bluuebunny/crossref_metadata_2025 huggingface dataset:
PIXE analysis of human brain tissue
Authors: Boruchowska M. , Lankosz M. , Adamek D. , Korman A.
Published: January 2005

The proton induced x‐ray emission (PIXE) technique was used for localized analysis of trace elements in small quantities of medical samples. Both white and gray matter of the human brain were studied. The tissue samples were taken at autopsy from patients aged from 17 to 88 years. Qualitative and quantitative analyses were performed. NIST SRM 1577b Bovine Liver and SRM 1566a Oyster Tissue were used as external standards for the determination of trace element mass fractions in the brain specimens. The main goal of these preliminary studies was to evaluate approaches for the quantitative analysis of medical materials using PIXE taking into account the effect of patient age on the accumulation of elements and the regional distribution of elements in human brain. Detection and quantification limits were calculated for selected elements. Elevation of Zn concentration with age of patients was observed for white mater of the human brain. Elements such as S, K, Ca, Mn, Fe, Cu and Zn clearly exhibit higher mass fractions in grey matter than in white matter in all cases. This investigation confirms that PIXE is a useful technique for multielement analysis of tissue samples with good sensitivity. Copyright © 2001 John Wiley & Sons, Ltd.
X‐ray waveguide phenomenon in thin layers under grazing incidence conditions.
Authors: Ebel Horst , Svagera Robert , Ebel Maria F.
Published: January 2005

Hayashi et al. published a paper on refracted x‐rays propagating near the surface under grazing incidence conditions. For pure silicon wafers the refraction can be described by Snell's law, whereas for thin n‐C33H86 layers on silicon wafers an additional beam occurs. An interesting feature of this beam is the constant photon energy over a wide range of take‐off angles. The authors suggested that the layer acts as a waveguide and a suitable x‐ray refraction theory for thin films is required. The present investigation deals with the interpretation of the waveguide phenomenon by the concept of an interference between two plane wave fields propagating under angles ±ϕ. The experimental results of Hayashi et al. are in good agreement with our calculated values. Copyright © 2001 John Wiley & Sons, Ltd.
Chronological lifespan of stationary phase yeast cells; a model for investigating the factors that might influence the ageing of postmitotic tissues in higher organisms
Authors: MacLean Morag , Harris Nicholas , Piper Peter W.
Published: January 2005

Budding yeast can be considered to have two distinct lifespans: (a) a replicative (budding, non‐chronological) lifespan, measured as the number of daughters produced by each actively dividing mother cell; and (ii) a chronological lifespan, measured as the ability of stationary cultures to maintain viability over time. In non‐dividing cells, essential components that become damaged cannot be diluted out through cell division but must, of necessity, be turned over and renewed. By elevating stress resistances, many of the activities needed for such renewal should be elevated with commensurate reduction in the steady‐state levels of damaged cell components. Therefore, chronological lifespan in particular might be expected to relate to stress resistance. For yeast to attain a full chronological lifespan requires the expression of the general stress response. It is more important, though, that the cells should be efficiently adapted to respiratory maintenance, since it is cultures grown to stationary phase on respiratory media that usually display the longest chronological lifespans. For this reason, respiration‐adapted cells potentially provide a better model of chronological ageing than cultures pre‐grown on glucose. Copyright © 2001 John Wiley & Sons, Ltd.
The activity of plasma membrane H+‐ATPase is strongly stimulated during Saccharomyces cerevisiae adaptation to growth under high copper stress, accompanying intracellular acidification
Authors: Fernandes Alexandra R. , Sá‐Correia Isabel
Published: January 2005

