bluuebunny/crossref_metadata_2025 huggingface dataset:
Auxetic behaviour from rotating rigid units
Authors: Grima J. N. , Alderson A. , Evans K. E.
Published: February 2005

Auxetic materials exhibit the unexpected feature of becoming fatter when stretched and narrower when compressed, in other words, they exhibit a negative Poisson's ratio. This counter‐intuitive behaviour imparts many beneficial effects on the material's macroscopic properties that make auxetics superior to conventional materials in many commercial applications. Recent research suggests that auxetic be‐haviour generally results from a cooperative effect between the material's internal structure (geometry setup) and the deformation mechanism it undergoes when submitted to a stress. Auxetic behaviour is also known to be scale‐independent, and thus, the same geometry/deformation mechanism may operate at the macro‐, micro‐ and nano‐ (molecular) level. A considerable amount of research has been focused on the ‘re‐entrant honeycomb structure’ which exhibits auxetic behaviour if deformed through hinging at the joints or flexure of the ribs, and it was proposed that this ‘re‐entrant’ geometry plays an impor‐ tant role in generating auxetic behaviour in various forms of materials ranging from nanostructured polymers to foams. This paper discusses an alternative mode of deformation involving ‘rotating rigid units’ which also results in negative Poisson's ratios. In its most ideal form, this mechanism may be construc‐ ted in two dimensions using ‘rigid polygons’ connected together through hinges at their vertices. On application of uniaxial loads, these ‘rigid polygons’ rotate with respect to each other to form a more open structure hence giving rise to a negative Poisson's ratio. This paper also discusses the role that ‘rotating rigid units’ are thought to have in various classes of materials to give rise to negative Poisson's ratios. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Searching for auxetics with DYNA3D and ParaDyn
Authors: Hoover Wm. G. , Hoover C. G.
Published: February 2005

We sought to simulate auxetic behavior by carrying out dynamic analyses of mesoscopic model structures. We began by generating nearly periodic cellular structures. Four‐node “Shell” elements and eight‐node “Brick” elements are the basic building blocks for each cell. The shells and bricks obey standard elastic‐plastic continuum mechanics. The dynamical response of the structures was next determined for a three‐stage loading process: (1) homogeneous compression; (2) viscous relaxation; (3) uniaxial compression. The simulations were carried out with both serial and parallel computer codes – DYNA3D and ParaDyn – which describe the deformation of the shells and bricks with a robust contact algorithm. We summarize the results found here. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Simulation of a superconducting granular system on a honeycomb structure
Authors: Mancini G. , Natali R.
Published: February 2005

A simulation of an elementary system of metallic superconducting grains arranged on a single honeycomb cell shows how, in the temperature region belowTcthe supercurrent depends on the structure angle. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical study of reaction channels for the weakly bound complex systems created with HF, CO2, and various amines
Authors: Chen Shyh‐Jong , Chen Cheng , Hong Yaw‐Shun
Published: February 2005

This investigation conducted reaction channels of weakly bound complexes CO2…HF, CO2…HF…NH3, CO2…HF…NH2CH3, CO2…HF…NH(CH3)2, and CO2…HF…N(CH3)3 systems, using the Gaussian 98 package at the B3LYP/6‐311++G(3df,2pd) level. The syn‐fluoroformic acid or syn‐fluoroformic acid plus NH3 or amine conformers are more stable than the related anti‐fluoroformic acid or anti‐fluoroformic acid plus NH3 or amine conformers. However, the above‐mentioned weakly bound complexes are more stable than both the related syn‐ and anti‐type fluoroformic acid or acid plus NH3 or amine conformers and their related decomposed into CO2 + HF or CO2 + NHR3F (RH, CH3) combined molecular systems. Five reaction channels of the weakly bound complexes exist. Each channel includes weakly bound complexes and their related above‐mentioned systems. Moreover, each reaction channel contains two transition states. The transition state between the weakly bound complex and anti‐fluoroformic acid type structure (T13) is significantly higher than that of internal rotation (T23) between syn‐ and anti‐FCO2H (or FCO2H…NR3) structures. However, the above‐mentioned T13 can significantly decrease its energy by adding the third molecule NH3 or NR3 (RH or CH3). The more CH3 that is substituted in NR3 of the reaction channel, the lower the activation energy of the transition state in the system is affected. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Trapping 4‐fluorobenzyl chloride in human plasma with chemical derivatization followed by quantitative bioanalysis using high‐performance liquid chromatography/tandem mass spectrometry
Authors: Yang Eric , Wang Sherry , Bowen Chester , Kratz John , Cyronak Matthew J. , Dunbar Jacob R.
Published: February 2005

