bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterogeneous PrPC metabolism in skeletal muscle cells
Authors: Massimino Maria Lina , Ferrari Jessica , Sorgato Maria Catia , Bertoli Alessandro
Published: January 2006

Recent reports have shown that prions, the causative agent of transmissible spongiform encephalopathies, accumulate in the skeletal muscle of diseased animals and man. In an attempt to characterise in this tissue the prion protein (PrPC), whose conformational rearrangement governs the generation of prions, we have analysed the protein in primary cultured murine myocytes and in different skeletal muscle types. Our results indicate that the expression and cellular processing of PrPC change during myogenesis, and in muscle fibres with different contractile properties. These findings imply a potential role for PrPC in the skeletal muscle physiology, but may also explain the different capability of muscles to sustain prion replication.
High‐throughput screening of cell death inducible short peptides from TNF‐related apoptosis‐inducing ligand sequence
Authors: Okochi Mina , Nakanishi Mari , Kato Ryuji , Kobayashi Takeshi , Honda Hiroyuki
Published: January 2006

Therapeutic peptides and small molecules, rationally designed to trigger cell death have attracted strong attention. Cell death inducible peptides were screened from amino acid sequence of tumor necrosis factor‐related apoptosis‐inducing ligand (TRAIL). Using Fmoc solid phase synthesis, cellulose membrane‐bound octameric peptide library of TRAIL scan was prepared and cell viability assay was directly performed on peptide disk with Jurkat cells. Six peptide sequences that could induce cell death were found. Peptide sequence with RNSCWSKD (TRAIL227–234) that exist in the zinc‐binding site revealed high cell death inducible activity. Apoptotic cell death was observed when cells were treated with soluble synthesized peptide.
A novel yeast two‐hybrid approach to identify CDPK substrates: Characterization of the interaction between AtCPK11 and AtDi19, a nuclear zinc finger protein1
Authors: Rodriguez Milla Miguel A. , Uno Yuichi , Chang Ing-Feng , Townsend Jared , Maher Eileen A. , Quilici David , Cushman John C.
Published: January 2006

Calcium‐dependent protein kinases (CDPKs) are sensor‐transducer proteins capable of decoding calcium signals in diverse phosphorylation‐dependent calcium signaling networks in plants and some protists. Using a novel yeast two‐hybrid (YTH) approach with constitutively active and/or catalytically inactive forms of AtCPK11 as bait, we identified AtDi19 as an AtCPK11‐interacting protein. AtDi19 is a member of a small family of stress‐induced genes. The interaction was confirmed using pull‐down assays with in vitro translated AtCPK11 and GST–AtDi19 and localization studies in Arabidopsis protoplasts cotransfected with AtCPK11:GFP and AtDi19:DsRed2 protein fusions. We further showed that the interaction of AtDi19 is specific to both AtCPK4 and AtCPK11, whereas other closely related CPKs from Arabidopsis interacted weakly (e.g., AtCPK12) or did not interact (e.g., AtCPK26, AtCPK5 and AtCPK1) with AtDi19. Deletion analyses showed that a region containing two predicted nuclear localization signals (NLS) and a nuclear export signal (NES) of AtDi19 is essential for interaction with AtCPK11. We further demonstrated that AtDi19 is phosphorylated by AtCPK11 in a Ca2+‐dependent manner at Thr105 and Ser107 within the AtDi19 bipartite NLS using in vitro kinase assays. Our data suggest that disruption of the autoinhibitor domain leading to the formation of a constitutively active CDPK may stabilize kinase–substrate interactions without affecting specificity.
Kidney claudin‐19: Localization in distal tubules and collecting ducts and dysregulation in polycystic renal disease
Authors: Lee Nikki P.Y. , Tong Man K. , Leung Pauline P. , Chan Vivian W. , Leung Simon , Tam Po-Chor , Chan Kwok-Wah , Lee Kai-Fai , Yeung William S.B. , Luk John M.
Published: January 2006

Tight junction (TJ) constitutes the barrier by controlling the passage of ions and molecules via paracellular pathway and the movement of proteins and lipids between apical and basolateral domains of the plasma membrane. Claudins, occludin, and junctional adhesion molecules are the major three transmembrane proteins at TJ. This study focuses a newly identified mammalian TJ gene, claudin‐19, in kidneys. Mouse claudin‐19 composes of 224 amino acids and shares 98.2% and 95% amino acid homology with rat and human, respectively; the most evolutionary‐related claudins are claudin‐1 and ‐7, which share ∼75% DNA sequence homology with claudin‐19. Claudin‐19 is abundantly expressed in the mouse and rat kidneys among the organs examined by Northern blots, and to a much less extent, also found in brain by RT‐PCR. Claudin‐19 and zonula occludens‐1 (ZO‐1) are localized at junctional regions of Madin–Darby canine kidney (MDCK) cells by immunofluorescent microscopy. In addition, ZO‐1 is found in the claudin‐19‐associated protein complexes in MDCK cells by co‐immunoprecipitation. Using aquaporin‐1 and aquaporin‐2 antibodies as markers for different renal segment, strong expression of claudin‐19 was observed in distal tubules of the cortex as well as in the collecting ducts of the medulla. To less extent, claudin‐19 is also present in the proximal tubules (cortex) and in the loop of Henle (medulla). Furthermore, intense claudin‐19 immunoreactivity is found co‐localized with the ZO‐1 in kidneys from postnatal day 15, day 45, and adult rats and mice. Similar localizations of claudin‐19 and ZO‐1 are also observed in human kidneys. Since these renal segments are mainly for controlling the paracellular cation transport, it is suggested that claudin‐19 may participate in these processes. In human polycystic kidneys, decreased expression and dyslocalization of claudin‐19 are noticed, suggesting a possible correlation between claudin‐19 and renal disorders. Taken together, claudin‐19 is a claudin isoform that is highly and specifically expressed in renal tubules with a putative role in TJ homeostasis in renal physiology.
Mechanism of toxicity of the branched‐chain fatty acid phytanic acid, a marker of Refsum disease, in astrocytes involves mitochondrial impairment
Authors: Reiser Georg , Schönfeld Peter , Kahlert Stefan
Published: January 2006