For the adaptation of cells of Saccharomyces cerevisiae, a period of latency is necessary before exponential growth is resumed in a medium supplemented with a highly inhibitory concentration of copper. In this work, we have examined some physiological responses occurring during this period of adaptation. The results revealed that plasma membrane H+‐ATPase (PM‐ATPase) activity is strongly stimulated (up to 24‐fold) during copper‐induced latency in growth medium with glucose, reaching maximal levels when the cells were about to start inhibited exponential growth. This in vivo activation of the ATPase activity by copper was accompanied by the stimulation of the H+‐pumping activity of the enzyme in vivo and was essentially due to the increase of the apparent Vmax for MgATP. Although the exact molecular basis of the reported plasma membrane ATPase activation was not clarified, no increase in the mRNA levels from the encoding genes PMA1 and PMA2 was apparently detected during copper‐induced latency. The physiological response reported here may allow the cells to cope with copper‐induced lipid peroxidation and consequent decrease in plasma membrane lipid ordering and increase in the non‐specific permeability to protons. The consequences of these copper deleterious effects were revealed by the decrease of the intracellular pH (pHi) of the yeast population, from approximately pHi 6 to pHi 5, during copper‐induced latency in growth medium at pH 4.3. The time‐dependent patterns of plasma membrane ATPase activation and of the decrease of pHi during the period of adaptation to growth with copper correlate, suggesting that the regulation of this membrane enzyme activity may be triggered by intracellular acidification. Consistent with this idea, when exponential growth under copper stress was resumed and the pHi of the yeast population recovered up to physiological values, plasma membrane ATPase activity simultaneously decreased from the highly stimulated level attained during the adaptation period of latency. Copyright © 2001 John Wiley & Sons, Ltd.
A new family of yeast vectors and S288C‐derived strains for the systematic analysis of gene function
Authors: Tomlin Gregory C. , Wixon Joanne L. , Bolotin‐Fukuhara Monique , Oliver Stephen G.
Published: January 2005

The yeast genome has been shown to contain a significant number of gene families with more than three members. In order to study these families it is often necessary to generate strains carrying deletions of all members of the family, which can require a wide range of auxotrophic markers. To facilitate such studies, we have generated yeast strains containing deletions of a selection of nutritional marker genes (ade2, ade4, ade8, met3 and met14). We have also cloned the corresponding cognate genes, allowing their use in PCR‐based gene disruptions. Two new pRS family Saccharomyces cerevisiae–Escherichia coli shuttle vectors containing ADE8 (one low‐copy, pRS4110, and one high‐copy, pRS4210) have been produced for use in conjunction with the new strains. A system for easier synthetic lethal screening using one of these new markers is also presented. The ADE8 and HIS3 genes have been cloned together on a high‐copy vector (pRS4213), providing a plasmid for red–white colour screening in the ade2Δ0 ade8Δ0 strains we have generated. In contrast to some conventional systems, this plasmid allows for screening using gene libraries constructed in URA3 plasmids. Copyright © 2001 John Wiley & Sons, Ltd.
Assessment of prediction accuracy of protein function from protein–protein interaction data
Authors: Hishigaki Haretsugu , Nakai Kenta , Ono Toshihide , Tanigami Akira , Takagi Toshihisa
Published: January 2005

Functional prediction of open reading frames coded in the genome is one of the most important tasks in yeast genomics. Among a number of large‐scale experiments for assigning certain functional classes to proteins, experiments determining protein–protein interaction are especially important because interacting proteins usually have the same function. Thus, it seems possible to predict the function of a protein when the function of its interacting partner is known. However, in vitro experiments often suffer from artifacts and a protein can often have multiple binding partners with different functions. We developed an objective prediction method that can systematically include the information of indirect interaction. Our method can predict the subcellular localization, the cellular role and the biochemical function of yeast proteins with accuracies of 72.7%, 63.6% and 52.7%, respectively. The prediction accuracy rises for proteins with more than three binding partners and thus we present the open prediction results for 16 such proteins. Copyright © 2001 John Wiley & Sons, Ltd.
Hut1 proteins identified in Saccharomyces cerevisiae and Schizosaccharomyces pombe are functional homologues involved in the protein‐folding process at the endoplasmic reticulum
Authors: Nakanishi Hideki , Nakayama Ken‐ichi , Yokota Ayako , Tachikawa Hiroyuki , Takahashi Nobuhiro , Jigami Yoshifumi
Published: January 2005