A quantitative bioanalytical method involving chemical derivatization, solid phase extraction (SPE) and high‐performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) was developed for the determination of 4‐fluorobenzyl chloride (4FBCl) in human plasma. 4FBCl is a volatile and reactive molecule that is very unstable in human plasma. In order to stabilize 4FBCl in plasma samples prior to storage, 4‐dimethylaminopyridine (DMAP) was added, forming a stable quaternary amine salt derivative. A three‐step weak cation‐exchange SPE procedure was then employed to remove excess DMAP. The plasma extracts were analyzed by HPLC/MS/MS using a TurboIonspray interface and multiple reaction monitoring. Unlike 4FBCl, the quaternary amine derivative shows excellent sensitivity in electrospray mass spectrometry. The method was validated over a concentration range of 0.5–500 ng/mL using 45 μL of plasma. The maximum within‐run and between‐run precision observed in a three‐run validation for quality control (QC) samples was 12.5 and 7.6%, respectively. The maximum percentage bias observed at all QC sample concentrations was 11.9%. The method has proven to be robust and compatible with high‐throughput bioanalysis. Copyright © 2005 John Wiley & Sons, Ltd.
Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry of 4‐sulfophenyl isothiocyanate‐derivatized peptides on AnchorChip™ sample supports using the sodium‐tolerant matrix 2,4,6‐trihydroxyacetophenone and diammonium citrate
Authors: Oehlers Leon P. , Perez Amy N. , Walter Ronald B.
Published: February 2005

The reagent 4‐sulfophenyl isothiocyanate (SPITC) is an effective, stable, and inexpensive alternative to commercially available reagents used in the N‐terminal sulfonation of peptides for enhanced postsource decay (PSD) in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometric (MALDI‐TOFMS) analyses. However, suppression of ionization of sulfonated peptides due to sample and matrix contaminants such as sodium can be a problem when using prestructured MALDI target sample supports, such as the Bruker Daltonics AnchorChip™. We show that use of the salt‐tolerant matrix 2,4,6‐trihydroxyacetophenone containing diammonium citrate (THAP/DAC) as an alternative to α‐cyanohydroxycinnamic acid (HCCA) reduces the need for extensive washing of ZipTip‐bound peptides or additional on‐target sample clean‐up steps. Use of the THAP/DAC matrix results in selective ionization of sulfonated peptides with greater peptide coverage, as well as detection of higher mass derivatized peptides, than was observed for HCCA or THAP alone. The THAP/DAC matrix is quite tolerant of sodium contamination, with SPITC‐peptides detectable in preparations containing up to 50 mM NaCl. In addition, THAP/DAC matrix was found to promote efficient PSD fragmentation of sulfonated peptides. We demonstrated the utility of using the THAP/DAC MALDI matrix for peptide sequencing with DNA polymerase β tryptic peptide mixture, as well as tryptic peptides derived from Xiphophorus maculatus brain extract proteins previously separated by two‐dimensional polyacrylamide gel electrophoresis (2D‐PAGE). Copyright © 2005 John Wiley & Sons, Ltd.
Testing treatment effects in the presence of competing risks
Authors: Freidlin Boris , Korn Edward L.
Published: February 2005

Competing risks are often encountered in clinical research. In the presence of multiple failure types, the time to the first failure of any type is typically used as an overall measure of the clinical impact for the patients. On the other hand, use of endpoints based on the type of failure directly related to the treatment mechanism of action allows one to focus on the aspect of the disease targeted by treatment. We review the methodology commonly used for testing failure specific treatment effects. Simulation results demonstrate that the cause‐specific log‐rank test is robust (in the sense of preserving the nominal level of the test) and has good power properties for testing for differences in the marginal latent failure‐time distributions, whereas the use of a popular cumulative incidence based approach may be problematic for this aim. Published in 2005 by John Wiley & Sons, Ltd.
High-affinity folate binding in human mammary gland
Authors: Holm Jan , Hansen Steen Ingemann , Høier-Madsen Mimi
Published: February 2005

High-affinity 3H-folate binding in Triton X-100 solubilized human mammary gland tissue displayed characteristics, e.g. apparent positive cooperativity and increasing affinity with decreasing concentration of folate binding protein, shown to be typical of specific folate binding. Radioligand dissociation was slow at pH 7.4. A major fraction of the bound radioligand dissociated rapidly at pH 3.5, while a residual binding of 20% persisted even after prolonged dialysis at pH 3.5. Gel chromatography revealed two major folate binding proteins (Mr ≈ 100 kDa and 25 kDa). However, only one single band was detectable on SDS-PAGE immunoblotting. The highest folate binding activity per g protein was associated with the upper triglyceride-containing layer of the 1000 g supernatant of the homogenate. The folate binding protein extracted from this layer had a low cross-reactivity (<5%) with rabbit antibodies against 25 kDa human milk folate binding protein. The folate binding protein in the 1000 g pellet and the aqueous phase of the 1000 g supernatant was present at a low concentration and had a cross-reactivity of 100%.
Intracellular signalling of epinephrine in rat hepatocytes during fetal development and hepatic regeneration
Authors: Leoni S. , Spagnuolo S. , Terenzi F. , Marino M. , Bolaffi C. , Pulcinelli F. M. , Mangiantini M. T.
Published: February 2005

The changes in intracellular calcium concentration and IP3 production after the addition of epinephrine were analysed in adult, fetal (20th–22nd day of intrauterine life), and regenerating rat hepatocytes (4 h–24 h after partial hepatectomy) to determine whether the signal transduction is the same in quiescent proliferating and differentiating cells.

