bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrohydrodynamic force and aerodynamic flow acceleration in surface dielectric barrier discharge
Authors: Boeuf J. P. , Pitchford L. C.
Published: May 2005

Surface discharges created in dielectric barrier discharge (DBD) configurations have been proposed as actuators for flow control in aerodynamic applications. We focus on DBDs operating in a glow regime, i.e., where the discharge is sustained by ion-induced secondary electron emission from the surface and volume ionization. After a brief discussion of the force per unit volume acting on the flow and due to the momentum transfer from charged particles to neutral molecules, we present calculations of this force based on a two-dimensional fluid model of the surface discharge. We show that this force is of the same nature as the electric wind in a corona discharge. However, the force in a DBD is localized in the cathode sheath region of the discharge expanding along the dielectric surface. While its intensity is much larger than the analogous force in a direct-current corona discharge, it is active during less than one hundred nanoseconds for each discharge pulse and the time-averaged forces in the two cases are comparable, at least for the conditions we have chosen for this study.
On asymptotic Hopf invariant for Hamiltonian systems
Authors: Deryabin Mikhail V.
Published: May 2005

We give a definition and discuss main properties of the asymptotic Hopf invariant, or helicity, for Hamiltonian systems. The definition relies on a technical construction which is a definition of a relative Hopf invariant for divergence-free vector fields in multiconnected domains of the following type: (flatdomaininR2)×(circle). We prove correctness of the definitions, and discuss ergodic interpretation of the Hamiltonian Hopf invariant, together with its relation with the Calabi invariant.
Tailored blast wave formation: Developing experiments pertinent to laboratory astrophysics
Authors: Moore Alastair S. , Symes Daniel R. , Smith Roland A.
Published: May 2005

The first production of “tailored” blast waves in a cluster media using an intense, 2×1016Wcm−2, laser pulse is reported. This new technique produces cylindrical blast waves with a strong axial modulation of variable spatial frequency as a seed for instability growth. Spherical or cylindrical colliding blast waves can also be produced. Energy deposition in the cluster medium was modified using moderate-power (<1015Wcm−2) “laser-machining,” which destroyed clusters in selected regions while keeping the atomic density constant. Electron density profiles track the time evolution showing the production of strongly modulated blast waves and the development of a thin shell after ≈6ns in H2. Similarity parameters suggest that the hydrogen results are hydrodynamically scalable, but instabilities are precluded by the lack of radiation and low Reynolds number. Similar argon and xenon experiments do not form blast waves on the studied time scale, but indicate that radiation might become influential later in the evolution.
Neveu–Schwarz fivebrane and tachyon condensation
Authors: Ghoshal Debashis , Jatkar Dileep P. , Kreuzer Maximilian
Published: May 2005

We argue that a semi-infinite D6-brane ending on an NS5-brane can be obtained from the condensation of the tachyon on the unstable D9-brane of type IIA theory. The construction uses a combination of the descriptions of these branes as solitons of the worldvolume theory of the D9-brane. The NS5-brane, in particular, involves a gauge bundle which is operator valued, and hence is better thought of as a gerbe.
Synthesis and memory effect study of Ge nanocrystals embedded in LaAlO3 high-k dielectrics
Authors: Lu X. B. , Lee P. F. , Dai J. Y.
Published: May 2005

A floating gate memory structure utilizing Ge nanocrystals embedded in LaAlO3 (LAO) high-k dielectric films has been fabricated by pulsed-laser deposition. A cross-sectional high-resolution transmission electron microscopy study revealed that the floating gate structure contains 5-nm-diam spherelike Ge nanocrystals embedded in amorphous LAO. A significant memory effect with a very high density of charge storage up to 2×1013∕cm2 in the Ge nanocrystals and a maximum flat band voltage shift of 3.2 V have been achieved for the trilayer structure of LAO(8nm)∕Ge∕LAO(3nm)∕Si. The memory structure utilizing the Ge nanocrystals grown in 1 min showed excellent charge retention characteristics, whereas the decay in memory capacitance after 104s of stress under a flat band voltage was only 8%. These results suggest that this memory structure utilizing Ge nanocrystals embedded in a LAO dielectric offers a high potential for the further scaling of floating gate memory devices. In addition, the effects of Ge growth time, and thus the size and density of the Ge nanocrystals, to the charge storage and charge retention characteristics were also studied.
Size-dependent electronic structures of ZnO nanowires
Authors: Wang Juan , An Xipo , Li Quan , Egerton R. F.
Published: May 2005

ZnO nanowires with a diameter distribution from 20 to 100 nm were fabricated by a simple thermal evaporation process. Two different types of nanowire (circular versus hexagonal cross section) were obtained by controlling the growth conditions. The size-dependent electronic structures of both types of samples were investigated using valence electron energy-loss spectroscopy. Both the common features (surface plasmon, bulk plasmon width) and the differences (O 2s interband transition, bulk plasmon energy) between the two types of samples are discussed. The experimental results strongly suggest that ZnO nanowires with hexagonal cross section and low-index terminating surfaces are of high electronic quality, even at 20 nm diameter, and can thus serve as effective building blocks for optoelectronic nanodevices.
Analysis of thermal images from diode lasers: Temperature profiling and reliability screening
Authors: Kozlowska Anna , Latoszek Mateusz , Tomm Jens W. , Weik Fritz , Elsaesser Thomas , Zbroszczyk Mariusz , Bugajski Maciej , Spellenberg B. , Bassler M.
Published: May 2005