The Saccharomyces cerevisiae HUT1 gene (scHUT1) and the Schizosaccharomyces pombe hut1+ gene (sphut1+) encode hydrophobic proteins with approximately 30% identity to a human UDP–galactose transporter‐related gene (UGTrel1) product. These proteins show a significant similarity to the nucleotide sugar transporter and are conserved in many eukaryotic species, but their physiological functions are not known. Both scHUT1 and sphut1+ genes are non‐essential for cell growth under normal conditions, and their disruptants show no defects in the modification of O‐ and N‐linked oligosaccharides, but are sensitive to a membrane‐permeable reducing agent, dithiothreitol (DTT). Consistent with this phenotype, scHUT1 has genetic interaction with ERO1, which plays an essential role in the oxidation of secretory proteins at the endoplasmic reticulum (ER). Overexpression of the MPD1 or MPD2 genes, which were isolated as multicopy suppressors of protein disulphide isomerase (PDI) depletion, could not replace the essential function of PDI in Δhut1 S. cerevisiae cells. Our results indicate that scHut1p and spHut1p are functional homologues, and their physiological function is to maintain the optimal environment for the folding of secretory pathway proteins in the ER. Copyright © 2001 John Wiley & Sons, Ltd.
Multicopy suppressors of the sly1 temperature‐sensitive mutation in the ER–Golgi vesicular transport in Saccharomyces cerevisiae
Authors: Kosodo Yoichi , Imai Keita , Hirata Aiko , Noda Yoichi , Takatsuki Akira , Adachi Hiroyuki , Yoda Koji
Published: January 2005

Saccharomyces cerevisiae Sly1 protein is a member of the Sec1/Munc18‐family proteins, which are essential for vesicular trafficking, but their exact biological roles are yet to be determined. A temperature‐sensitive sly1 mutant arrests the vesicular transport from the ER to Golgi compartments at 37°C. We screened for multicopy suppressor genes that restore the colony formation of the sly1ts mutant to discover functionally interacting components. The suppressor genes obtained were classified as: (1) those that encode a multifunctional suppressor, SSD1; (2) heat shock proteins, SSB1 and SSB2; (3) cell surface proteins, WSC1, WSC2 and MID2; (4) ER–Golgi transport proteins, USO1 and BET1; and (5) an as‐yet‐uncharacterized protein, HSD1 (high‐copy suppressor of SLY1 defect 1). By epitope tagging of the gene product, we found that Hsd1 protein is an ER‐resident membrane protein. Its overproduction induced enlargement of ER‐like membrane structures. Copyright © 2001 John Wiley & Sons, Ltd.
Identification and characterization of Saccharomyces cerevisiae strains isolated from West African sorghum beer
Authors: van der Aa Kühle Alis , Jesperen Lene , Glover Richard L.K. , Diawara Bréhima , Jakobsen Mogens
Published: January 2005

The occurrence and characterization of yeasts isolated from sorghum beer produced in Ghana and Burkina Faso, West Africa, were investigated. The yeasts involved in the fermentations were found to consist of Saccharomyces spp. almost exclusively. Of the isolates investigated, 45% were identified as Saccharomyces cerevisiae, whereas more than half of the isolates (53%) had physiological properties atypical of S. cerevisiae or any other member of the complex sensu strictu, as they were able to assimilate only glucose, maltose and ethanol as carbon sources. Both ITS–PCR RFLP and PFGE strongly indicated that these isolates were related to S. cerevisiae, regardless of their phenotypic characteristics. Sequencing of the D1/D2 domain of the 26S rDNA confirmed the close relatedness to S. cerevisiae with 0.5% nucleotide differences. The MAL1 and MAL3 loci were found for all isolates as the only recognized MAL loci. Besides, for 40% of the isolates the MAL61 probe hybridized to a position of about 950 kbp, which has not formerly been described as a MAL locus. The results showed that the spontaneous fermentation of West African sorghum beer is dominated by a variety of strains of S.cerevisiae not previously described, among which starter cultures should be selected. Copyright © 2001 John Wiley & Sons, Ltd.
Expression and activity of the Hxt7 high‐affinity hexose transporter of Saccharomyces cerevisiae
Authors: Ye Ling , Berden Jan A. , van Dam Karel , Kruckeberg Arthur L.
Published: January 2005

