whether this spatial organization of natural biofilms is reflected in the community structure. We analyzed bacterial community differentiation between the base and streamers (filamentous structures floating in the water) of stream biofilms under various flow conditions using denaturing gradient gel electrophoresis (DGGE) and sequencing. Fourth-corner analysis showed pronounced deviation from random community structure suggesting that streamers constitute a more competitive zone within the biofilm than its base. The same analysis also showed members of the α-Proteobacteria and Gemmatimonadetes to preferentially colonize the biofilm base, whereas β-Proteobacteria and Bacteroidetes were comparatively strong competitors in the streamers. We suggest this micro-scale differentiation as a response to the environmental dynamics in natural ecosystems.
Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight
Authors: Mastroleo Felice , Van Houdt Rob , Leroy Baptiste , Benotmane M Abderrafi , Janssen Ann , Mergeay Max , Vanhavere Filip , Hendrickx Larissa , Wattiez Ruddy , Leys Natalie
Published: July 2009

In view of long-haul space exploration missions, the European Space Agency initiated the Micro-Ecological Life Support System Alternative (MELiSSA) project targeting the total recycling of organic waste produced by the astronauts into oxygen, water and food using a loop of bacterial and higher plant bioreactors. In that purpose, the α-proteobacterium, Rhodospirillum rubrum S1H, was sent twice to the International Space Station and was analyzed post-flight using a newly developed R. rubrum whole genome oligonucleotide microarray and high throughput gel-free proteomics with Isotope-Coded Protein Label technology. Moreover, in an effort to identify a specific response of R. rubrum S1H to space flight, simulation of microgravity and space-ionizing radiation were performed on Earth under identical culture set-up and growth conditions as encountered during the actual space journeys. Transcriptomic and proteomic data were integrated and permitted to put forward the importance of medium composition and culture set-up on the response of the bacterium to space flight-related environmental conditions. In addition, we showed for the first time that a low dose of ionizing radiation (2 mGy) can induce a significant response at the transcriptomic level, although no change in cell viability and only a few significant differentially expressed proteins were observed. From the MELiSSA perspective, we could argue the effect of microgravity to be minimized, whereas R. rubrum S1H could be more sensitive to ionizing radiation during long-term space exploration mission.
Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean
Authors: Hewson Ian , Poretsky Rachel S , Dyhrman Sonya T , Zielinski Brian , White Angelicque E , Tripp H James , Montoya Joseph P , Zehr Jonathan P
Published: July 2009

Trichodesmium are responsible for a large fraction of open ocean nitrogen fixation, and are often found in complex consortia of other microorganisms, including viruses, prokaryotes, microbial eukaryotes and metazoa. We applied a community gene expression (metatranscriptomic) approach to study the patterns of microbial gene utilization within colonies of Trichodesmium collected during a bloom in the Southwest Pacific Ocean in April 2007. The survey generated 5711-day and 5385-night putative mRNA reads. The majority of mRNAs were from the co-occurring microorganisms and not Trichodesmium, including other cyanobacteria, heterotrophic bacteria, eukaryotes and phage. Most transcripts did not share homology with proteins from cultivated microorganisms, but were similar to shotgun sequences and unannotated proteins from open ocean metagenomic surveys. Trichodesmium transcripts were mostly expressed photosynthesis, N2 fixation and S-metabolism genes, whereas those in the co-occurring microorganisms were mostly involved in genetic information storage and processing. Detection of Trichodesmium genes involved in P uptake and As detoxification suggest that local enrichment of N through N2 fixation may lead to a P-stress response. Although containing similar dominant transcripts to open ocean metatranscriptomes, the overall pattern of gene expression in Trichodesmium colonies was distinct from free-living pelagic assemblages. The identifiable genes expressed by Trichodesmium and closely associated microorganisms reflect the constraints of life in well-lit and nutrient-poor waters, with biosynthetic investment in nutrient acquisition and cell maintenance, which is in contrast to gene transcription by soil and coastal seawater microbial assemblages. The results provide insight into aggregate microbial communities in contrast to planktonic free-living assemblages that are the focus of other studies.
Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge
Authors: Hesselsoe Martin , Füreder Stephanie , Schloter Michael , Bodrossy Levente , Iversen Niels , Roslev Peter , Nielsen Per Halkjær , Wagner Michael , Loy Alexander
Published: July 2009