Phytanic acid is a saturated branched‐chain fatty acid, which is formed by bacterial degradation of chlorophyll in the intestinal tract of ruminants. The methyl group in β‐position prevents degradation of phytanic acid by the β‐oxidation pathway. Therefore, degradation of phytanic acid is initiated by α‐oxidation in peroxisomes. The inherited peroxisomal disorder Refsum disease is characterised by accumulation of phytanic acid. Unusually high concentrations of phytanic acid can be found in the plasma of Refsum disease patients, who suffer from neurodegeneration and muscle dystrophy. Phytanic acid has been suggested to be causally involved in the clinical symptoms. To elucidate the pathogenic mechanism, we investigated the influence of phytanic acid in rat hippocampal astrocytes by monitoring the cytosolic Ca2+ concentration, the mitochondrial membrane potential (Δψm), the generation of reactive oxygen species as well as the cellular ATP level. In response to phytanic acid (100 μM) cytosolic Ca2+ was quickly increased. The phytanic acid‐evoked Ca2+ response was transient and involved activation of intracellular Ca2+ stores. In isolated rat brain mitochondria, phytanic acid dissipated Δψm in a reversible and dose‐dependent manner. Moreover, phytanic acid released cytochrome c from mitochondria. Depending on the mitochondrial activity state, phytanic acid either stimulated or inhibited the electron flux within the respiratory chain. In addition, phytanic acid induced substantial generation of reactive oxygen species in isolated mitochondria as well as in intact cells. Phytanic acid caused cell death of astrocytes within a few hours of exposure. In conclusion, we suggest that phytanic acid initiates astrocyte cell death by activating the mitochondrial route of apoptosis.
Using replication research for just‐in‐time purchasing construct development
Authors: Kaynak Hale , Hartley Janet L.
Published: January 2006

Using replication research, the validity of the just‐in‐time purchasing (JITP) construct is established. Although empirical researchers have examined JITP over the last two decades, a consistent set of valid, reliable factors has not been used. The lack of valid construct is a barrier to hypotheses testing and meta‐analyses on JITP. This study confirmed the validity of six JITP factors: top management commitment, employee relations, training, supplier quality management, transportation, and quantities delivered using two different data sets and testing the first‐ and second‐order structure of the JITP construct. Content validity, reliability, unidimensionality, convergent validity, discriminant validity, criterion‐related validity, and an invariant factorial structure of the JITP construct were empirically established.
The importance of private lands for ocelot Leopardus pardalis conservation in the United States
Authors: Haines Aaron M. , Janecka Jan E , Tewes Michael E. , Grassman Jr Lon I. , Morton Patricia
Published: January 2006

The distribution of ocelots Leopardus pardalis in the USA is limited to southern Texas. Identification and monitoring of ocelot populations enables biologists to assess population health and status. Use of camera traps has been successfully used to monitor numerous populations of wild felids, including the ocelot. Our objectives were to identify ocelot presence within southern Texas and estimate ocelot population size and density. We used camera traps to survey for ocelots on four study sites in southern Texas. We recorded ocelot presence on one study site with an abundance estimate of three individuals and a density estimate of 0.30±SE 0.03 ocelots km−2. The conservation implications of this study suggest concentrating conservation efforts in and around the study site (Yturria Ranch) found to have ocelots. In addition, this study emphasizes the importance of including private landowners in the ocelot recovery process.
Declining populations of the Javan warty pig Sus verrucosus
Authors: Semiadi Gono , Meijaard Erik
Published: January 2006

We conducted an interview-based survey for the Javan warty pig Sus verrucosus, endemic to the islands of Java and Bawean in Indonesia. The species occurs in 10 isolated areas, although some additional, probably very small populations, may remain. Compared to a survey conducted in 1982, 17 of the 32 (53%) populations are extinct or have dropped to levels so low that local hunters have failed to encounter the species in recent years. This indicates a rapid population decline. We hypothesize that this loss is primarily caused by a decline in suitable habitat, especially stands of teak Tectona grandis forest or similar forest plantations, and by high hunting pressure. Competition from and hybridization with the Eurasian wild boar Sus scrofa may be further threats to S. verrucosus. Rapid action is needed to prevent extinction in the wild. We recommend effective protection of selected S. verrucosus populations, lobbying of the Government to give protected status to S. verrucosus, conducting ecological research and investigating crop damage issues, and establishment of conservation breeding programmes.
Planning the conservation of the breeding population of cinereous vultures Aegypius monachus in the Republic of Georgia
Authors: Gavashelishvili Alexander , McGrady Mike J. , Javakhishvili Zura
Published: January 2006