High‐affinity hexose transport is required for efficient utilization of low hexose concentrations by the baker's yeast Saccharomyces cerevisiae. These low concentrations occur during the late exponential phase of batch growth on hexoses, during hexose‐limited chemostat or fed‐batch culture, or during growth on sugars such as sucrose and raffinose that are hydrolysed to hexoses outside the cell. The expression of the Hxt7 high‐affinity glucose transporter of S. cerevisiae was examined during batch growth on glucose medium in a wild‐type strain and a strain expressing only HXT7 (i.e. with null mutations in HXT1–HXT6). In the wild‐type strain, HXT7 transcription was repressed at high glucose and was detected when the glucose in the culture approached depletion. In the HXT7‐only strain, transcription of HXT7 was constitutive throughout the glucose growth phase and was increased further at low glucose concentrations. After glucose depletion, the levels of HXT7 mRNA declined rapidly in both strains. In contrast, the Hxt7 protein was relatively stable after glucose depletion. By monitoring the subcellular localization of an Hxt7::GFP fusion protein it was observed that Hxt7 was localized in the plasma membrane, even when expressed at high glucose concentrations in the HXT7‐only strain. After glucose depletion Hxt7 was gradually endocytosed and targeted to the vacuole for degradation. The Hxt7::GFP fusion protein was a fully functional hexose transporter with a catalytic centre activity of approximately 200/sec. It is concluded that repression of HXT7 and degradation of Hxt7 at high glucose concentrations is dependent on a high glucose transport capacity. Copyright © 2001 John Wiley & Sons, Ltd.
Amino acid residues important for substrate specificity of the amino acid permeases Can1p and Gnp1p in Saccharomyces cerevisiae
Authors: Regenberg Birgitte , Kielland‐Brandt Morten C.
Published: January 2005

Deletion of the general amino acid permease gene GAP1 abolishes uptake of L‐citrulline in Saccharomyces cerevisiae, resulting in the inability to grow on L‐citrulline as sole nitrogen source. Selection for suppressor mutants that restored growth on L‐citrulline led to isolation of 21 mutations in the arginine permease gene CAN1. One similar mutation was found in the glutamine‐asparagine permease gene GNP1. L‐[14C]citrulline uptake measurements confirmed that suppressor mutations in CAN1 conferred uptake of this amino acid, while none of the mutant permeases had lost the ability to transport L‐[14C]arginine. Substrate specificity seemed to remain narrow in most cases, and broad substrate specificity was only observed in the cases where mutations affect two proline residues (P148 and P313) that are both conserved in the amino acid–polyamine–choline (APC) transporter superfamily. We found mutations affecting six predicted domains (helices III and X, and loops 1, 2, 6 and 7) of the permeases. Helix III and loop 7 are candidates for domains in direct contact with thetransported amino acid. Helix III was affected in both CAN1 (Y173H, Y173D) and GNP1 (W239C) mutants and has previously been found to be important for substrate preference in other members of the family. Furthermore, the mutations affecting loop 7 (residue T354, S355, Y356) are close to a glutamate side chain (E367) potentially interacting with the positively charged substrate, a notion supported by conservation of the side chain in permeases for cationic substrates. Copyright © 2001 John Wiley & Sons, Ltd.
The flow field and bare-spot formation in spin-up from rest of a two-layer fluid about a vertical axis
Authors: UNGARISH M. , MANG J.
Published: January 2005

The spin-up from rest of a two-layer fluid with a free surface in a cylindrical container
rotating about a vertical axis is investigated for small Ekman numbers. Numerical
results from the axisymmetric Navier–Stokes equations, supported by comparisons
with improved boundary-layer approximations, show that the Ekman-type layer on the
bottom pushes the dense fluid of the lower layer to the periphery, and consequently
the interface between the layers curves upward near the sidewall and descends near the
centre. When the lower layer of fluid is sufficiently thin a bare spot appears at the
bottom, i.e. a region where the light fluid is in direct contact with the horizontal
boundary. The lower-layer fluid is spun-up quickly by the bottom Ekman layer, but
the angular motion in the upper layer is provided by the much weaker detached
Ekman layer on the interface between the two fluids, and hence the global spin-up
process is prolonged compared with the homogeneous fluid case. The influence of the
various dimensionless parameters and the connection with the continuous stratified
case are discussed.
Coherent structures in oscillatory boundary layers
Authors: COSTAMAGNA PAOLA , VITTORI GIOVANNA , BLONDEAUX PAOLO
Published: January 2005

The dynamics of the vortex structures appearing in an oscillatory boundary layer
(Stokes boundary layer), when the flow departs from the laminar regime, is investigated by means of flow visualizations and a quantitative analysis of the velocity and
vorticity fields. The data are obtained by means of direct numerical simulations of the
Navier–Stokes and continuity equations. The wall is flat but characterized by small
imperfections. The analysis is aimed at identifying points in common and differences
between wall turbulence in unsteady flows and the well-investigated turbulence structure in the steady case. As in Jimenez & Moin (1991), the goal is to isolate the basic
flow unit and to study its morphology and dynamics. Therefore, the computational
domain is kept as small as possible.