Imaging thermography in the 3–5μm wavelength range is applied to the analysis of thermal properties of high-power diode lasers. We investigate these devices by inspecting their front facets as well as their active regions along the resonator. The latter is done through top windows within the substrate. Raw data are found to be mostly interfered by thermal radiation traveling through the substrate, which is transparent for infrared light. Substracting this contribution and recalibration allows for obtaining realistic temperature profiles along laser structures. Facet heating is analyzed complementary by micro-Raman spectroscopy. We show how hot spots at the front facet, in the substrate, or even in the active region within the substrate are discovered. Our approach paves the way for an advanced methodology of device screening.
Terahertz cavity-enhanced attenuated total reflection spectroscopy
Authors: Schiwon Robert , Schwaab Gerhard , Bründermann Erik , Havenith Martina
Published: May 2005

We realized cavity-enhanced absorption spectroscopy in the terahertz spectral region by combining multilayer mirrors with an attenuated total reflection technique. Using this technique, we were able to observe an absorbance of biological samples with a minimum detectable concentration as low as 8×10−10mol∕mm2. The absorbance between 75cm−1 and 115cm−1 was measured using a monolithic resonator of high-purity silicon. We demonstrate that the sensitivity of the attenuated total reflection design is significantly improved by adding multilayer mirrors for the THz region.
Studies of superconducting field effect transistors with sheet resistances close to the quantum resistance
Authors: Logvenov G. Yu. , Schneider C. W. , Mannhart J. , Barash Yu. S.
Published: May 2005

The effects of applied electric fields on bilayer heterostructures with sheet resistances close to the quantum resistance RQ=h∕4e2 have been studied. The field effect provides evidence that at low temperatures the DS channels consist of superconducting islands coupled by underdoped weak links. By applying electric fields, the critical temperature of the channels is shifted by 10 K and the zero bias anomalies of the weak links are reversed.
Lattice distortion∕disordering and local amorphization in the dendrites of a Ti66.1Cu8Ni4.8Sn7.2Nb13.9 nanostructure–dendrite composite during intersection of shear bands
Authors: Kim K. B. , Das J. , Baier F. , Eckert J.
Published: May 2005

The dendrites in the Ti66.1Cu8Ni4.8Sn7.2Nb13.9 nanostructure–dendrite composite deformed up to 25% reveal an interaction of primary and secondary shear bands. A detailed analysis of the lattice images of the interaction regions in the dendrites using high resolution transmission electron microscopy indicates local amorphization and lattice distortion∕disordering near to the apex of the primary shear bands in the dendrite. Furthermore, moiré fringes are formed at the edge of the interaction regions between the primary and secondary shear bands suggesting gradual structural changes in the dendrites.
NiGe on Ge(001) by reactive deposition epitaxy: An in situ ultrahigh-vacuum transmission-electron microscopy study
Authors: Nath R. , Soo C. W. , Boothroyd C. B. , Yeadon M. , Chi D. Z. , Sun H. P. , Chen Y. B. , Pan X. Q. , Foo Y. L.
Published: May 2005

We use an ultrahigh-vacuum transmission-electron microscopy, equipped with an electron-beam evaporator directed at a heating stage in the pole piece, to follow the reaction pathway of Ni on Ge(001) substrate at 300 °C. Using reactive deposition, we illustrate that epitaxial orthorhombic NiGe (a=5.381Å, b=3.428Å, and c=5.811Å) phase can be grown directly without the initial formation of metal-rich Ni2Ge phase. The epitaxial orientation of the NiGe islands and the underlying Ge(001) substrate were found to be NiGe(1¯01)∕∕Ge(001) and NiGe[010]∕∕Ge[110].
Threshold current density of electromigration in eutectic SnPb solder
Authors: Yeh Y. T. , Chou C. K. , Hsu Y. C. , Chen Chih , Tu K. N.
Published: May 2005

Electromigration has emerged as an important reliability issue in the microelectronics packaging industry since the dimension of solder joints has continued to shrink. In this letter, we report a technique that enables the precise measurement of the important parameters of solder electromigration, such as activation energy, critical length, threshold current density, effective charge numbers, and electromigration rate. Patterned Cu∕Ti films in a Si trench were employed for eutectic SnPb solder to be reflowed on, and thus solder Blech specimens were fabricated. Atomic force microscope was used to measure the depletion volume caused by electromigration on the cathode end. The threshold current density is estimated to be 8.5×103A∕cm2 at 100 °C, which relates directly to the maximum allowable current that a solder joint can carry without electromigration damage. This technique facilitates the scientifically systematic investigation of electromigration in solders.
Observation of In concentration variations in InGaN∕GaN quantum-well heterostructures by scanning capacitance microscopy
Authors: Zhou X. , Yu E. T. , Florescu D. I. , Ramer J. C. , Lee D. S. , Ting S. M. , Armour E. A.
Published: May 2005