Occupied and potential nesting areas of Near Threatened cinereous vulture Aegypius monachus in the Republic of Georgia were examined to model its nesting habitat. The intention is to support its conservation within the context of the ongoing establishment of a system of protected areas. Data were manipulated and analysed using a geographical information system, univariate statistical analysis and logistic regression. The best model suggested that in Georgia plots were more likely to contain a cinereous vulture nest if the slope was >30° and faced north, was situated in rugged terrain away from unprotected and populated areas, and was relatively dry. North-facing slopes were where suitable nest trees could be found, whereas ruggedness, protected areas and remoteness from populated areas made access to the nest trees by humans difficult. Low annual rainfall provided better soaring and breeding conditions. The model suggested that the breeding range of cinereous vulture in Georgia could expand if seasonal grazing, which is the primary source of disturbance, is properly managed. Because neither nesting places nor food availability appeared to be limiting, human disturbance and climate seem to best explain the current distribution of nesting cinereous vultures in Georgia, and probably elsewhere in the Caucasus.
Tolkien the storyteller
Authors: Smith Ross
Published: January 2006

The 20th century’s most popular novelist? – the third of three articles. The year 2005 marks the 50th anniversary of the publication of J.R.R. Tolkien’s prose epic The Lord of the Rings: voted ‘the book of the century’ in a poll conducted in 1997 by the UK book retailer Waterstones and ‘the UK’s best loved book’ in a BBC survey carried out in 2003. TLOTR was adapted to the screen in 2001 by the New Zealand-based director Peter Jackson and released, to widespread acclaim, in three parts between 2001 and 2003. The present is the third of three linked discussions of Tolkien’s work and the media through which it has been channelled (text and film), and of why it has been so phenomenally popular.
Assimilation to /r/ in English initial consonant clusters
Authors: Stahlke Herbert F. W.
Published: January 2006

THE RECENT Bulley-Davidson discussion of English initial consonant clusters (ET80, ET81, ET83) brings attention to the need for phonetic rigor and some phonological understanding when describing the sounds and sound patterns of English. Three topics the two writers deal with would benefit from such rigor: /tr/ and /dr/ clusters, the status and function of /j/ in initial clusters before /u/, and the role of syllable structure in the description of consonant clusters.
“Binary Synthesis”: Goethe's Aesthetic Intuition in Literature and Science
Authors: Stephenson Roger H.
Published: January 2006

Argument

This essay seeks to identify the cultural significance of Goethe's scientific writings. He reformulates, in the light of his own concrete experience, “crucial turning-points” (Hauptmomente) in the history of science – key ideas, the historical understanding of which is vital to present understanding – thus situating his own scientific work at the bi-polar center of the Western scientific tradition, conceived as the dramatic interplay over centuries of two opposing modes of thought. For in his experimentation he recaptures the glimpse of living form gained in aesthetic perception (Anschauung), from which such inherited theoretical positions are ultimately derived. At each stage of this process, imagination, in its aesthetic modality, is essential, for it alone reveals the world as it truly is. The literary quality of his writings on nature, as on culture, reveals Goethe's stylistic achievement in devising a medium in which the insights gained in contemplation may be so transmitted as to make a similar, imaginative, appeal to his reader – re-enacting the abstract-concrete equilibrium characterizing all aesthetic experience. Matching his style to the subtle, delicate, connectedness of Nature, Goethe recreates the delights of participating in natural creativity. His Janus-faced, scientific-literary, style illustrates “binary synthesis,” the principle that unites Goethe's science with his art.

Beauty is the normal state.

(Ralph Waldo Emerson, The Conduct of Life)

There can be no such thing as an eclectic philosophy, but there can be eclectic philosophers. But an eclectic is anyone who, from whatever exists and is happening round about, appropriates the things he or she finds congenial to her or his nature; and this context validly includes all that can be called culture and progress in a theoretical and practical sense. It follows that two eclectic philosophers could turn into the greatest opponents if they are antagonistic to one another, each picking out whatever suits him or her in every traditional system of philosophy.

(Goethe, Wilhelm Meister's Journeyman Years)
Genetic Code, Text, and Scripture: Metaphors and Narration in German Molecular Biology
Authors: Brandt Christina
Published: January 2006

Argument

This paper examines the role of metaphors in science on the basis of a historical case study. The study explores how metaphors of “genetic information,” “genetic code,” and scripture representations of heredity (i.e. the metaphorical comparison of DNA with text and alphabet) entered molecular biology and reshaped experimentation during the 1950s and 1960s. Following the approach of the philosopher Hans Blumenberg, I will argue that metaphors are not merely a means of popularization or a specific kind of modeling (by building analogies) but rather are representations that can unfold an operational force of their own.