The epinephrine treatment causes a significative cytosolic calcium transient in hepatocytes isolated in the last day of fetal life (22-day old) and in the early stage of regeneration (4 h). This effect is not significant in the previous stage of fetal life (20-day old) and at the onset of M phase of cell cycle after partial hepatectomy (24 h).

[3H]myo inositol incorporation into IP3 and IP4 is higher in 20 day fetal and regenerating hepatocytes with respect to the control. In these cells the epinephrine does not affect basal level of IP3 and IP4, while it causes a substantial increase of these inositol phosphates in adult hepatocytes.

[3H]myo inositol incorporation into PIP2 is very low at the 20th day of fetal life. Epinephrine has no effect on this parameter in fetal and regenerating hepatocytes.

Our results show that the epinephrine signal is mediated differently in proliferating and in quiescent hepatocytes.
A novel copper-containing protein from spinach: A blue oxidase with unique properties
Authors: Sarkissian Levon Kh. , Nalbandyan Robert M.
Published: February 2005

A copper-containing protein resembling in its optical and EPR spectra stellacyanin from latex was isolated from spinach leaves. The protein oxidizes ferrocyanide and catechol. The activity was highest at acidic pt4. It was shown that similar proteins isolated from cucumber and squash also possess the oxidase activity to ferrocyanide.
Binding of mitochondrial ATPase from ox heart to its naturally occurring inhibitor protein: Localization by antibody binding
Authors: Jackson Philip J. , Harris David A.
Published: February 2005

The naturally occurring ATPase inhibitor protein from ox heart mitochondria was cross-linked to its binding site on the mitochondrial ATPase using 1-ethyl-3-(dimethylamino)propyl carbodiimide. The cross-linked product, when transferred electrophoretically to a nitrocellulose sheet, reacted with antibodies directed against the inhibitor protein and the β-subunit of the ATPase. It was concluded that the binding site for the inhibitor protein lies on the β-subunit.
Two-dimensional structure of phospholipase induced crystals of Ca2+-ATPase from sarcoplasmic reticulum
Authors: Misra M. , Malhotra S. K.
Published: February 2005

A two-dimensional projection map was computed of the Ca2+-ATPase molecules in sarcoplasmic reticulum, isolated from rabbit skeletal muscle. Crystalline arrays of Ca2+-ATPase molecules were formed by incubating the membrane vesicles with phospholipase A2 and dialysing against Tris/HCl buffer. Ca2+-ATPase molecules appear as quasi-triangular blobs in the projection map and seem to form dimers. The projection map seems to indicate an enzyme conformation somewhat similar to vanadate-induced crystals but different from lanthanide-induced crystals of Ca2*-ATPase.
Roles of Cyclophilins in Cancers and Other Organ Systems
Authors: Yao Qizhi , Li Min , Yang Hui , Chai Hong , Fisher William , Chen Changyi
Published: February 2005

Cyclophilins are originally identified as cellular binding proteins for the immunosuppressive drug cyclosporin A. Many cyclophilins, including CypA, CypB, CypC, CypD, and Cyp40, have been discovered and shown to be ubiquitously distributed in many types of cells and organ systems. Recent investigations have uncovered many important properties and functions for cyclophilins including peptidyle‐prolyl‐isomerase activity and protein folding/repair; maintaining mitochondrial functions and involvement in apoptosis; roles in regulation of T‐cell function and inflammation; interaction with CD147; and pathogenesis of vascular disease, human immunodeficiency virus infection, and rheumatoid arthritis. Furthermore, the expression and functions of cyclophilins may be correlated with tumor biology of several types of cancers including pancreatic carcinoma. Molecular mechanisms of cyclophilin‐mediated biologic events and future directions of research are discussed in this review. Understanding the roles of cyclophilins in cancers and other organ systems will be crucial in determining clinical applications for the treatment or diagnosis of human diseases.
Role of Gastrointestinal Hormones in Neuroblastoma
Authors: Gustafson W. Clay , De Berry Brittany B. , Evers B. Mark , Chung Dai H.
Published: February 2005

As a neuroendocrine tumor, neuroblastoma expresses various gastrointestinal (GI) hormones, such as vasoactive intestinal peptide, gastrin‐releasing peptide (GRP), neurotensin, and somatostatin, which exert diverse cellular functions in neuroblastoma. In particular, we have recently found that GRP and its cell surface receptor, GRP‐R, are abundantly expressed in neuroblastomas. Moreover, more advanced‐stage neuroblastomas demonstrated an increased level of GRP‐R, suggesting an important role of GRP in aggressive tumor behavior. This review describes the role of several GI hormones commonly expressed in neuroblastoma and discusses in depth the mitogenic actions of GRP in neuroblastoma. In addition, the molecular mechanisms involved in the GRP‐induced stimulation of neuroblastoma cell growth are discussed. Our study results demonstrate a role of GRP as an autocrine/paracrine growth factor and elucidate involvement of specific intracellular signaling, the phosphatidylinositol 3‐kinase pathway, in the growth regulation of neuroblastoma.
Viability theory for an ecosystem approach to fisheries
Authors: Cury Philippe M. , Mullon Christian , Garcia Serge M. , Shannon Lynne J.
Published: February 2005