Scanning capacitance microscopy and spectroscopy have been used to analyze nanoscale variations in electronic properties in In0.15Ga0.85N∕GaN quantum-well structures grown by metalorganic chemical vapor deposition. Scanning capacitance imaging reveals that localized regions within the In0.15Ga0.85N quantum well, up to ∼25nm in radius and present at densities in the range of 109–1010cm−2, exhibit markedly increased electron accumulation relative to surrounding areas. Spatially resolved scanning capacitance spectroscopy combined with numerical simulations indicates that these regions of enhanced electron accumulation are characterized by locally increased In concentration in the quantum well. The presence of these localized In-rich regions is correlated with reported observations of increased luminescence efficiency, presumably due to carrier localization and consequently enhanced radiative recombination, in very similarly grown samples. In addition, these results demonstrate the ability, using a surface characterization technique, to image variations in composition in a subsurface quantum well with nanoscale spatial resolution.
Observation of tip-to-sample heat transfer in near-field optical microscopy using metal-coated fiber probes
Authors: Gucciardi P. G. , Patanè S. , Ambrosio A. , Allegrini M. , Downes A. D. , Latini G. , Fenwick O. , Cacialli F.
Published: May 2005

Metal-coated scanning near-field optical microscopy fiber probes can undergo significant heating due to partial absorption of the coupled light by the metallic film covering the apical zone. In this letter we report experimental evidence of tip-to-sample heat transfer on a 7,7′,8,8′-tetracyanoquinodimethane molecular crystal. Local melting is observed at nanometric tip–sample distances, when increasing the laser power injected into the fiber above a threshold of 8.8mW. Hole formation and material displacement are observed, as well as failure of the shear-force-based imaging process, due to partial sticking of the melted material to the probe.
Nitrogen incorporation effects on gain properties of GaInNAs lasers: Experiment and theory
Authors: Thränhardt A. , Kuznetsova I. , Schlichenmaier C. , Koch S. W. , Shterengas L. , Belenky G. , Yeh J.-Y. , Mawst L. J. , Tansu N. , Hader J. , Moloney J. V. , Chow W. W.
Published: May 2005

Gain properties of GaInNAs lasers with different nitrogen concentrations in the quantum wells are investigated experimentally and theoretically. Whereas nitrogen incorporation induces appreciable modifications in the spectral extension and the carrier density dependence of the gain, it is found that the linewidth enhancement factor is reduced by inclusion of nitrogen, but basically unaffected by different nitrogen content due to the balancing between gain and index changes.
Nonlinear response of a superconducting filter: To compress or not to compress
Authors: Salkola M. I.
Published: May 2005

Nonlinearities in passive superconducting filters give rise to gain and intermodulation distortions that can diminish their ability to attenuate large interfering signals. It is shown that the departure from gain linearity depends on the phase of a nonlinear interaction. If the nonlinear interaction arises from the kinetic inductance of a superconducting state, the signal frequency determines whether the superconducting filter exhibits gain expansion or compression. The absence of gain expansion is a signature of the nonlinear interaction that is mainly resistive.
Chemical sputtering of carbon by nitrogen ions
Authors: Jacob W. , Hopf C. , Schlüter M.
Published: May 2005

Chemical sputtering of amorphous hydrogenated carbon layers by nitrogen molecular ions was studied as a function of the ion energy in the range from 30to900eV. The sputtering yield shows only a very weak variation with energy in the range from 900 down to 50eV. For lower energies it decreases significantly. This behavior is interpreted as an indication of chemical sputtering.
Effect of atomic configuration and liquid stability on the glass-forming ability of Ca-based metallic glasses
Authors: Park E. S. , Kim D. H.
Published: May 2005

In the present study, we report a Ca–Mg–Ni alloy exhibiting significantly improved glass-forming ability (GFA). The Ca60Mg25Ni15 bulk metallic glass (BMG) with a diameter of 13mm is successfully fabricated by a conventional copper mold casting method in air atmosphere. The ΔTx, Trg, K, and γ parameters exhibit very poor correlation with the GFA. However, the σ parameter exhibits a far better correlation with GFA, indicating that the liquid phase stability and atomic size mismatch dominantly affect the GFA of Ca-based ternary BMGs. The GFA of alkaline-earth-metal-based ternary BMGs such as Ca- and Mg-based BMGs cannot be described properly only by considering thermodynamic and/or kinetic criterion (ΔTx, Trg, K, and γ parameters), but can well be described by considering atomic configuration criterion as well as thermodynamic criterion (σ parameter).
Using Geographic Information Systems to Measure District Change, 2000–2002
Authors: Crespin Michael H.
Published: May 2005

In this article, I use geographic information systems to develop a continuous measure of district continuity and change following the 2000–02 congressional redistricting cycle. The new measure provides details of where the new population in a district came from and how the old population was distributed within new districts. This measure is then used to demonstrate the independent and interactive influence of district change on competition for congressional elections.
Bias in Conditional and Unconditional Fixed Effects Logit Estimation: A Correction
Authors: Coupé Tom
Published: May 2005