The elementary process which maintains turbulence in oscillatory boundary layers
is found to be similar to that of steady flows. Indeed, when turbulence is generated,
a sequence of events similar to those observed in steady boundary layers is observed.
However, these events do not occur randomly in time but with a repetition time scale
which is about half the period of fluid oscillations. At the end of the accelerating
phases of the cycle, low-speed streaks appear close to the wall. During the early
part of the decelerating phases the strength of the low-speed streaks grows. Then the
streaks twist, oscillate and eventually break, originating small-scale vortices. Far from
the wall, the analysis of the vorticity field has revealed the existence of a sequence of
streamwise vortices of alternating circulation pumping low-speed fluid far from the
wall as suggested by Sendstad & Moin (1992) for steady flows. The vortex structures
observed far from the wall disappear when too small a computational domain is
used, even though turbulence is self-sustaining. The present results suggest that the
streak instability mechanism is the dominant mechanism generating and maintaining
turbulence; no evidence of the well-known parent vortex structures spawning offspring
vortices is found. Although wall imperfections are necessary to trigger transition to
turbulence, the characteristics of the coherent vortex structures, for example the
spacing of the low-speed streaks, are found to be independent of wall imperfections.
Frictional two-layer exchange flow
Authors: ZAREMBA LILLIAN J. , LAWRENCE G. A. , PIETERS R.
Published: January 2005

A numerical model is developed to study the effects of friction on the steady exchange
flow that evolves when a barrier is removed from a constriction separating two
reservoirs of slightly different densities. The model has excellent agreement with an
analytical solution and laboratory measurements of exchange flows through channels
of constant width and depth. The model reveals three viscous flow regimes for a
convergent–divergent contraction of constant depth, and three additional viscous
flow regimes when an offset sill is introduced. Each regime is characterized by a
different set of internal hydraulic control locations. Examination of the predicted
interface profiles reveals that it is not possible to distinguish between different flow
regimes on the basis of these profiles alone.
The World Health Organization adult ADHD self-report scale (ASRS): a short screening scale for use in the general population
Authors: KESSLER RONALD C. , ADLER LENARD , AMES MINNIE , DEMLER OLGA , FARAONE STEVE , HIRIPI EVA , HOWES MARY J. , JIN ROBERT , SECNIK KRISTINA , SPENCER THOMAS , USTUN T. BEDIRHAN , WALTERS ELLEN E.
Published: January 2005

Background. A self-report screening scale of adult attention-deficit/hyperactivity disorder (ADHD), the World Health Organization (WHO) Adult ADHD Self-Report Scale (ASRS) was developed in conjunction with revision of the WHO Composite International Diagnostic Interview (CIDI). The current report presents data on concordance of the ASRS and of a short-form ASRS screener with blind clinical diagnoses in a community sample.

Method. The ASRS includes 18 questions about frequency of recent DSM-IV Criterion A symptoms of adult ADHD. The ASRS screener consists of six out of these 18 questions that were selected based on stepwise logistic regression to optimize concordance with the clinical classification. ASRS responses were compared to blind clinical ratings of DSM-IV adult ADHD in a sample of 154 respondents who previously participated in the US National Comorbidity Survey Replication (NCS-R), oversampling those who reported childhood ADHD and adult persistence.

Results. Each ASRS symptom measure was significantly related to the comparable clinical symptom rating, but varied substantially in concordance (Cohen's κ in the range 0·16–0·81). Optimal scoring to predict clinical syndrome classifications was to sum unweighted dichotomous responses across all 18 ASRS questions. However, because of the wide variation in symptom-level concordance, the unweighted six-question ASRS screener outperformed the unweighted 18-question ASRS in sensitivity (68·7% v. 56·3%), specificity (99·5% v. 98·3%), total classification accuracy (97·9% v. 96·2%), and κ (0·76 v. 0·58).

Conclusions. Clinical calibration in larger samples might show that a weighted version of the 18-question ASRS outperforms the six-question ASRS screener. Until that time, however, the unweighted screener should be preferred to the full ASRS, both in community surveys and in clinical outreach and case-finding initiatives.
Karl Barth: from fighter against the ‘Roman heresy’ to leading thinker for the ecumenical movement
Authors: Welker Michael
Published: January 2005

Karl Barth saw himself as a ‘Randfigur’, a boundary figure, in ecumenical theology, while important members of the ecumenical movement regarded him as a ‘Wegbereiter de Okumene des 20. Jahrhunderts’, a pioneer of the ecumene in the twentieth century. Which characterisation is correct?