Maintenance of overall ecosystem complexity is perceived as critical to the sustainability of ecosystem use. The development of an operational basis for an ecosystem approach to fisheries, however, faces many difficulties. On the research side, the challenge is in defining proper long-term, ecosystem-related objectives; determining meaningful reference values and indicators for desirable or undesirable states of the ecosystem; and developing appropriate data collection, analytical tools and models. The “viability” concept developed in economics by Jean-Pierre Aubin can be used to assist in the definition, selection of, and interaction among long-term objectives at an ecosystem level. It recognizes that ecosystems are complex assemblages of interacting and self-organizing natural and human components that cannot be predicted. Viability models define an ensemble of “viable states”, in contrast to undesirable states defined as such by ecological, economic, and/or social constraints. These constraints can be derived from fisheries objectives, conservation principles, scientific results of modelling, or precautionary principles, and correspond to limit reference points to be avoided. Viability theory does not attempt to choose any “optimal solution” according to given criteria, but selects “viable evolutions”. These evolutions are compatible with the constraints in the sense that they satisfy them at each time and can be delineated by the viability kernel. The southern Benguela marine ecosystem is presented as a first attempt for the application of this theory. In defining ecosystem-based objectives (and related issues such as target reference points), it seems more difficult to reach consensus among stakeholders on what is desirable than on what is undesirable (e.g. biological or economic collapse, species extinction, displacement of local rural communities). Expressed in the negative form or as limit reference points, ecosystem-based constraints can be considered simultaneously with current target reference points, such as maximum sustainable yield, using viability models. The viability approach can help to progressively integrate ecosystem considerations, such as conservation, into fisheries management.
An application of two techniques for the analysis of short, multivariate non-stationary time-series of Mauritanian trawl survey data
Authors: Erzini Karim , Inejih Cheikh A. O. , Stobberup Kim A.
Published: February 2005

Min/max autocorrelation factor analysis (MAFA) and dynamic factor analysis (DFA) are complementary techniques for analysing short (>15–25 y), non-stationary, multivariate data sets. We illustrate the two techniques using catch rate (cpue) time-series (1982–2001) for 17 species caught during trawl surveys off Mauritania, with the NAO index, an upwelling index, sea surface temperature, and an index of fishing effort as explanatory variables. Both techniques gave coherent results, the most important common trend being a decrease in cpue during the latter half of the time-series, and the next important being an increase during the first half. A DFA model with SST and UPW as explanatory variables and two common trends gave good fits to most of the cpue time-series.
The trophic spectrum: theory and application as an ecosystem indicator
Authors: Gascuel Didier , Bozec Yves-Marie , Chassot Emmanuel , Colomb Audrey , Laurans Martial
Published: February 2005

Trophic spectra represent the distribution of biomass, abundance, or catch by trophic level, and may be used as indicators of the trophic structure and functioning of aquatic ecosystems in a fisheries context. As a theoretical background, we present a simple ecosystem model of biomass flow reflecting predation and ontogenetic processes. Biomass trophic spectrum of total biomass can be modelled as the result of three major factors and processes: trophic efficiency, transfer kinetics, and extent of top-down control. In the simulations, changes in the spectrum highlight fishing impacts on trophic structure and reveal some functional characteristics of the underlying ecosystem. As examples of potential applications, three case studies of trophic spectra are presented. Catch trophic spectra allow description of structural differences among European fishing areas and periods. Abundance trophic spectra of coral-reef fish assemblages display different trophic signatures, characterizing different reef habitats in New Caledonia and highlighting fishing effects in a marine protected area context. Biomass trophic spectra of demersal resources off Northwest Africa show a shift in ecosystem structure that can be attributed to the rapid increase in fishing pressure during the past few decades. Off Senegal, total biomass remained fairly constant, suggesting a strong top-down control linked to fisheries targeting high trophic level species. Off Guinea, exploitation rates are spread over a wider range of trophic levels, and the total biomass of demersal resources tended to decrease. The trophic spectrum is concluded to be a useful indicator describing and comparing systems in time and space, detecting phase shifts linked to natural or anthropogenic perturbations, and revealing differences in ecosystem functioning.
A framework for ecosystem impacts assessment using an indicator approach
Authors: Livingston P.A. , Aydin K. , Boldt J. , Ianelli J. , Jurado-Molina J.
Published: February 2005

Assessment of the historical, present, and future states of marine ecosystems and the effects that humans and climate have on the state of an ecosystem are crucial to the scientific advice required to implement an ecosystem-based fishery management system. Management of federal groundfish fisheries in Alaska considers not just the target fishery, but also the possible impact those fisheries might have on other species and the ecosystem. Management actions have ranged from providing protection of endangered species in the region to preventing new fisheries from starting on key foodweb components such as forage fish. A scientific framework for providing ecosystem-based advice that puts the ecosystem first has been evolving over the past few years. This framework provides a way of assessing ecosystem factors that influence target species, the impact the target fishery may have on associated species, and ecosystem-level impacts of fishing. An indicator approach that describes ecosystem status, and trends and measures of human and climate influence has been developed to provide advice to fishery managers. This approach is now being expanded to utilize a variety of models to predict possible future trends in various ecosystem indicators. Future implementation challenges include the refinement of these predictive models, and the inclusion of climate into the models. Identification of sensitive and meaningful ecosystem indicators is also required before a more formalized decision-making process, one that includes ecosystem considerations, can be developed. Most important, the culture of fishery management and research organizations needs to change to embrace the ecosystem-based protections already mandated by various laws.
Developmental deficits in social perception in autism: the role of the amygdala and fusiform face area
Authors: Schultz Robert T.
Published: February 2005