While the influence of cybernetics and information theory on molecular biology is well documented in historical analysis throughout recent years, this paper offers new insights into the metaphysical and religious resonances of textual metaphors in the life sciences. The main focus will be on developments in Germany, in particular on the work of the German biochemist Gerhard Schramm. In this historical case study the interaction between metaphors and experimental practices will be discussed. The paper analyzes different phases in the use of metaphors during the 1950s and 1960s: it will explore how the metaphors of a “genetic alphabet” or of “genetic code” (which were used with an illustrative purpose in the 1950s) developed into a new research program and eventually attained ontological status in the early 1960s. At that time Schramm's use of textual metaphors was reminiscent of nineteenth-century German natural philosophy. In this case, the metaphorical shift shows how the metaphor of a “genetic text” or a “genetic code,” which were central for the emerging molecular biology, drew on older cultural traditions with all of their metaphysical and religious preoccupations.
Use of in situ cloud condensation nuclei, extinction, and aerosol size distribution measurements to test a method for retrieving cloud condensation nuclei profiles from surface measurements
Authors: Ghan Steven J. , Rissman Tracey A. , Elleman Robert , Ferrare Richard A. , Turner David , Flynn Connor , Wang Jian , Ogren John , Hudson James , Jonsson Haflidi H. , VanReken Timothy , Flagan Richard C. , Seinfeld John H.
Published: January 2006

If the aerosol composition and size distribution below cloud are uniform, the vertical profile of cloud condensation nuclei concentration can be retrieved entirely from surface measurements of CCN concentration and particle humidification function and surface‐based retrievals of relative humidity and aerosol extinction or backscatter. This provides the potential for long‐term measurements of CCN concentrations near cloud base. We have used a combination of aircraft, surface in situ, and surface remote sensing measurements to test various aspects of the retrieval scheme. Our analysis leads us to the following conclusions. The retrieval works better for supersaturations of 0.1% than for 1% because CCN concentrations at 0.1% are controlled by the same particles that control extinction and backscatter. If in situ measurements of extinction are used, the retrieval explains a majority of the CCN variance at high supersaturation for at least two and perhaps five of the eight flights examined. The retrieval of the vertical profile of the humidification factor is not the major limitation of the CCN retrieval scheme. Vertical structure in the aerosol size distribution and composition is the dominant source of error in the CCN retrieval, but this vertical structure is difficult to measure from remote sensing at visible wavelengths.
Crustal magnetization of Mars controlled by lithology or cooling rate in a reversing dynamo?
Authors: Rochette P.
Published: January 2006

To explain the lack of magnetization in large portions of the Noachian crust, a lithological origin has been put forward, corresponding to the lack of formation of magnetic minerals in the crustal rocks. An alternative hypothesis is proposed here, with constant amount of magnetic minerals, but variable reduction of total magnetization over the magnetic thickness, due to variable record of successive polarities of the magnetizing field. Large crustal cooling rates would correspond to strongly magnetized zone, and slow cooling rates to poorly magnetized zone. Based on this model we derive an explanation for the proposed confinement of magnetized zones within the inter‐tropical band.
Entropy‐based member selection in a GCM ensemble forecasting
Authors: Tapiador F. J. , Gallardo C.
Published: January 2006

We present a method for choosing a member in a global circulation model (GCM) ensemble forecasting. We show that the r2 correlation between members and independent data is related to the flux of information entropy contained into the forecasts. This allows to classify the members in terms of goodness‐of‐fit. To validate the method we use several ECMWF‐ensemble forecast from the DEMETER project, and the ERA‐40 database. We compare ERA‐40 actual estimates with our entropy‐based choice of the DEMETER members in each of the 180 days, obtaining consistent results. Our hypothesis is based on energy‐balance, maximum entropy production considerations so that the method might only be applicable to global simulations.
Contrasts between the summertime surface energy balance and boundary layer structure at Dome C and Halley stations, Antarctica
Authors: King J. C. , Argentini S. A. , Anderson P. S.
Published: January 2006

The Antarctic research stations of Dome C and Halley lie at similar latitudes (∼75°S) and are thus subject to similar diurnal variation of solar radiation at the top of the atmosphere. However, the response of the atmospheric boundary layer to this diurnally varying forcing differs greatly at the two stations. At Dome C during summer there is a strong diurnal cycle in near‐surface temperature and wind speed, and a shallow (∼350 m) convective boundary layer is observed to grow in response to diurnal heating. At Halley, diurnal variations in temperature and wind speed are smaller than those at Dome C, and there is no clear diurnal variability in boundary layer depth. Analysis of the summertime surface energy budget for both stations indicates that the main reason for the different diurnal variability at the two stations is the greater partitioning of available energy into latent heat flux at the warmer Halley station. We argue that the diurnally varying convective boundary layer observed at Dome C will not be typical of the whole of the East Antarctic plateau.
Groundwater pumping and land subsidence in the Emilia‐Romagna coastland, Italy: Modeling the past occurrence and the future trend
Authors: Teatini P. , Ferronato M. , Gambolati G. , Gonella M.
Published: January 2006