Extensive physiological analyses of different microbial community members in many samples are difficult because of the restricted number of target populations that can be investigated in reasonable time by standard substrate-mediated isotope-labeling techniques. The diversity and ecophysiology of Rhodocyclales in activated sludge from a full-scale wastewater treatment plant were analyzed following a holistic strategy based on the isotope array approach, which allows for a parallel functional probing of different phylogenetic groups. Initial diagnostic microarray, comparative 16S rRNA gene sequence, and quantitative fluorescence in situ hybridization surveys indicated the presence of a diverse community, consisting of an estimated number of 27 operational taxonomic units that grouped in at least seven main Rhodocyclales lineages. Substrate utilization profiles of probe-defined populations were determined by radioactive isotope array analysis and microautoradiography-fluorescence in situ hybridization of activated sludge samples that were briefly exposed to different substrates under oxic and anoxic, nitrate-reducing conditions. Most detected Rhodocyclales groups were actively involved in nitrogen transformation, but varied in their consumption of propionate, butyrate, or toluene, and thus in their ability to use different carbon sources in activated sludge. This indicates that the functional redundancy of nitrate reduction and the functional versatility of substrate usage are important factors governing niche overlap and differentiation of diverse Rhodocyclales members in this activated sludge.
The p24 family and selective transport processes at the ER—Golgi interface
Authors: Strating Jeroen R.P.M. , Martens Gerard J.M.
Published: July 2009

The secretory pathway is of vital importance for eukaryotic cells and has a pivotal role in the synthesis, sorting, processing and secretion of a large variety of bioactive molecules involved in intercellular communication. One of the key processes in the secretory pathway concerns the transport of cargo proteins from the ER (endoplasmic reticulum) to the Golgi. Type‐I transmembrane proteins of ∼24 kDa are abundantly present in the membranes of the early secretory pathway, and bind the COPI and COPII coat complexes that cover vesicles travelling between the membranes. These p24 proteins are thought to play an important role in the selective transport processes at the ER—Golgi interface, although their exact functioning is still obscure. One model proposes that p24 proteins couple cargo selection in the lumen with vesicle coat recruitment in the cytosol. Alternatively, p24 proteins may furnish subcompartments of the secretory pathway with the correct subsets of machinery proteins. Here we review the current knowledge of the p24 proteins and the various roles proposed for the p24 family members.
Interaction of mitochondrial thioredoxin with glucocorticoid receptor and NF-κB modulates glucocorticoid receptor and NF-κB signalling in HEK-293 cells
Authors: Psarra Anna-Maria G. , Hermann Stefan , Panayotou George , Spyrou Giannis
Published: July 2009

Trx2 (mitochondrial thioredoxin) is an antioxidant and anti-apoptotic factor essential for cell viability. Trx1 (cytoplasmic thioredoxin) is a co-factor and regulator of redox-sensitive transcription factors such as the GR (glucocorticoid receptor) and NF-κB (nuclear factor κB). Both transcription factors have been detected in mitochondria and a role in mitochondrial transcription regulation and apoptosis has been proposed. In the present study, we show using SPR (surface plasmon resonance) and immunoprecepitation that GR and the p65 subunit of NF-κB are Trx2-interacting proteins. The interaction of Trx2 with GR is independent of the presence of GR ligand and of redox conditions. The p65 subunit of NF-κB can interact with Trx2 in the oxidized, but not the reduced, form. Using HEK (human embryonic kidney)-293 cell lines with increased or decreased expression of Trx2, we show that Trx2 modulates transcription of GR and NF-κB reporter genes. Moreover, Trx2 overexpression modulates the mRNA levels of the COX1 (cytochrome oxidase subunit I) and Cytb (cytochrome b), which are known to be regulated by GR and NF-κB. Increased expression of Trx2 differentially affects the expression of Cytb. The glucocorticoid dexamethasone potentiates the expression of Cytb, whereas TNFα (tumour necrosis factor α) down-regulates it. These results suggest a regulatory role for Trx2 in GR and NF-κB signalling pathways.
GDI-1 preferably interacts with Rab10 in insulin-stimulated GLUT4 translocation
Authors: Chen Yu , Deng Yongqiang , Zhang Jinzhong , Yang Lu , Xie Xiangyang , Xu Tao
Published: July 2009