In a recent paper published in this journal, Katz (2001) compares the bias in conditional and unconditional fixed effects logit estimation using Monte Carlo Simulation. This note shows that while Katz's (2001) specification has “wrong” fixed effects (in the sense that the fixed effects are the same for all individuals), his conclusions still hold if I correct his specification (so that the fixed effects do differ over individuals). This note also illustrates the danger, when using logit, of including dummies when no fixed effects are present.
Age-dependent residual tensile strains are present in the dura mater of rats
Authors: Henderson James H , Nacamuli Randall P , Zhao Betty , Longaker Michael T , Carter Dennis R
Published: May 2005

The objectives of this study were to determine whether residual tensile strains exist in the dura mater of mammalsin vivo, and whether the strains are age-dependent. We made incisions in the parietal dura mater of immature and mature rats, and measured the retraction of the dura mater from each incision. We then used a finite-element model to calculate the strain present in the parietal dura mater of each rat. We found that age-dependent residual tensile strains are present in the dura mater of rats. The mean average residual strain of the immature rats was significantly larger than that of the mature rats (4.96±1.54% (s.d.) versus 0.39±0.13%,p<0.0001), with the mean strain calculated in the mature rats of the order of the minimum measurement that could be made using our experimental approach. In addition, in the immature rats mean residual strain in the longitudinal direction was significantly larger than mean residual strain in the transverse direction (6.11±3.62% versus 3.82±2.64%,p=0.0218). Our findings show that age-dependent residual tensile strains exist in the dura mater of rats. We speculate that these strains may reflect the rate and direction of cranial growth and may also influence cranial healing.
Linear response of Venice storm gates to incident waves
Authors: Adamo Andrea , Mei Chiang C
Published: May 2005

In laboratory experiments, it is known that the mobile storm barriers designed for Venice inlets can be excited subharmonically by incident waves to oscillate in modes that can reduce the efficiency of protection against storm tides. Based on the idealization that a barrier is composed of many gates across the middle of an infinitely long channel, resonance of the articulated structure has been shown to originate from the existence of trapped modes, and is possible only via a nonlinear mechanism. In reality, the inlet geometry is different in that two parallel jetties are present only on the sea side; the barrier faces a large open space in the lagoon. Here we give a linear scattering theory for such a geometry. An energy identity is derived to provide a global check for numerical computations. Gate responses are first carried out for a wide range of incident wave frequencies. Resonances are found at frequencies close to the natural frequencies predicted recently by Li and Mei (Li & Mei 2003
Appl. Ocean Res.
25
, 115–126). Responses to random incident waves described by JONSWAP spectrum are discussed.
Iron-Sulfur Cluster Biogenesis in Chloroplasts. Involvement of the Scaffold Protein CpIscA
Authors: Abdel-Ghany Salah E. , Ye Hong , Garifullina Gulnara F. , Zhang Lihong , Pilon-Smits Elizabeth A.H. , Pilon Marinus
Published: May 2005

The chloroplast contains many iron (Fe)-sulfur (S) proteins for the processes of photosynthesis and nitrogen and S assimilation. Although isolated chloroplasts are known to be able to synthesize their own Fe-S clusters, the machinery involved is largely unknown. Recently, a cysteine desulfurase was reported in Arabidopsis (Arabidopsis thaliana; AtCpNifS) that likely provides the S for Fe-S clusters. Here, we describe an additional putative component of the plastid Fe-S cluster assembly machinery in Arabidopsis: CpIscA, which has homology to bacterial IscA and SufA proteins that have a scaffold function during Fe-S cluster formation. CpIscA mRNA was shown to be expressed in all tissues tested, with higher expression level in green, photosynthetic tissues. The plastid localization of CpIscA was confirmed by green fluorescent protein fusions, in vitro import, and immunoblotting experiments. CpIscA was cloned and purified after expression in Escherichia coli. Addition of CpIscA significantly enhanced CpNifS-mediated in vitro reconstitution of the 2Fe-2S cluster in apo-ferredoxin. During incubation with CpNifS in a reconstitution mix, CpIscA was shown to acquire a transient Fe-S cluster. The Fe-S cluster could subsequently be transferred by CpIscA to apo-ferredoxin. We propose that the CpIscA protein serves as a scaffold in chloroplast Fe-S cluster assembly.
Toward Supportive Data Collection Tools for Plant Metabolomics
Authors: Jenkins Helen , Johnson Helen , Kular Baldeep , Wang Trevor , Hardy Nigel
Published: May 2005