The article sheds light on Karl Barth as an ‘ecumenical theologian’ in eight different phases of his life: his wrestling with Roman Catholicism in Göttingen and Munster, particularly with the help of the Munich Jesuit Erich Przywara; his encounter and interaction with ecumenical leaders such as Visser't Hooft and Pierre Maury at the beginning of the Nazi dictatorship and his disappointment about the failing resistance of the ecumenical institutions against Hitler; his search for a clear ecumenical course during the Second World War and the Cold War thereafter; his contribution to the meeting of the World Council of Churches in Amsterdam in 1948 and in the preparation of this meeting; his complex and complicated dealing with the ‘fundamental ecumenical question’ of church and Israel; the reception of his theology in Roman Catholicism in the 1950s and 1960s through von Balthasar, Kung and other young theologians and Barth's interaction with them; Barth's engagement with Vatican II and his trip to Rome; finally, his personal ‘ecumenical existence’ in the last years of his life.

The contribution explores continuities and discontinuities in his stance towards ‘ecumenical theology’ – ecumenical theology in its various meanings. It depicts Barth in his journey from a fighter against the ‘Roman heresy’ to a critical pioneer of ecumenical theology in general and the institutionalised ecumene in particular.
The character of Christian realism
Authors: Sonderegger Katherine
Published: January 2005

This article aims to set out a modest, ’pre-theoretical’ or common sense account of metaphysical realism in Christian theology. The essay defends and explores the claim that Christian theology does not rest on definitions or world views when it speaks about ’realism’. Christian realism is not a method, especially not a method spinning free of its proper content, nor a theory about schools of realism. Christian theology is ordered to God's own ways and works: it is a realism in which the God of Israel is both agent and sovereign, both object and subject in the world we inhabit. Christian realism is reflection upon the reality created and blessed by the Creator.
‘Smoke cities’: northern industrial towns in late Georgian England
Authors: BARKER HANNAH
Published: January 2005

The industrial towns of northern England have been largely overlooked during the late eighteenth and early nineteenth centuries. This article examines newspaper advertising, directories, public building and improvement in Manchester, Leeds and Sheffield and identifies a middling, consumerist society, where urban culture was firmly rooted in the localities in which it developed. The nature of this culture challenges simplistic understandings of metropolitan dominance and questions the utility of national models of consumerism and ‘politeness’ that ignore the importance of regional variation and provincialism.
Gender, occupation, illiteracy and the urban economic environment: Leicester, 1760–1890
Authors: BROWN ELAINE
Published: January 2005

This article examines the relationship between gender, occupation, illiteracy and economic development in Leicester from 1760 to 1890. Although Leicester's economy was at a proto-industrial stage of development, heavily dependent on domestic and workshop-based industries, interesting comparisons may be made with industrializing factory towns. There was similar reliance on child and female labour, and the industries appeared to develop in a climate of illiteracy. This new local case study is especially important for previous research concerning gender, occupation, illiteracy and economic development has tended to focus on urban market towns or newly developing factory towns.
Research in urban history: a review of recent theses
Authors: MILLER CAROLINE L.
Published: January 2005

Defining what constitutes urban history has always proved challenging; however, employing this review's usual wide definition has resulted in the identification of theses from a range of disciplines. This review covers theses produced in 2003 and drawn from the Index of Theses located at http://www.theses.com/ and Dissertations International located at http://wwwlib.umi.com/ dissertations. This year for the first time it has become necessary to limit coverage in the face of what can only be described as a boom in theses addressing aspects of urban life. This blossoming of interest should not be unexpected given the increasing urbanization of the world's population, leading to a curiosity about the origins and nature of urban life. Consequently this year's review again includes shorter summaries in an attempt to allow coverage of 53 theses.
Simulated carbon sink response of shortgrass steppe, tallgrass prairie and forest ecosystems to rising [CO2], temperature and nitrogen input
Authors: Pepper D. A. , Del Grosso S. J. , McMurtrie R. E. , Parton W. J.
Published: January 2005