Insulin stimulates GLUT4 (glucose transporter 4) translocation in adipocytes and muscles. An emerging picture is that Rab10 could bridge the gap between the insulin signalling cascade and GLUT4 translocation in adipocytes. In the present study, two potential effectors of Rab10, GDI (guanine-nucleotide-dissociation inhibitor)-1 and GDI-2, are characterized in respect to their roles in insulin-stimulated GLUT4 translocation. It is shown that both GDI-1 and GDI-2 exhibit similar distribution to GLUT4 and Rab10 at the TGN (trans-Golgi network) and periphery structures. Meanwhile, GDI-1 clearly interacts with Rab10 with higher affinity, as shown by both immunoprecipitation and in vivo FRET (fluorescence resonance energy transfer). In addition, the participation of GDIs in GLUT4 translocation is illustrated when overexpression of either GDI inhibits insulin-stimulated GLUT4 translocation in 3T3-L1 adipocytes. Taken together, we propose that GDI-1 is preferentially involved in insulin-stimulated GLUT4 translocation through facilitating Rab10 recycling.
Molecular recognition of physiological substrate noradrenaline by the adrenaline-synthesizing enzyme PNMT and factors influencing its methyltransferase activity
Authors: Drinkwater Nyssa , Gee Christine L. , Puri Munish , Criscione Kevin R. , McLeish Michael J. , Grunewald Gary L. , Martin Jennifer L.
Published: July 2009

Substrate specificity is critically important for enzyme catalysis. In the adrenaline-synthesizing enzyme PNMT (phenylethanolamine N-methyltransferase), minor changes in substituents can convert substrates into inhibitors. Here we report the crystal structures of six human PNMT complexes, including the first structure of the enzyme in complex with its physiological ligand R-noradrenaline. Determining this structure required rapid soak methods because of the tendency for noradrenaline to oxidize. Comparison of the PNMT–noradrenaline complex with the previously determined PNMT–p-octopamine complex demonstrates that these two substrates form almost equivalent interactions with the enzyme and show that p-octopamine is a valid model substrate for PNMT. The crystal structures illustrate the adaptability of the PNMT substrate binding site in accepting multi-fused ring systems, such as substituted norbornene, as well as noradrenochrome, the oxidation product of noradrenaline. These results explain why only a subset of ligands recognized by PNMT are methylated by the enzyme; bulky substituents dictate the binding orientation of the ligand and can thereby place the acceptor amine too far from the donor methyl group for methylation to occur. We also show how the critical Glu185 catalytic residue can be replaced by aspartic acid with a loss of only 10-fold in catalytic efficiency. This is because protein backbone movements place the Asp185 carboxylate almost coincident with the carboxylate of Glu185. Conversely, replacement of Glu185 by glutamine reduces catalytic efficiency almost 300-fold, not only because of the loss of charge, but also because the variant residue does not adopt the same conformation as Glu185.
Role of MCP-1 in cardiovascular disease: molecular mechanisms and clinical implications
Authors: Niu Jianli , Kolattukudy Pappachan E.
Published: July 2009

Many of the major diseases, including cardiovascular disease, are widely recognized as inflammatory diseases. MCP-1 (monocyte chemotactic protein-1) plays a critical role in the development of cardiovascular diseases. MCP-1, by its chemotactic activity, causes diapedesis of monocytes from the lumen to the subendothelial space where they become foam cells, initiating fatty streak formation that leads to atherosclerotic plaque formation. Inflammatory macrophages probably play a role in plaque rupture and the resulting ischaemic episode as well as restenosis after angioplasty. There is strong evidence that MCP-1 plays a major role in myocarditis, ischaemia/reperfusion injury in the heart and in transplant rejection. MCP-1 also plays a role in cardiac repair and manifests protective effects under certain conditions. Such protective effects may be due to the induction of protective ER (endoplasmic reticulum) stress chaperones by MCP-1. Under sustained ER stress caused by chronic exposure to MCP-1, the protection would break down resulting in the development of heart failure. MCP-1 is also involved in ischaemic angiogenesis. The recent advances in our understanding of the molecular mechanisms that might be involved in the roles that MCP-1 plays in cardiovascular disease are reviewed. The gene expression changes induced by the signalling events triggered by MCP-1 binding to its receptor include the induction of a novel zinc-finger protein called MCPIP (MCP-1-induced protein), which plays critical roles in the development of the pathophysiology caused by MCP-1 production. The role of the MCP-1/CCR2 (CC chemokine receptor 2) system in diabetes, which is a major risk factor for cardiovascular diseases, is also reviewed briefly. MCP-1/CCR2- and/or MCPIP-targeted therapeutic approaches to intervene in inflammatory diseases, including cardiovascular diseases, may be feasible.
Multimodal optical workstation for simultaneous linear, nonlinear microscopy and nanomanipulation: Upgrading a commercial confocal inverted microscope
Authors: Mathew Manoj , Santos Susana I. C. O. , Zalvidea Dobryna , Loza-Alvarez Pablo
Published: July 2009