Over recent years, a number of initiatives have proposed standard reporting guidelines for functional genomics experiments. Associated with these are data models that may be used as the basis of the design of software tools that store and transmit experiment data in standard formats. Central to the success of such data handling tools is their usability. Successful data handling tools are expected to yield benefits in time saving and in quality assurance. Here, we describe the collection of datasets that conform to the recently proposed data model for plant metabolomics known as ArMet (architecture for metabolomics) and illustrate a number of approaches to robust data collection that have been developed in collaboration between software engineers and biologists. These examples also serve to validate ArMet from the data collection perspective by demonstrating that a range of software tools, supporting data recording and data upload to central databases, can be built using the data model as the basis of their design.
Genome Cluster Database. A Sequence Family Analysis Platform for Arabidopsis and Rice
Authors: Horan Kevin , Lauricha Josh , Bailey-Serres Julia , Raikhel Natasha , Girke Thomas
Published: May 2005

The genome-wide protein sequences from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) spp. japonica were clustered into families using sequence similarity and domain-based clustering. The two fundamentally different methods resulted in separate cluster sets with complementary properties to compensate the limitations for accurate family analysis. Functional names for the identified families were assigned with an efficient computational approach that uses the description of the most common molecular function gene ontology node within each cluster. Subsequently, multiple alignments and phylogenetic trees were calculated for the assembled families. All clustering results and their underlying sequences were organized in the Web-accessible Genome Cluster Database (http://bioinfo.ucr.edu/projects/GCD) with rich interactive and user-friendly sequence family mining tools to facilitate the analysis of any given family of interest for the plant science community. An automated clustering pipeline ensures current information for future updates in the annotations of the two genomes and clustering improvements. The analysis allowed the first systematic identification of family and singlet proteins present in both organisms as well as those restricted to one of them. In addition, the established Web resources for mining these data provide a road map for future studies of the composition and structure of protein families between the two species.
The Institute for Genomic Research Osa1 Rice Genome Annotation Database
Authors: Yuan Qiaoping , Ouyang Shu , Wang Aihui , Zhu Wei , Maiti Rama , Lin Haining , Hamilton John , Haas Brian , Sultana Razvan , Cheung Foo , Wortman Jennifer , Buell C. Robin
Published: May 2005

We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 nontransposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.
The Maize Genetics and Genomics Database. The Community Resource for Access to Diverse Maize Data
Authors: Lawrence Carolyn J. , Seigfried Trent E. , Brendel Volker
Published: May 2005

The Maize Genetics and Genomics Database (MaizeGDB) serves the maize (Zea mays) research community by making a wealth of genetics and genomics data available through an intuitive Web-based interface. The goals of the MaizeGDB project are 3-fold: to provide a central repository for public maize information; to present the data through the MaizeGDB Web site in a way that recapitulates biological relationships; and to provide an array of computational tools that address biological questions in an easy-to-use manner at the site. In addition to these primary tasks, MaizeGDB team members also serve the community of maize geneticists by lending technical support for community activities, including the annual Maize Genetics Conference and various workshops, teaching researchers to use both the MaizeGDB Web site and Community Curation Tools, and engaging in collaboration with individual research groups to make their unique data types available through MaizeGDB.
MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research
Authors: Zhang Peifen , Foerster Hartmut , Tissier Christophe P. , Mueller Lukas , Paley Suzanne , Karp Peter D. , Rhee Seung Y.
Published: May 2005

MetaCyc (http://metacyc.org) contains experimentally determined biochemical pathways to be used as a reference database for metabolism. In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome. To increase the breadth of pathways and enzymes, more than 60 plant-specific pathways have been added or updated in MetaCyc recently. In contrast to MetaCyc, which contains metabolic data for a wide range of organisms, AraCyc is a species-specific database containing only enzymes and pathways found in the model plant Arabidopsis (Arabidopsis thaliana). AraCyc (http://arabidopsis.org/tools/aracyc/) was the first computationally predicted plant metabolism database derived from MetaCyc. Since its initial computational build, AraCyc has been under continued curation to enhance data quality and to increase breadth of pathway coverage. Twenty-eight pathways have been manually curated from the literature recently. Pathway predictions in AraCyc have also been recently updated with the latest functional annotations of Arabidopsis genes that use controlled vocabulary and literature evidence. AraCyc currently features 1,418 unique genes mapped onto 204 pathways with 1,156 literature citations. The Omics Viewer, a user data visualization and analysis tool, allows a list of genes, enzymes, or metabolites with experimental values to be painted on a diagram of the full pathway map of AraCyc. Other recent enhancements to both MetaCyc and AraCyc include implementation of an evidence ontology, which has been used to provide information on data quality, expansion of the secondary metabolism node of the pathway ontology to accommodate curation of secondary metabolic pathways, and enhancement of the cellular component ontology for storing and displaying enzyme and pathway locations within subcellular compartments.
Evaluation of left ventricular volumes and ejection fraction by automated gated myocardial SPECT versus cardiovascular magnetic resonance
Authors: Persson Eva , Carlsson Marcus , Palmer John , Pahlm Olle , Arheden Håkan
Published: May 2005

Background:  Electrocardiogram‐gated myocardial single‐photon emission computed tomography (SPECT) with 99mTc‐tetrofosmin allows simultaneous evaluation of myocardial perfusion and function. In this study, left ventricular volumes, ejection fraction (LVEF), and left ventricular wall volume (LVWV) derived from gated SPECT were compared with measurements from cardiovascular magnetic resonance (CMR), performed within a few hours.