The Emilia‐Romagna coastland south of the Po River delta, Italy, has experienced a dramatic land settlement mainly due to the large groundwater withdrawal related to the local economic and tourist development started in the early 1950s. Although the use of surface water has reduced the settlement rate over the last three decades, anthropogenic land subsidence still continues in a few kilometer wide coastal strip at a rate larger than the natural one. The occurrence is reconstructed since 1946 with the aid of advanced finite element flow and poromechanical models implemented with a realistically detailed geology of the regional shallow multiaquifer system. The models have been calibrated against the piezometric, leveling, and extensometer records observed over the last 50 years, and a land subsidence prediction in 2016 is performed. The results show that the extensive groundwater pumping that occurred in the past is most likely the main cause of the recent land settlement as well because of the delayed compaction of the clay aquitards comprised between the depleted aquifers. However, the available pumping data do not allow for a thorough understanding of the current local settlement process along the coastline, which is the most vulnerable area of the Emilia‐Romagna region from an environmental viewpoint. If the planned scenario of groundwater resource management will be implemented, anthropogenic land subsidence is bound to become a marginal problem for the central and northern portion of the Emilia‐Romagna coastland.
Land surface state and flux estimation using the ensemble Kalman smoother during the Southern Great Plains 1997 field experiment
Authors: Dunne Susan , Entekhabi Dara
Published: January 2006

The ensemble Kalman smoother (EnKS) is employed to estimate surface and subsurface soil moisture and surface energy fluxes during the Southern Great Plains 1997 (SGP97) experiment through the assimilation of observed L band radiobrightness temperatures. Previous work using the ensemble Kalman filter (EnKF) and a simple smoother demonstrated that soil moisture estimation is a reanalysis‐type problem. The EnKF uses observations as they become available to update the current state. The EnKS takes the EnKF estimate as its first guess. However, in addition to updating the current state it also updates the best estimate at previous times. The performance of the EnKS is compared to the EnKF and the ensemble open loop in which no measurements are assimilated. Estimated surface soil moisture is compared to gravimetric observations at three locations. Root zone (5–100 cm) soil moisture is evaluated by comparing the resultant latent heat flux to flux tower observations. In a fixed lag smoother, observations are used to update past estimates within a fixed time window. The EnKS can be implemented in a fixed lag formulation in problems with limited memory such as soil moisture estimation. It is shown that there is a trade‐off to be made between the improved accuracy with longer lag and the increased computational cost incurred. It is demonstrated that the EnKS is a relatively inexpensive state estimation algorithm suited to operational data assimilation.
Density fitting of two-electron integrals in extended systems with translational periodicity: The Coulomb problem
Authors: Varga Štefan , Milko Matúš , Noga Jozef
Published: January 2006

Density fitting approach to Coulomb integrals for infinite systems with translational periodicity is reformulated in direct space. Despite of the Coulomb infinite decay of some integrals, direct-space calculation is shown to be feasible. Moreover, we show that the direct-space ansatz is completely equivalent to our previous formulation in reciprocal space. Computational demands scale linearly with the number of unit cells. In addition, direct-space treatment has some practical advantages over the reciprocal-space formulation. The efficiency of our scheme is demonstrated on systems with translational periodicity in one dimension. Computation time takes only a small fraction of the conventional calculation with exact integrals. We show that for infinite systems auxiliary basis sets of equally good quality as for molecules can be constructed in a systematic way.
Diagnosed internal temperatures and shock evolution provide insight on dynamic-Hohlraum’s axial radiation production and asymmetry
Authors: Sanford T. W. L. , Nash T. J. , Mock R. C. , Apruzese J. P. , Peterson D. L.
Published: January 2006

Measurements and analyses [J. P. Apruzese et al., Phys. Plasmas 12, 012705 (2005)] of Al and MgK-shell lines from tracer layers symmetrically embedded in cylindrical dynamic-Hohlraum (DH) targets, driven by two nested tungsten-wire arrays in a z pinch, suggest that the radiation temperatures near either end of top or bottom radiation exit holes (REHs) of the DHs are similar. Moreover, the measured radii inferred for the shock developed within the targets converge towards the z axis symmetrically when viewed simultaneously through either end of the Hohlraums. These two results support the earlier observation [T. W. L. Sanford et al., Phys. Plasmas 12, 022701 (2005)] that the anticorrelation of the axial power with the magnitude of tungsten-wire material flowing near (or across) the given REH is due to increased tungsten opacity at the REH. This mechanism appears to be dominant in affecting the top-bottom (anode-cathode) symmetry in axial power, rather than there being any significant up-down difference in Hohlraum temperature or shock development. Additionally, we show that the insertion of two thin annular pedestals extending into the anode-cathode gap from either electrode, just radially outside of the REHs, improves the up-down power symmetry, decreases the rise time of the axial radiation, and decreases the shot-to-shot variation in the radiation pulse shape, and shock velocity. These improvements suggest that the quality of the plasma shell, which forms within the central region of the implosion, is superior to that adjacent to either electrode. Finally, enhanced emission on axis is observed, prior to the arrival of the main mass-driven shock from the impact of the wire arrays on the target. This phenomenon is consistent with the existence of a radiation-driven shock in the foam target which calculations indicate forms from radiation generated when the outer wire-array plasma impacts the inner array of the nest.
Microcoils for transport of magnetic beads
Authors: Ramadan Qasem , Yu Chen , Samper Victor , Poenar Daniel Puiu
Published: January 2006