In this work we propose and build a multimodal optical workstation that extends a commercially available confocal microscope (Nikon Confocal C1-Si) to include nonlinear/multiphoton microscopy and optical manipulation/stimulation tools such as nanosurgery. The setup allows both subsystems (confocal and nonlinear) to work independently and simultaneously. The workstation enables, for instance, nanosurgery along with simultaneous confocal and brightfield imaging. The nonlinear microscopy capabilities are added around the commercial confocal microscope by exploiting all the flexibility offered by this microscope and without need for any mechanical or electronic modification of the confocal microscope systems. As an example, the standard differential interference contrast condenser and diascopic detector in the confocal microscope are readily used as a forward detection mount for second harmonic generation imaging. The various capabilities of this workstation, as applied directly to biology, are demonstrated using the model organism Caenorhabditis elegans.
Energetics investigation on encapsulation of protein/peptide drugs in carbon nanotubes
Authors: Chen Qu , Wang Qi , Liu Ying-Chun , Wu Tao , Kang Yu , Moore Joshua D. , Gubbins Keith E.
Published: July 2009

This work focuses on the dynamic properties and energetics of the protein/peptide drug during its transport through carbon nanotubes (CNTs). A systematic study was performed on the interaction between the peptide and the CNTs. In the molecular dynamics (MD) simulations, the protein/peptide molecule Zadaxin® is observed to be encapsulated inside the nanotube after its spontaneous insertion and oscillates around the center of the tube, where the van der Waals interaction energy is observed to be a minimum. Furthermore, it is found by performing steered MD simulations that the pulling force applied to the peptide reaches a maximum value, which demonstrates the ability of the CNTs to trap protein/peptide drugs. Such effects, attributed to van der Waals interactions, can be influenced by varying the lengths and diameters of the CNTs. Longer nanotubes provide a broader area to trap the peptide, while smaller nanotubes are able to encapsulate the peptide with a deeper interaction energy well. This investigation provides insights into nanoscale pharmaceutical drug delivery devices.
Hybrid core-multishell nanowire forests for electrical connector applications
Authors: Kapadia Rehan , Ko Hyunhyub , Chueh Yu-Lun , Ho Johnny C. , Takahashi Toshitake , Zhang Zhenxing , Javey Ali
Published: July 2009

Electrical connectors based on hybrid core-multishell nanowire forests that require low engagement forces are demonstrated. The physical binding and electrical connectivity of the nanowire electrical connectors arise from the van der Waals interactions between the conductive metallic shells of the engaged nanowire forests. Specifically, the nanofibrillar structure of the connectors causes an amplification of the contact area between the interpenetrating nanowire arrays, resulting in strong adhesion with relatively low interfacial resistance. The nanowire electrical connectors may enable the exploration of a wide range of applications involving reversible assembly of micro- and macroscale components with built-in electrical interfacing.
Mechanical testing of glassy and rubbery polymers in numerical simulations: Role of boundary conditions in tensile stress experiments
Authors: Makke Ali , Perez Michel , Lame Olivier , Barrat Jean-Louis
Published: July 2009

We use coarse-grained molecular dynamics simulations to perform tensile test deformation on glassy and rubbery polymer samples using two types of driving for the deformation. We compare the outcome from a standard homogeneous deformation procedure with that of a boundary driven procedure in which the sample is driven by the nanometric equivalent of grips. No significant difference is observed in both uniaxial and triaxial tensile experiments. Implications for testing the behavior of nonhomogeneous polymer materials are briefly discussed.
Exploring dark current voltage characteristics of micromorph silicon tandem cells with computer simulations
Authors: Sturiale A. , Li Hongbo T. , Rath J. K. , Schropp R. E. I. , Rubinelli F. A.
Published: July 2009