Methods:  The study population included 55 patients with known or suspected coronary artery disease, including 13 patients with recent acute myocardial infarction. End‐diastolic (EDV) and end‐systolic (ESV) volumes, LVEF and LVWV were derived automatically from gated SPECT using commercially available software (QGS). In the CMR studies, manually delineated endocardial and epicardial borders on short‐axis slices were used to calculate the volumes.

Results:  Gated SPECT underestimated EDV by 35 ± 14 ml (mean ± SD) (P<0·001), ESV by 10 ± 13 ml (P<0·001), and LVEF by 4 ± 7 percentage points (P<0·001). There were no systematic difference in EDV, ESV or LVEF between the methods. SPECT underestimated LVWV by 49 ± 30 ml (P<0·001), with a trend towards increasing underestimation by SPECT for larger wall volumes.

Conclusion:  These findings show that gated SPECT slightly underestimates EDV, ESV and LVEF compared with CMR. This underestimation is systematic, however, indicating that ventricular volumes derived from gated SPECT are robust enough to guide clinical management. Estimates of LVWV in patients with large wall volumes are less accurate.
Nurses and the Genomic Revolution
Authors: Jenkins Jean , Grady Patricia A. , Collins Francis S.
Published: May 2005

Purpose

: To increase nurses' genetics and genomics literacy through a series of articles focused on genomic research discoveries and their importance for nursing education, practice, policy, and research.

Organizing Framework

: “Genomics for Health” is one of three themes, along with genomes to biology and genomes to society, emanating from applications of the Human Genome Project (HGP).

Methods

: In this series of articles, nurse scientists who are experts in genetics and genomics sciences explain terminology, provide background information about the HGP, discuss clinical examples, and recommend changes in nursing practice, education, and research.

Conclusions

: The HGP has already led to major changes in clinical practice, research, education, and policy, and even more dramatic changes are predicted for people throughout the world. Mastering this information is necessary for nurses globally because genomic information will ultimately pervade all of health care.
The Interface of Genomic Technologies and Nursing
Authors: Loescher Lois J. , Merkle Carrie J.
Published: May 2005

Purposes

: (a) to summarize views of the interface of technology, genomic technology, and nursing; (b) provide an overview of current and emerging genomic technologies; (c) present clinical exemplars of uses of genomic technology in two disease conditions; and (d) list genomic‐focused nursing research on genomic technologies.

Organizing Framework

: A discussion of genomic technology in the context of nurses' views of technology, the importance of genomic technology for nurses, linking the central dogma of molecular biology to state‐of‐the‐art tests and assays, and nurses' current use of technologies.

Conclusions

: Human genome discoveries will continue to be an integral part of disease prevention, diagnosis, treatment, and management. These discoveries also have the potential for being integrated into nursing science. Genomic technologies are becoming a driving force in patient management, so that nurses will be unable to provide quality care without knowledge of the types of genomic technologies, the rationale for their use, and the possible sequelae that can result from genetic diagnosis or treatment. Many nurses already are using genomic technologies to conduct genomic‐focused nursing research. The biobehavioral nature of much of this research further indicates the important contributions of nurses in genomics.
Preparing Nurses for the Global Pandemic of Chronic Obstructive Pulmonary Disease
Authors: Kara Magfiret
Published: May 2005

Purpose

: To raise awareness of the global pandemic of chronic obstructive pulmonary disease (COPD), its multiple underlying causes, and how to fight it, with particular attention to needs in nursing education.

Methods

: Integrative review of the literature.

Findings

: The main underlying causes of COPD are both individual and environmental factors, and the disease usually results from an interaction between these two factors. The prevalence of COPD is highest in countries where cigarette smoking has been, or still is, very common, and it is lowest in countries where smoking is less common, or total tobacco consumption per person is low. COPD is to some extent a preventable disease especially by preventing exposure to tobacco smoke and to occupational dusts and chemicals including vapours, irritants, fumes, and indoor and outdoor air pollution. The main implication for nurses and nursing curricula is to expand the focus from the individual to include population‐based intervention programmes.

Conclusions

: Addressing the underlying causes of COPD and providing appropriate interventions are within the scope of nursing practice and responsibility. Changes in nursing education are needed for nurses to be able to address the COPD pandemic.
Hopelessness as a Response to Physical Illness
Authors: Dunn Susan L.
Published: May 2005

Purpose

: To analyze hopelessness as a psychological response to physical illness, differentiate hopelessness from depression, and discuss measures of hopelessness.

Organizing Framework

: Walker and Avant's (1995) concept analysis strategy.

Method

: A review of the literature from 1983 to 2004 was completed, with a focus on hopelessness theory and measurement.

Findings

: Although hopelessness is closely related to depression, distinct characteristics of hopelessness were identified. A continuum of attributes of hopelessness and depression was derived. Hopelessness has been examined in a variety of populations with several different instruments. One established measure was selected for discussion.