Integrated magnetic devices were fabricated, consisting of arrays of microcoils of a novel structure, embedded in a silicon substrate, with small conductors asymmetrically shaped and with ferromagnetic pillars made of a magnetic alloy (NiCoP) as magnetic cores. These structures generated large magnetic field gradients that very effectively attracted magnetic beads. By alternatively injecting currents in an array of such microcoils placed in a microfluidic chamber, magnetic beads were guided in different movement modes and step sizes in a continuous flow.
Growth and characteristics of low dislocation density GaN grown on Si(111) from a single process
Authors: Chen X. , Uesugi T.
Published: January 2006

From one uninterrupted growth process, GaN films were deposited on maskless stripe-patterned Si(111) substrates using the facet-initiated growth technique. The epilayer with a flat surface has a thickness of ∼1.3μm. The influence of stress on the behavior of dislocations in the crystal during growth was observed by the transmission electron microscopy (TEM). Concentrated lines of dislocations were found along the coalescence boundaries by atomic force microscopy (AFM). Few dislocations were detected in the other area. The average threading dislocation density of the GaN layer was decreased to ∼1.7×108cm−2. These dislocations have pure or partial screw dislocation characteristics.
Banana regime pressure anisotropy in a bumpy cylinder magnetic field
Authors: García-Perciante A. L. , Callen J. D. , Shaing K. C. , Hegna C. C.
Published: January 2006

The pressure anisotropy is calculated for a plasma in a bumpy cylindrical magnetic field in the low collisionality (banana) regime for small magnetic-field modulations (ϵ≡ΔB∕2B⪡1). Solutions are obtained by integrating the drift-kinetic equation along field lines in steady state. A closure for the local value of the parallel viscous force B∙∇∙Π‖ is then calculated and is shown to exceed the flux-surface-averaged parallel viscous force ⟨B∙∇∙Π‖⟩ by a factor of O(1∕ϵ). A high-frequency limit (ω⪢ν) for the pressure anisotropy is also determined and the calculation is then extended to include the full frequency dependence by using an expansion in Cordey eigenfunctions.
Relativistic quasidegenerate perturbation theory with four-component general multiconfiguration reference functions
Authors: Miyajima Makoto , Watanabe Yoshihiro , Nakano Haruyuki
Published: January 2006

Relativistic quasidegenerate perturbation theory (QDPT) using general multiconfiguration (GMC) reference functions is developed and implemented. It is the relativistic counterpart of the nonrelativistic QDPT with GMC reference and thus retains all the advantages of the nonrelativistic GMC reference QDPT, such as applicability to any configuration space and small computational cost compared to the complete configuration-space case. The method is applied to the potential-energy curves of the ground states of I2 and Sb2 molecules, the excitation energies of CH3I, and the energies of the lowest terms of C, Si, and Ge atoms, and is shown to provide a balanced description of potential-energy curves and accurate transition energies for systems containing heavy elements and to provide much better results compared to the reference function (i.e., active space configuration interaction) level.
Oxide-free InSb (100) surfaces by molecular hydrogen cleaning
Authors: Tessler R. , Saguy C. , Klin O. , Greenberg S. , Weiss E. , Akhvlediani R. , Edrei R. , Hoffman A.
Published: January 2006

We report that annealing of an oxidized InSb (100) single-crystal sample at 250°C under molecular hydrogen flow [molecular hydrogen cleaning (MHC)] results in complete desorption of the surface oxides. Following this process, the surface morphology is found to be very smooth at the nanometric scale without any droplet structure and a nearly 1:1 In:Sb stoichiometry. MHC was applied to remove the native oxide of an epi-ready InSb(100) substrate used for molecular beam epitaxy growth of InSb films. These results suggest that MHC of InSb can be used as a very effective cleaning process for epitaxial film growth.
Kinetic theory of the stability of the inhomogeneous plasmas with transverse inhomogeneous electric field
Authors: Mikhailenko Vladimir S. , Mikhailenko Vladimir V.
Published: January 2006

The stability of a magnetized inhomogeneous plasma with transverse inhomogeneous electric field is analyzed by using a kinetic formalism. It is found that for a smooth profile of the flow velocity, drift and ion-cyclotron waves are damped due to resonant interaction with ions. On the other hand, drift and drift-cyclotron kinetic instabilities modified by shear flow are excited by inverse electron Landau damping. A renormalized nonlinear dispersion equation, which accounts for random scattering of ions in the presence of the inhomogeneous transverse shear flow, is derived and applied to determine the saturation level of the drift-cyclotron instability in a plasma with transverse shear flow.
Effect of negative-ion flux on ion distribution around a spherical probe in electronegative plasmas
Authors: Denysenko I. , Yu M. Y. , Azarenkov N. A.
Published: January 2006

The electric potential and the electron- and ion-density profiles near a spherical probe in electronegative plasmas containing negative as well as positive ions are studied. It is shown that for relatively large probe radius and neutral-gas pressure, and/or small electron-to-ion temperature ratio, the density profile of the negative ions can differ from that of Boltzmann if their flux near the probe is outwards. The existence of stationary states is considered and the corresponding maximum negative-ion flux is obtained.
Combined role of frequency variation and magnetic field on laser electron acceleration
Authors: Gupta D. N. , Suk H.
Published: January 2006