Autism is a severe developmental disorder marked by a triad of deficits, including impairments in reciprocal social interaction, delays in early language and communication, and the presence of restrictive, repetitive and stereotyped behaviors. In this review, it is argued that the search for the neurobiological bases of the autism spectrum disorders should focus on the social deficits, as they alone are specific to autism and they are likely to be most informative with respect to modeling the pathophysiology of the disorder. Many recent studies have documented the difficulties persons with an autism spectrum disorder have accurately perceiving facial identity and facial expressions. This behavioral literature on face perception abnormalities in autism is reviewed and integrated with the functional magnetic resonance imaging (fMRI) literature in this area, and a heuristic model of the pathophysiology of autism is presented. This model posits an early developmental failure in autism involving the amygdala, with a cascading influence on the development of cortical areas that mediate social perception in the visual domain, specifically the fusiform “face area” of the ventral temporal lobe. Moreover, there are now some provocative data to suggest that visual perceptual areas of the ventral temporal pathway are also involved in important ways in representations of the semantic attributes of people, social knowledge and social cognition. Social perception and social cognition are postulated as normally linked during development such that growth in social perceptual skills during childhood provides important scaffolding for social skill development. It is argued that the development of face perception and social cognitive skills are supported by the amygdala–fusiform system, and that deficits in this network are instrumental in causing autism.
Paleoecology of Beringian “packrat” middens from central Yukon Territory, Canada
Authors: Zazula Grant D. , Froese Duane G. , Westgate John A. , La Farge Catherine , Mathewes Rolf W.
Published: February 2005

Rodent middens from ice-rich loess deposits are important new paleoenvironmental archives for Eastern Beringia. Plant macrofossils recovered from three middens associated with Dawson tephra (ca. 24,00014C yr B.P.) at two sites in Yukon Territory include diverse graminoids, forbs, and mosses. These data suggest substantial local scale floristic and habitat diversity in valley settings, including steppe-tundra on well-drained soils, moist streamside meadows, and hydric habitats. Fossil arctic ground squirrel burrows and nesting sites indicate that permafrost active layers were thicker during Pleistocene glacial periods than at present on north-facing slopes.
Origins and variation of terrestrial energetic neutral atoms outflow
Authors: Wilson G. R. , Moore T. E.
Published: February 2005

Analysis of ENA data from the LENA instrument on the IMAGE spacecraft shows that the terrestrial atmosphere is a copious emitter of energetic neutral atoms (<300 eV) under all conditions. When activity is low, the observed emissions are concentrated close to the Earth and are presumed to be the high‐energy tail of the warm oxygen geocorona, with energies <2 eV. When activity increases, the relative abundance of the higher‐energy neutrals increases, and the emissions can be seen farther from the Earth. Because of the close correlation between the postperigee ENA flux (fluxes seen 1–2 hours after spacecraft perigee) and Ap and the fact that the postperigee fluxes are seen when no magnetic storm is in progress we conclude that many of the emitted ENA come from the auroral zone and are produced by energized ionospheric ions rather than by precipitating energetic ions. In more spectacular events, such as the Bastille Day storm event (14–16 July 2000), oxygen neutral emissions produced by precipitation of keV ring current oxygen ions can also make an important contribution to the total neutral emission. We conclude that diurnal variation in ENA emissions is a winter hemisphere feature that is absent in the summer hemisphere. As activity increases, the altitude range of the auroral oval ENA emission region increases.
A dynamic similarity subgrid model for chemical transformations in large‐eddy simulation of the atmospheric boundary layer
Authors: Vinuesa J.‐F. , Porté‐Agel F.
Published: February 2005

In large‐eddy simulations (LESs) of atmospheric reacting flows, homogeneous and instantaneous mixing of reactants within a grid‐cell is usually assumed. However, highly reactive species are often segregated or pre‐mixed at small scales. In this paper, we propose a parameterization to account for the effect of the unresolved scales on the chemical transformations. Its formulation relies on the description of the subgrid unresolved reactant covariance as a function of the resolved covariance by using scale‐similarity arguments. A dynamic procedure is used to compute the model coefficient from the resolved reactant concentration fields, therefore not requiring any parameter specification or tuning. In simulations of a convective boundary layer with a fast second‐order reaction, using the new model is found to perform better than ignoring subgrid chemistry effects.
Active mesopelagic prokaryotes support high respiration in the subtropical northeast Atlantic Ocean
Authors: Arístegui Javier , Duarte Carlos M. , Gasol Josep M. , Alonso‐Sáez Laura
Published: February 2005