Conclusions

: Continued study of hopelessness as a psychological response to physical illness is needed, including the continued differentiation of hopelessness from depression, further analysis of the continuum of hopelessness and depression, and the differentiation of state from trait hopelessness. Research to validate this conceptualization will enhance accuracy of the diagnosis of hopelessness and testing of nursing inteventions.
Hospital Ethical Climates and Registered Nurses' Turnover Intentions
Authors: Hart Sara Elizabeth
Published: May 2005

Purpose

: To investigate (a) the effects of hospital ethical climates on positional and professional turnover intentions of registered nurses, and (b) the relationships among demographic factors, employment characteristics, and positional and professional turnover intentions of registered nurses.

Design

: A cross‐sectional study of randomly selected registered nurses (n=463) in Missouri, USA, conducted in 2003 and 2004.

Methods

: A self‐administered questionnaire containing the Hospital Ethical Climate Survey, the Anticipated Turnover Scale, and the Nursing Retention Index was used to assess registered nurses' perceptions of the hospital ethical climate and their intentions to leave their position or the nursing profession. Descriptive statistics, Pearson product‐moment correlations, and hierarchical regression techniques were used to analyze the data.

Findings

: The hospital ethical climate explained 25.4% of the variance in positional turnover intentions and 14.7% of the variance in professional turnover intentions. Together, hospital ethical climate, control over practice, the use of educational reimbursement as a retention strategy, gender, and staff sufficiency explained 29.7% of the variance in positional turnover intentions. Hospital ethical climate, patient load, and control over practice together explained 15.8% of the variance in professional turnover intentions.

Conclusions

: Of the variables included in this analysis, the hospital ethical climate was most important in explaining nurses' positional and professional turnover intentions.
Simulation of thermal fatigue in hot strip mill work rolls
Authors: Mercado‐Solis R. D. , Beynon J. H.
Published: May 2005

The surface deterioration of work rolls constitutes a significant constraint on the operation of hot mills, as the duration of rolling campaigns are greatly restricted by the surface condition of the rolls. Work roll changes account for a large proportion of downtime in the operation of hot strip mills, resulting in financial penalties for the mill operators in terms of lost production and roll maintenance.

It is generally accepted that thermal fatigue represents one of the main factors influencing work roll wear in the finishing stands of a hot strip mill. In order to assess the thermal fatigue behaviour of typical work roll alloy grades, a series of tests were performed on high‐speed steel (HSS) and high‐carbon high‐chromium steel samples using a stand alone twin‐disc simulation machine under conditions that are comparable to those of hot rolling of steel. The progressive changes in surface condition of the roll samples were monitored and analysed by means of stylus profilometry, optical and scanning electron microscopy. The experimental results were compared with fragments of scrapped work rolls taken from the mill. Tests performed on the HSS samples did not result in appreciable surface degradation of the test sample. On the other hand, examination of the high‐carbon high‐chromium samples after testing revealed thermal crack morphologies and surface defects comparable to those observed in mill roll samples.
A study on the structural analysis of aluminium drosses and processing of industrial aluminium salty slags
Authors: Hazar A. Binnaz Yoruç , Saridede Muhlis Nezihi , Çiğdem Mustafa
Published: May 2005

In aluminium‐melting operations, a dross layer containing 85% metallic Al forms on the surface of the molten aluminium bath. Therefore, a significant amount of metal is removed from the furnace with the dross. Melt losses are one of the most important economical points in the melting operations. In the first part of the present study, a series of reverbaratory furnace drosses received from several aluminium plants located in Turkey were examined to determine their compositional and structural characteristics. Following crushing and grinding operations, drosses were dimensionally classified into 5 groups. Metallic Al, Mg, Zn, Fe and SiO2 contents of each group were analyzed separately. The metallic aluminium content of the group +4 mm is found to be approximately 75% while that of −0.5 mm group is 25%. Another fundamental finding is the high Mg content present in the drosses. Furthermore, Fe and SiO2 contents increase with decreasing particle size of the dross. In the second part of the investigation, experiments were carried out on the treatment of the salty slags to obtain salt, aluminium and non‐metallic products which can be used for various purposes. Leaching and crystallization in an evaporator is employed to determine the optimum conditions for the recovery of flux from the salty slag.
Photodynamic therapy in dermatology – an update
Authors: Babilas Philipp , Karrer Sigrid , Sidoroff Alexis , Landthaler Michael , Szeimies Rolf‐Markus
Published: May 2005