Laser-induced acceleration of an electron injected initially at an angle to the direction of a short laser pulse with frequency variation in the presence of an axial static magnetic field has been investigated. Due to the combined effect of frequency variation of the laser and a magnetic field, the electron escapes from the laser pulse near the pulse peak. The electron gains considerable energy and retains it even after passing of the laser pulse in the presence of magnetic field in vacuum. The frequency variation plays an important role to enhance the electron energy in the presence of a static magnetic field in vacuum.
The relativistic kinetic Weibel instability: General arguments and specific illustrations
Authors: Schaefer-Rolffs U. , Lerche I. , Schlickeiser R.
Published: January 2006

A general description is developed of the kinetic Weibel [Phys. Rev. Lett. 2, 83 (1959)] instability in relativistic plasmas for arbitrary plasma distribution functions. Then general conditions for the existence of the relativistic instability are given as well as the influence of limits on the wave-number range and so on the instability rate. A comparison with previous works on bi-Gaussian distributions is also provided. Furthermore, ultrarelativistic and also weakly anisotropic relativistic distributions are investigated in general. Finally, isolated Weibel modes (in which both the frequency and wave number are fixed) are derived for asymmetric relativistic plasma distributions and constraints on these isolated modes are presented.
Electron microscopy study on structure of rolled-up semiconductor nanotubes
Authors: Jin-Phillipp N. Y. , Thomas J. , Kelsch M. , Deneke Ch. , Songmuang R. , Schmidt O. G.
Published: January 2006

By releasing strained epitaxial layers from their substrates, the layers roll up to form nanotubes. The structures of InAs∕GaAs and SiGe∕Si rolled-up nanotubes (RUNTs) are characterized by using transmission electron microscopy (TEM), electron diffraction, high-resolution TEM, and spatially resolved electron energy-loss spectroscopy. Freestanding RUNTs as well as their cross sections are investigated. It is found that the walls of the nanotubes are composed of alternating crystalline and noncrystalline oxide-containing layers. Defects may form in some nanotubes, where the rolling involves a misorientation.
Radially propagating fluctuation structures in the scrape-off layer of Alcator C-Mod
Authors: Grulke O. , Terry J. L. , LaBombard B. , Zweben S. J.
Published: January 2006

Radially propagating spatiotemporal fluctuation structures are observed in the scrape-off layer of Alcator C-Mod [I. H. Hutchinson et al., Phys. Plasmas 1, (1994)] using the combination of electric probes, a radial array of views measuring Dα emission, and two-dimensional imaging of Dα emission. For a specific magnetic-field configuration the electric probe and the Dα array measured plasma density and potential fluctuations along the same magnetic-flux tube. Calculations of the cross-correlation functions of Dα intensity fluctuations with ion saturation current fluctuations and floating potential fluctuations, respectively, reveal that the potential associated with fluctuation structures is of dipole type, consistent with fundamental models for radial blob propagation. Radial and poloidal velocities of fluctuation structures are obtained by two-dimensional spatiotemporal turbulence imaging using an ultrafast framing camera observing the Dα emission intensity in the poloidal plane. In the poloidal direction the fluctuation structures are predominantly propagating in direction of background E×B velocity. Measured radial velocities are directed outwards with a magnitude of typically 1% of the ion sound speed.
Rashba effect in InGaAs∕InP parallel quantum wires
Authors: Guzenko V. A. , Knobbe J. , Hardtdegen H. , Schäpers Th. , Bringer A.
Published: January 2006

We report on the Rashba effect in InGaAs∕InP quantum wires with an effective width ranging from 1.18μm down to 210nm. By measuring 160 wires in parallel universal conductance, fluctuations could be suppressed so that the characteristic beating effect in the magnetorestistance was observable down to very low magnetic fields. A characteristic shift of the nodes in the beating pattern was found for decreasing wire width. By assuming a realistic soft-wall potential, the experimentally observed node positions could be reproduced. For the range of measured wires, our study confirms that the Rashba coupling parameter does not change with wire width.
Surface microstructure analysis of cubic boron nitride films by transmission electron microscopy
Authors: Meng X. M. , Zhang W. J. , Chan C. Y. , Lee C. S. , Bello I. , Lee S. T.
Published: January 2006

A simple coating technique was introduced to preserve the surface structure of samples for transmission electron microscopy (TEM) characterization, and used to study boron nitride (BN) films. A gold film precoated on the surface of BN films served to protect the BN surface against ion damages during sample preparation, and to separate and distinguish the film surface structure from the TEM glue. The technique enabled the observation of detailed surface microstructures of cubic BN (cBN) films, which provided direct evidences for understanding cBN growth mechanisms. The TEM sample technique is expected to be generally applicable to other film systems, particularly those with an amorphous topmost layer.
SiC pore surfaces: Surface studies of 4H–SiC(11¯02) and 4H–SiC(1¯102¯)
Authors: Starke U. , Lee W. Y. , Coletti C. , Saddow S. E. , Devaty R. P. , Choyke W. J.
Published: January 2006