Here we provide evidence, based on prokaryote metabolic proxies and direct estimates of oxygen consumption, that the mesopelagic prokaryote assemblage in the subtropical Northeast Atlantic is an active one. It supports a high respiration (0.22 ± 0.05 μmol O2 l−1 d−1, corresponding to 68 ± 8 mmol CO2 m−2 d−1), comparable to that of the epipelagic zone during the same period (64–97 mmol C m−2 d−1). Our findings suggest that mesopelagic prokaryotes in the NE subtropical Ocean, as well as in other eastern boundary regions, are important carbon sinks for organic matter advected from the highly productive coastal systems, and would play a key role in the global carbon cycle of the oceans.
Organic reactions increasing the absorption index of atmospheric sulfuric acid aerosols
Authors: Nozière B. , Esteve W.
Published: February 2005

Unlike most environments present at Earth's surface atmospheric aerosols can be favorable to organic reactions. Among them, the acid‐catalyzed aldol condensation of aldehydes and ketones produces light‐absorbing compounds. In this work the increase of the absorption index of sulfuric acid solutions 50–96 wt. % resulting from the uptake of gas‐phase acetaldehyde, acetone, and 2‐butanone (methyl ethyl ketone), has been measured in the near UV and visible range. Our results indicate that the absorption index between 200 and 500 nm for stratospheric sulfuric aerosols exposed to 100 pptV of acetaldehyde (1 pptV = 10−12 v/v) would increase by four orders of magnitude over a two‐year lifetime. Rough estimates based on previous radiative calculations suggest that this reaction could result in an increase of the radiative forcing of sulfate aerosols of the order of 0.01 W m−2, and that these processes are worth further investigation.
High‐latitude aurora during steady northward interplanetary magnetic field and changing IMF By
Authors: Cumnock J. A.
Published: February 2005

High‐latitude transpolar arcs (TPAs) are often observed during northward interplanetary magnetic field (IMF); of these, theta aurora are seen when transpolar arcs move in the dawn or dusk direction across the entire polar region in response to IMF By changes. Periods of study were chosen when By changes sign during steady northward IMF in order to determine the influence of IMF Bx, By, the strength of the IMF, the solar wind, and Earth dipole tilt on the occurrence and motion of high‐latitude TPAs forming theta aurora. For a 4.5‐year period there are 55 events for which IMF Bz is northward for at least 2 hours before and at least 3 hours after a By sign change. Of these, 19 occurred when the Polar satellite was over the Northern Hemisphere for the duration of the event. We find that for northward IMF and a By sign change theta aurora are almost always formed in the Northern Hemisphere, regardless of Bx and dipole tilt. This implies that theta aurorae form simultaneously in both hemispheres. IMF By does not appear to influence the intensity and duration of the arc. Strongest UV emissions occur in the summer hemisphere. Evolution time has a fairly complex dependence on solar wind parameters.
Unifying large and small wave‐generated ripples
Authors: Williams Jon J. , Bell Paul S. , Thorne Peter D.
Published: February 2005

Frequently, in field and laboratory studies of wave‐generated bed forms on beds of sandy sediments, both large and small wave‐generated ripples (LWRs and SWRs) are observed and in some situations may be superimposed upon one another. The present paper examines relationships between measured wave conditions and the geometry of LWRs and SWRs and shows that existing empirical equations used to predict the dimensions of SWRs perform badly for LWRs. To address this problem, relationships found between ripple geometry and the wave Reynolds number are used as the basis for new expressions for prediction of ripple height, wavelength, and steepness that improve the accuracy of existing approaches for both LWRs and SWRs. The present results indicate strongly that SWRs and LWRs are related and their superposition in certain conditions reflects the time lag between the response of the bed to changing hydrodynamic conditions. They must be considered therefore when estimating the total bed roughness in a range of practical engineering and numerical modeling applications.
Cascading‐driven upwelling in submarine canyons at high latitudes
Authors: Kämpf Jochen
Published: February 2005

Numerical simulations and laboratory experiments confirm my initial research hypothesis stating that dense‐water cascading down a submarine canyon induces localized upwelling of deeper water onto the shelf. This process, not described before, is associated with internal deformation radii inherent in the cascading process being less the canyon width and geostrophic adjustment of a density front that establishes along the canyon axis. Since submarine canyons are common to continental margins, this paper has identified a key process triggering the renewal of shelf waters at high latitudes.
Climatology of short‐period gravity waves observed over northern Australia during the Darwin Area Wave Experiment (DAWEX) and their dominant source regions
Authors: Pautet P.‐D. , Taylor M. J. , Liu A. Z. , Swenson G. R.
Published: February 2005