Topical photodynamic therapy (PDT) is a well‐established treatment modality which has mainly shown to be effective for dermatooncologic conditions like actinic keratoses (AK), Bowen's disease, in situ squamous cell carcinoma and superficial basal cell carcinoma (BCC). However, a therapeutical benefit of PDT is also evident for inflammatory dermatoses like localized scleroderma, acne vulgaris and granuloma annulare. Recent work has been focused on the development and evaluation of topical photosensitizers like the heme precursor 5‐aminolevulinic acid (5‐ALA) or its methyl ester (methyl aminolevulinate) inducing photosensitizing porphyrins. These drugs do not induce strong generalized cutaneous photosensitization like the systemically applied porphyrins or their derivatives. For dermatological purposes, incoherent lamps or light‐emitting diode arrays can be used for light activation. Depending on the applied light dose and the concentration of the photosensitizer either cytotoxic effects resulting in tumor destruction or immunomodulatory effects improving the inflammatory conditions occur. Treating superficial oncologic lesions (tumor thickness <2–3 mm) cure rates achieved by PDT are equal to the cure rates of the respective standard therapeutic procedure. The benefits of PDT are the low level of invasiveness and the excellent cosmetic results after treatment.
Refractory livedoid vasculitis responding to PUVA: a report of four cases
Authors: Tuchinda C. , Leenutaphong V. , Sudtim S. , Lim H. W.
Published: May 2005

Livedoid vasculitis is a chronic disease characterized by recurrent painful irregularly shaped ulcers, which heal with scars, most commonly located on feet or lower extremities. This condition is often resistant to the therapy. We report four cases with refractory livedoid vasculitis that responded to systemic psoralens and ultraviolet A radiation therapy.
Inhibition of adipose tissue lipolysis increases intramuscular lipid and glycogen use in vivo in humans
Authors: van Loon Luc J. C. , Thomason-Hughes Michaela , Constantin-Teodosiu Dumitru , Koopman René , Greenhaff Paul L. , Hardie D. Grahame , Keizer Hans A. , Saris Wim H. M. , Wagenmakers Anton J. M.
Published: May 2005

This study investigates the consequences of inhibition of adipose tissue lipolysis on skeletal muscle substrate use. Ten subjects were studied at rest and during exercise and subsequent recovery under normal, fasting conditions (control trial, CON) and following administration of a nicotinic acid analog (low plasma free fatty acid trial, LFA). Continuous [U-13C]palmitate and [6,6-2H2]glucose infusions were applied to quantify plasma free fatty acid (FFA) and glucose oxidation rates and to estimate intramuscular triacylglycerol (IMTG) and glycogen use. Muscle biopsies were collected to measure 1) fiber type-specific IMTG content; 2) allosteric regulators of hormone-sensitive lipase (HSL), glycogen phosphorylase, and pyruvate dehydrogenase; and 3) the phosphorylation status of HSL at Ser563and Ser565. Administration of a nicotinic acid analog (acipimox) substantially reduced plasma FFA rate of appearance and subsequent plasma FFA concentrations ( P < 0.0001). At rest, this substantially reduced plasma FFA oxidation rates, which was compensated by an increase in the estimated IMTG use ( P < 0.05). During exercise, the progressive increase in FFA rate of appearance, uptake, and oxidation was prevented in the LFA trial and matched by greater IMTG and glycogen use. Differential phosphorylation of HSL or relief of its allosteric inhibition by long-chain fatty acyl-CoA could not explain the increase in muscle TG use, but there was evidence to support the contention that regulation may reside at the level of the glucose-fatty acid cycle. This study confirms the hypothesis that plasma FFA availability regulates both intramuscular lipid and glycogen use in vivo in humans.
Nutrient regulation of PKCε is mediated by leucine, not insulin, in skeletal muscle
Authors: Vary Thomas C. , Goodman Stacy , Kilpatrick Laurie E. , Lynch Christopher J.
Published: May 2005

Nutrients enhance signaling pathways involved in skeletal muscle growth through an increased rate of protein synthesis. These studies have led to an understanding of the potential role of the mammalian target of rapamycin (mTOR) in this process. However, activation of mTOR cannot account for all the stimulatory effects of nutrients. The purpose of these experiments was to examine the effect of nutrients on the cellular distribution and activation state of novel PKC isoforms (PKCε and PKCδ) in the gastrocnemius of rats by use of modification state-dependent phosphopeptide-specific antibodies. The phosphorylation of PKCε on the catalytic domain autophosphorylation site (Ser729) was elevated during feeding and then returned to basal levels when the feeding period ended. Meal feeding augmented the phosphorylation of the downstream effectors of mTOR, namely S6K1 and 4E-BP1. In contrast, the phosphorylation of PKCδ on either the catalytic domain autophosphorylation site (Ser643) or activation loop site (Thr505) was unaffected. Similar results were obtained when animals were given leucine either acutely via gavage or chronically by dietary supplementations. The effect of leucine was not mimicked by injecting animals with insulin but could be induced by gavage with norleucine, a structural analog of leucine that does not increase plasma insulin concentration. Thus rises in insulin secondary to meal intake or leucine gavage are probably not responsible for increased phosphorylation of PKCε in response to meal feeding. Elevating the leucine concentration stimulated the phosphorylation of PKCε in gastrocnemius from perfused hindlimb and caused a shift in the distribution of PKCε from the membrane fraction to the cytosolic fraction. The results indicate that leucine leads to an activation (autophosphorylation) and subcellular redistribution of PKCε, but not PKCδ, in gastrocnemius both in vivo and in vitro. Furthermore, activation of the mTOR signaling pathway above basal conditions does not appear to be necessary to induce phosphorylation or translocation of PKCε, suggesting that multiple signaling pathways become activated with leucine.