The morphology and atomic structure of 4H–SiC(11¯02) and 4H–SiC(1¯102¯) surfaces, i.e., the surfaces found in the triangular channels of porous 4H–SiC, have been investigated using atomic force microscopy, low-energy electron diffraction (LEED), and Auger electron spectroscopy (AES). After hydrogen etching, the surfaces show steps parallel and perpendicular to the c axis, yet drastically different morphologies for the two isomorphic orientations. Both surfaces immediately display a sharp LEED pattern. Together with the presence of oxygen in the AES spectra, this indicates the development of an ordered oxide. Both surfaces show an oxygen-free well-ordered surface after Si deposition and annealing.
Large-orbit coaxial-structure cyclotron autoresonance maser
Authors: Zhang Shi-Chang , Thumm Manfred
Published: January 2006

We present a conceptual proposal for a large-orbit coaxial-structure cyclotron autoresonance maser (CARM), wherein the rf structure is a coaxial waveguide or cavity and a large-orbit electron beam encircles the axis of the coaxial structure. Both dispersion analysis and nonlinear simulations demonstrate the feasibility of the proposal. The large-orbit coaxial-structure CARM could be expected to operate in millimeter and submillimeter wave ranges with high power, low operating magnetic field, and ultrahigh gain. It is found that electron-beam velocity spread substantially decreases the power of CARMs, but this adverse influence might be offset by a proper taper of the axial magnetic field.
Multicellularity and the functional interdependence of motility and molecular transport
Authors: Solari Cristian A. , Ganguly Sujoy , Kessler John O. , Michod Richard E. , Goldstein Raymond E.
Published: January 2006

Benefits, costs, and requirements accompany the transition from motile totipotent unicellular organisms to multicellular organisms having cells specialized into reproductive (germ) and vegetative (sterile soma) functions such as motility. In flagellated colonial organisms such as the volvocalean green algae, organized beating by the somatic cells' flagella yields propulsion important in phototaxis and chemotaxis. It has not been generally appreciated that for the larger colonies flagellar stirring of boundary layers and remote transport are fundamental for maintaining a sufficient rate of metabolite turnover, one not attainable by diffusive transport alone. Here, we describe experiments that quantify the role of advective dynamics in enhancing productivity in germ soma-differentiated colonies. First, experiments with suspended deflagellated colonies ofVolvox carterishow that forced advection improves productivity. Second, particle imaging velocimetry of fluid motion around colonies immobilized by micropipette aspiration reveals flow fields with very large characteristic velocitiesUextending to length scales exceeding the colony radiusR. For a typical metabolite diffusion constantD, the associated Peclet numberPe= 2UR/D>> 1, indicative of the dominance of advection over diffusion, with striking augmentation at the cell division stage. Near the colony surface, flows generated by flagella can be chaotic, exhibiting mixing due to stretching and folding. These results imply that hydrodynamic transport external to colonies provides a crucial boundary condition, a source for supplying internal diffusional dynamics.
Intradialytic parenteral nutrition: comparison of olive oil versus soybean oilbasedlipid emulsions
Authors: Cano Noël J. M. , Saingra Yannick , Dupuy Anne-Marie , Lorec-Penet Anne-Marie , Portugal Henri , Lairon Denis , Cristol Jean-Paul , Come Adrien , Le Brun Alexia , Atlan Philippe , Leverve Xavier M.
Published: January 2006

Lipid, oxidative and inflammatory parameters are frequently altered in dialysis patients and may be worsened by intravenous lipid emulsions (ILE). We assessed the efficacy and tolerance of olive as compared with standard soybean oil-based ILE during intradialytic parenteral nutrition (IDPN). IDPN mixtures containing amino acids, glucose, and either olive oil (OO group,n17) or soybean oil-based ILE (SO group,n18) were administered in a 5-week randomized, double-blind study. On days 0 and 35, patients' nutritional status was assessed by BMI, normalized protein catabolic rate, predialytic creatinine, serum albumin and transthyretin; lipid metabolism by plasma LDL- and HDL-cholesterol, triacylglycerols, phospholipids, apo A-I, A-II, B, C-II, C-III, E and lipoprotein (a); oxidative status by α-tocopherol, retinol, selenium, glutathione peroxidase, malondialdehyde and advanced oxidized protein products; inflammatory status by serum C-reactive protein, orosomucoid, IL-2 and IL-6. No serious adverse event was observed. Significant changes were observed from day 0 to day 35 (P<0·05): nutritional criteria improved (albumin in OO; albumin, transthyretin and creatinine in SO); LDL-cholesterol, apo B, C-II, C-III and apo A-I/A-II ratio increased in both groups. HDL-cholesterol decreased in OO; apo E increased and lipoprotein (a) decreased in SO; α-tocopherol/cholesterol ratio increased in OO; malondialdehyde decreased in both groups; IL-2 increased in both groups. The between-group comparison only showed the following differences: α-tocopherol/cholesterol increased in OO; lipoprotein (a) decreased in SO. From these data, it was concluded that OO- and SO-based IDPNs similarly improved nutritional status and influenced plasma lipid, oxidative, inflammatory and immune parameters.