The transport mechanisms controlling the forward dark current-voltage characteristic of the silicon micromorph tandem solar cell were investigated with numerical modeling techniques. The dark current-voltage characteristics of the micromorph tandem structure at forward voltages show three regions: two with an exponential dependence and a third where the current grows more slowly with the applied voltage. In the first exponential region the current is entirely controlled by recombination through gap states of the top cell. In the second exponential region the current is controlled by the mixture of recombination through gap states of both the top and bottom cells and by free carrier diffusion along the a-Si:H intrinsic layer. In the third region the onset of the electron space charge limited current on the a-Si:H top cell can be observed along with some other mechanisms that are discussed in the paper. The high forward dark J-V curve of the tandem cell can be used as diagnosis tool to quickly inspect the efficiency of the recombination junction in recombining the electron-hole pairs generated under illumination in the top and bottom cells. The dark current at high forward voltages is highly influenced by the amount of electron-hole pairs thermally generated inside the recombination junction.
Monte Carlo simulation on ferroelectric response to magnetic field in an elastic Ising spin chain
Authors: Yao Xiaoyan , Lo Veng Cheong , Liu Jun-Ming
Published: July 2009

The fantastic ferroelectric response to the magnetic field observed in Ca3CoMnO6 compound, where the ferroelectricity is driven by the collinear magnetism, is investigated by using Monte Carlo simulation based on a one-dimensional elastic Ising model. The microscopic domain structures of spins and ionic displacements are evaluated at different temperatures under different external magnetic fields. It is revealed that the up-up-down-down (↑↑↓↓) spin domains clamped with the domains of ionic displacement are responsible for the exotic ferroelectric behavior upon different magnetic fields in the low temperature range.
Reversible gels of patchy particles: Role of the valence
Authors: Russo John , Tartaglia Piero , Sciortino Francesco
Published: July 2009

We simulate a binary mixture of colloidal patchy particles with two and three patches, respectively, for several relative concentrations and hence relative average valences. For these limited-valence systems, it is possible to reach low temperatures, where the lifetime of the patch-patch interactions becomes longer than the observation time without encountering phase separation in a colloid-poor (gas) and a colloid rich (liquid) phase. The resulting arrested state is a fully connected long-lived network where particles with three patches provide the branching points connecting chains of two-patch particles. We investigate the effect of the valence on the structural and dynamic properties of the resulting gel and attempt to provide a theoretical description of the formation and of the resulting gel structure based on a combination of the Wertheim theory for associated liquids and the Flory–Stockmayer approach for modeling chemical gelation.
The influence of Sn doping on the growth of In2O3 on Y-stabilized ZrO2(100) by oxygen plasma assisted molecular beam epitaxy
Authors: Bourlange A. , Payne D. J. , Palgrave R. G. , Zhang H. , Foord J. S. , Egdell R. G. , Jacobs R. M. J. , Veal T. D. , King P. D. C. , McConville C. F.
Published: July 2009

The influence of Sn doping on the growth of In2O3 on Y-stabilized ZrO2(100) by oxygen plasma assisted molecular beam epitaxy has been investigated over a range of substrate temperatures between 650 and 900 °C. The extent of dopant incorporation under a constant Sn flux decreases monotonically with increasing substrate temperature, although the n-type carrier concentration in “overdoped” films grown at 650 °C is lower than in films with a lower Sn concentration grown at 750 °C. The small increase in lattice parameter associated with Sn doping leads to improved matching with the substrate and suppresses breakup of the films into square islands observed in high temperature growth of undoped In2O3 on Y-stabilized ZrO2(100). Plasmon energies derived from infrared reflection spectra of Sn-doped films are found to be close to satellite energies in core level photoemission spectroscopy, but for a nominally undoped reference sample there is evidence for carrier accumulation at the surface. This influences both the In 3d core line shape and the intensity of a peak close to the Fermi energy associated with photoemission from the conduction band.
Doping-dependent nanofaceting on silicon nanowire surfaces
Authors: Li Fang , Nellist Peter D. , Cockayne David J. H.
Published: July 2009

Silicon nanowires with axially varying n- and p-doping were grown by the vapor-liquid-solid approach using gold as the catalyst. The nanowire sidewalls exhibit periodic nanofaceting, which is found to be dopant-dependent. It is shown that the nanofaceting occurs during the enhanced sidewall growth that arises when the diborane dopant gas is introduced. The nanowires are axially oriented along ⟨111⟩, and the crystallographic planes on which the nanofaceting occurs are determined to be {111} and {100}.
Silicon-rich SiO2/SiO2 multilayers: A promising material for the third generation of solar cell
Authors: Gourbilleau F. , Ternon C. , Maestre D. , Palais O. , Dufour C.
Published: July 2009