The Darwin Area Wave Experiment (DAWEX) was designed to investigate the generation and propagation of gravity waves from intense regions of localized convection that occur regularly over northern Australia (in the vicinity of Darwin) during the premonsoon period. This multinational program was conducted during the austral spring 2001 using a range of coordinated optical, radar, and in situ balloon measurements. As part of this program, all‐sky image observations of short‐period gravity wave events in the near infrared OH nightglow emission (altitude ∼87 km) were made from two well‐separated sites in northern Australia: Wyndham (15.5°S, 128.1°E) and Katherine (14.5°S, 132.3°E), over a 10‐day period during November 2001. A total of 25 extensive wave events were observed during this period, from which the dominant horizontal wave characteristics were determined to be: wavelength 25–35 km and observed phase speed 27–75 m/s, yielding observed periods from 7 to 14 min, consistent with previous measurements at other low‐latitude sites. A key finding of this study was a marked anisotropy in the wave propagation headings, with over 3/4 of the events exhibiting a strong southward component of motion and a clear preference for wave progression over the azimuthal range SE to SSW. Although this range encompasses gravity waves originating locally from the Darwin area, the majority of the wave events exhibited propagation headings consistent with more distant sources located to the north and northwest of Australia. Assuming deep convection was the dominant mechanism for the waves, the strong asymmetry in their velocity distribution appears to result from a combination of nonuniformity in the geographic occurrence of thunderstorms coupled together with significant wind filtering effects at the source altitude and within the middle atmosphere. These results are consistent with long‐range, short‐period wave propagation (most probably in the form of ducted waves) possibly from intense convective regions located ∼1000 km to the north over the Indonesian Island chain.
Cloud base temperature measurements using a simple longwave infrared cloud detection system
Authors: Riordan D. , Clay R. , Maghrabi A. , Dawson B. , Pace R. , Wild N.
Published: February 2005

We have studied the 10 μm temperature of overcast skies, as measured from the ground, in a coastal region of South Australia. The long‐term aim of this work is to be able to use measurements of the sky temperature, plus other readily measured ground‐based parameters, to recognize the presence, or otherwise, of clouds. Comparisons have been made between the 10 μm sky temperature and cloud height in overcast conditions, measured both with a ceilometer and radiosondes. A low‐altitude cloud exhibits a wide range of emissivities, such that clouds with base heights up to 1200 m have emissivities ranging from below 0.2 to close those expected for black bodies at those wavelengths. However, higher clouds exhibit different properties, as their temperatures approach those to be expected for a clear sky with water vapor.
Mineralogical and geochemical compositions of the eolian dust from the northeast equatorial Pacific and their implications on paleolocation of the Intertropical Convergence Zone
Authors: Hyeong Kiseong , Park Sung‐Hyun , Yoo Chan Min , Kim Ki‐Hyune
Published: February 2005

Eolian components of a 328‐cm‐long piston core collected from the northeast equatorial Pacific at 16°12′N and 125°59′W were investigated for mineral and geochemical compositions in order to constrain the sources of dust and determine the latitudinal position of the Intertropical Convergence Zone (ITCZ) recorded in the core. The eolian components below 250 cm are characterized by smectite‐ and phillipsite‐rich mineral composition, depleted rare earth elements (REEs), and high Eu/Sm ratios, indicative of volcanic‐rich composition. These characteristics are found in equatorial and south Pacific surface sediments, of which eolian particles are supplied from Central and South America. In contrast, eolian components above 250 cm are characterized by quartz‐ and illite‐rich mineralogy, and more shale‐like REE and trace element compositions, which are common in surface sediments of the central Pacific north of the ITCZ, where eolian particles are sourced from the Asia and North America. The observed changes are attributed to the shifting of its eolian sources from the Central and South America to the China and North America across the hemispheric dust barrier of the ITCZ. This result suggests that smectite‐illite transition, a phenomenon that smectite amount increases over illite at a depth, can be used as a tracking tool for the paleolocation of the ITCZ in the northeast and central Pacific. Backtrack path construction of Pacific plate indicates paleolocation of the ITCZ north of 12°N (±2°) prior to late Miocene.
An ensemble‐based reanalysis approach to land data assimilation
Authors: Dunne Susan , Entekhabi Dara
Published: February 2005

Future pathfinder missions such as NASA's Hydrosphere State (Hydros) and ESA's Soil Moisture and Ocean Salinity (SMOS) will provide satellite‐based global observations of surface (0–5 cm) soil moisture. In previous work an ensemble Kalman filter was used to estimate soil moisture, related states, and fluxes by merging noisy low‐frequency microwave observations with the forecasts from a conventional yet uncertain land surface model. Kalman filter estimates are only conditioned on observations prior to estimation times. Here it is argued that soil moisture estimation is a reanalysis‐type problem as observations beyond the estimation time are useful in the estimation. An ensemble smoother is used in which the state vector and measurement vector are distributed in time and updated as a batch. Its performance in a land data assimilation context is compared to that of the ensemble Kalman filter. Results demonstrate that smoothing yields an improved estimate compared to filtering, reflected in the decreased deviation from truth and the reduction in uncertainty associated with the estimate. Precipitation significantly impacts the performance of the smoother, acting as an information barrier between dry‐down events. An adaptive hybrid filter/smoother is presented in which brightness temperature is used to break the study interval into a series of dry‐down events. The smoother is used on dry‐down events, and the filter is used when precipitation is evident between estimation times. An improved estimate is obtained as all observations in a given dry‐down period are used to estimate soil moisture in that period, and backward propagation of information from subsequent precipitation events is avoided.
Consistent and mimetic discretizations in general relativity
Authors: Di Bartolo Cayetano , Gambini Rodolfo , Pullin Jorge
Published: February 2005