Si-rich-SiO2(SRSO)/SiO2 multilayers (MLs) have been grown by reactive magnetron sputtering. The presence of silicon nanoclusters (Si-ncls) within the SRSO sublayer and annealing temperature influence optical absorption as well as photoluminescence. The optimized annealing temperature has been found to be 1100 °C, which allows the recovery of defects and thus enhances photoluminescence. Four MLs with Si-ncl size ranging from 1.5 to 8 nm have been annealed using the optimized conditions and then studied by transmission measurements. Optical absorption has been modeled so that a size effect in the linear absorption coefficient α (in cm−1) has been evidenced and correlated with TEM observations. It is demonstrated that amorphous Si-ncl absorption is fourfold higher than that of crystalline Si-ncls.
The role of rotatable anisotropy in the asymmetric magnetization reversal of exchange biased NiO/Ni bilayers
Authors: Yang P. Y. , Song C. , Fan B. , Zeng F. , Pan F.
Published: July 2009

The angular dependence of asymmetric magnetization reversal in exchange biased NiO/Ni bilayers was investigated using a vectorial vibrating sample magnetometer. Different angular dependences of the exchange field, coercivity, and asymmetry were obtained by tuning the NiO layer thickness (tNiO). Comparing the experimental data with the theoretical calculations, we found that the asymmetric magnetization reversal of bilayers with larger tNiO was dominated by competing uniaxial and unidirectional anisotropies, and an additional rotatable anisotropy was required in the simulation to correctly describe the magnetization reversal of bilayers with smaller tNiO. The irreversible magnetization switches of a large amount of antiferromagnetic grains in thin NiO layers are responsible for the rotatable anisotropy, which may also significantly affect the shape of the hysteresis loops and the range of angles with symmetric magnetization reversal.
Effects of ultraviolet treatment on the contact resistivity and electronic transport at the Ti/ZnO interfaces
Authors: Lin Yow-Jon , Tsai Chia-Lung , Liu W.-R. , Hsieh W. F. , Hsu C.-H. , Tsao Hou-Yen , Chu Jian-An , Chang Hsing-Cheng
Published: July 2009

We report on the effect of ultraviolet (UV) treatment on the specific contact resistance (ρ) and electronic transport at the Ti/ZnO interfaces. The experimental results show the same barrier height of Ti/ZnO samples without UV treatment as Ti/ZnO samples with UV treatment and the higher ρ of Ti/ZnO samples with UV treatment than Ti/ZnO samples without UV treatment, suggesting the barrier-height independence of ρ. Based on the thermionic-emission model and x-ray photoelectron spectroscopy results, we found that the induced decrease in the number of the hydroxides at the surface region of ZnO by UV treatment resulted in decreases in the electron concentration near the surface region and the excess current component related to tunneling, increasing in ρ of Ti/ZnO samples.
Investigation on configuration of self-assembly in magnetic fluid film under a magnetic field
Authors: Kou Yao , Di Ziyun , Chen Xianfeng
Published: July 2009

We experimentally study transmittances of water-based magnetic fluid (MF) film and the behaviors of nanoparticles under an external magnetic field. The transmittances of two orthogonally polarized rays exhibit different curve shapes. The experimental data are used to determine the values of three important parameters that are related to the intensity of the field. Based on the relationship between these parameters and the field, the self-assembly of particles is discussed. The method introduced in this paper can be employed as an available means to inspect the behavior of the particles in MF.
Vertical electronic excitation with a dielectric continuum model of solvation including volume polarization. II. Implementation and applications
Authors: Chipman Daniel M.
Published: July 2009

A practical implementation is described for calculation of solute vertical electronic excitation with a new dielectric continuum model of solvation. Particular attention is given to the specific aspects associated with quantum mechanical treatment of the solute, which leads to volume polarization effects arising from penetration of the solute charge density outside the cavity nominally enclosing it. Some representative computations are presented using this method and several other related methods from the literature for the lowest vertical transitions of an acetone and a water molecule in dielectric continuum models of aqueous solution. These illustrate the two possible extreme behaviors wherein the acetone transition is found to be little affected by volume polarization, while the water transition is found to be quite sensitive to volume polarization, the latter so much so that approximate treatments of volume polarization are inadequate.