A discretization of a continuum theory with constraints or conserved quantities is called mimetic if it mirrors the conserved laws or constraints of the continuum theory at the discrete level. Such discretizations have been found useful in continuum mechanics and in electromagnetism. We have recently introduced a new technique for discretizing constrained theories. The technique yields discretizations that are consistent, in the sense that the constraints and evolution equations can be solved simultaneously, but it cannot be considered mimetic since it achieves consistency by determining the Lagrange multipliers. In this paper we would like to show that when applied to general relativity linearized around a Minkowski background the technique yields a discretization that is mimetic in the traditional sense of the word. We show this using the traditional metric variables and also the Ashtekar new variables, but in the latter case we restrict ourselves to the Euclidean case. We also argue that there appear to exist conceptual difficulties to the construction of a mimetic formulation of the full Einstein equations, and suggest that the new discretization scheme can provide an alternative that is nevertheless close in spirit to the traditional mimetic formulations.
Effect of bending and torsional mode excitation on the reaction Cl+CH4→HCl+CH3
Authors: Kim Zee Hwan , Bechtel Hans A. , Camden Jon P. , Zare Richard N.
Published: February 2005

A beam containing CH4, Cl2, and He is expanded into a vacuum chamber where CH4 is prepared via infrared excitation in a combination band consisting of one quantum of excitation each in the bending and torsional modes (ν2+ν4). The reaction is initiated by fast Cl atoms generated by photolysis of Cl2 at 355nm, and the resulting CH3 and HCl products are detected in a state-specific manner using resonance-enhanced multiphoton ionization (REMPI). By comparing the relative amplitudes of the action spectra of Cl+CH4(ν2+ν4) and Cl+CH4(ν3) reactions, we determine that the ν2+ν4 mode-driven reaction is at least 15% as reactive as the ν3 (antisymmetric stretch) mode-driven reaction. The REMPI spectrum of the CH3 products shows no propensity toward the formation of umbrella bend mode excited methyl radical, CH3(ν2=1), which is in sharp distinction to the theoretical expectation based on adiabatic correlations between CH4 and CH3. The rotational distribution of HCl(v=1) products from the Cl+CH4(ν2+ν4) reaction is hotter than the corresponding distribution from the Cl+CH4(ν3) reaction, even though the total energies of the two reactions are the same within 4%. An explanation for this enhanced rotational excitation of the HCl product from the Cl+CH4(ν2+ν4) reaction is offered in terms of the projection of the bending motion of the CH4 reagent onto the rotational motion of the HCl product. The angular distributions of the HCl(ν=0) products from the Cl+CH4(ν2+ν4) reaction are backward scattered, which is in qualitative agreement with theoretical calculation. Overall, nonadiabatic product vibrational correlation and mode specificity of the reaction indicate that either the bending mode or the torsional mode or both modes are strongly coupled to the reaction coordinate.
The performance of time-dependent density functional theory based on a noncollinear exchange-correlation potential in the calculations of excitation energies
Authors: Wang Fan , Ziegler Tom
Published: February 2005

In the present work we have studied the accuracy of excitation energies calculated from spin-flip transitions with a formulation of time-dependent density functional theory based on a noncollinear exchange-correlation potential proposed in a previous study. We compared the doublet-doublet excitation energies from spin-flip transitions and ordinary transitions, calculated the multiplets splitting of some atoms, the singlet-triplet gaps of some diradicals, the energies of excited quartet states with a doublet ground state. In addition, we attempted to calculate transition energies with excited states as reference. We compared the triplet excitation energies and singlet-triplet separations of the excited state from spin-flip and ordinary transitions. As an application, we show that using excited quartet state as reference can help us fully resolve excited states spin multiplets. In total the obtained excitation energies calculated from spin-flip transitions agree quite well with other theoretical results or experimental data.
Bonding behavior and thermal stability of C54Si6: A first-principles molecular dynamics study
Authors: Matsubara M. , Massobrio C.
Published: February 2005

By using a self-consistent plane-waves density functional approach we study the bonding behavior and the thermal properties of C54Si6 heterofullerenes. Calculations are carried out by employing a generalized gradient approximation. Our investigation improves upon previous findings on the same system obtained via the local density approximation approach. This is due to a much larger search in configurational space and the explicit account of temperature effects. Overall, isomers can be classified in two groups. In the first, nearest-neighboring Si atoms form a subnetwork, while in the second the Si atoms are farther apart on the cage. In addition to structural optimization, we carried out first-principles molecular dynamics for temperatures up to T=3000K on a time interval of 12 ps. These simulations show that Si–Si bond variations with temperature are less important when all Si atoms are found on a hexagon. Therefore, this structural arrangement is the most likely to be observed experimentally. Analysis of charge topology reveals that the amount of charge on each atom depends on the number of heterogeneous bonds, due to a significant charge transfer from the Si to the neighboring C atoms.
Origin of temperature dependent conductivity of α-polyvinylidene fluoride
Authors: Tuncer Enis , Wegener Michael , Frübing Peter , Gerhard-Multhaupt Reimund
Published: February 2005

The conductivity of α-polyvinylidene fluoride is obtained from dielectric measurements performed in the frequency domain at several temperatures. At temperatures above the glass-transition, the conductivity can be interpreted as an ionic conductivity, which confirms earlier results reported in the literature. Our investigation shows that the observed ionic conductivity is closely related to the amorphous phase of the polymer.