The response of plant ecosystems to environmental change will determine whether the terrestrial biosphere will remain a substantial carbon sink or become a source during the next century. We use two ecosystem models, the Generic Decomposition And Yield model (G'DAY) and the daily time step version of the Century model (DAYCENT), to simulate net ecosystem productivity (NEP) for three contrasting ecosystems (shortgrass steppe in Colorado, tallgrass prairie in Kansas, and Norway spruce in Sweden) with varying degrees of water, temperature, and nutrient limitation, to determine responses to gradual increases in atmospheric CO2 concentration ([CO2]), temperature, and nitrogen input over 100 years. Using G'DAY, under rising [CO2], there is evidence of C sink “saturation,” defined here as positive NEP reaching an upper limit and then declining toward zero, at all three sites (due largely to increased N immobilization in soil organic matter) but a positive C sink is sustained throughout the 100 years. DAYCENT also predicts a sustained C sink at all three sites under rising [CO2], with evidence of C sink saturation for the Colorado grassland and the C sink levels off after 80 years for the Kansas grassland. Warming reduces soil C and the C sink in both grassland ecosystems but increases the C sink in the forest. Warming increases decomposition and soil N mineralization, which stimulates net primary productivity (NPP) at all sites except when inducing water limitation. At the forest site some of the enhanced N release is allocated to a woody biomass pool with a low N:C ratio so that warming enhances NEP without increased N input at the forest site, but not at the grassland sites. Responses to combinations of treatments are generally additive for DAYCENT but more interactive for G'DAY, especially under combined rising [CO2] and warming at the strongly water‐ and N‐limited shortgrass steppe. Increasing N input alleviates C sink saturation and enhances NEP, NPP, and soil C at all sites. At the water‐limited grassland sites the effect of rising [CO2] on growth is greatest during the drier seasons. Key sensitivities in the simulations of NEP are identified and include NPP sensitivity to gradual increase in [CO2], N immobilization as a long‐term feedback, and the presence or not of plant biomass pools with low N:C ratio.
Carbon‐based ocean productivity and phytoplankton physiology from space
Authors: Behrenfeld Michael J. , Boss Emmanuel , Siegel David A. , Shea Donald M.
Published: January 2005

Ocean biogeochemical and ecosystem processes are linked by net primary production (NPP) in the ocean's surface layer, where inorganic carbon is fixed by photosynthetic processes. Determinations of NPP are necessarily a function of phytoplankton biomass and its physiological status, but the estimation of these two terms from space has remained an elusive target. Here we present new satellite ocean color observations of phytoplankton carbon (C) and chlorophyll (Chl) biomass and show that derived Chl:C ratios closely follow anticipated physiological dependencies on light, nutrients, and temperature. With this new information, global estimates of phytoplankton growth rates (μ) and carbon‐based NPP are made for the first time. Compared to an earlier chlorophyll‐based approach, our carbon‐based values are considerably higher in tropical oceans, show greater seasonality at middle and high latitudes, and illustrate important differences in the formation and demise of regional algal blooms. This fusion of emerging concepts from the phycological and remote sensing disciplines has the potential to fundamentally change how we model and observe carbon cycling in the global oceans.
Morphological and geochemical variations along the eastern Galápagos Spreading Center
Authors: Christie David M. , Werner Reinhard , Hauff Folkmar , Hoernle Kaj , Hanan Barry B.
Published: January 2005

As the eastern Galápagos Spreading Center (GSC) shallows westward toward the Galápagos Archipelago, axial morphology evolves from a low‐relief, valley‐and‐ridge terrain to an increasingly prominent axial ridge, closely mirroring the western GSC. Between the Inca Transform (∼85.5°W) and its western termination near 91°W, the eastern GSC comprises seven morphological segments, separated by five morphological discontinuities and the eastward propagating 87°W overlapping spreading center. Combined morphologic and geochemical data divide the eastern GSC into two domains independent of the fine‐scale morphologic segmentation. The western domain is defined by its axial ridge morphology and highly variable lava population. Elemental data define steep along‐axis gradients, reflecting a complex source that includes one or more hot spot–related components in addition to a highly depleted component. The eastern domain is defined by transitional, valley‐and‐ridge morphologies and a surprisingly invariant lava population. This population is dominated by shallow crystal fractionation processes and displays significantly less variability attributable to multiple source components. The Galápagos hot spot has long been known to have a symmetrical, long‐wavelength influence on crustal accretion along the GSC. Existing isotopic and new elemental data define twin “geochemical peaks” that we interpret as loci for transfer of distinct source components from the Galápagos plume to the GSC. Although Na8 and Fe8 values lie within the negatively correlated global array, Na8 increases with decreasing axial depth, contrary to global trends and consistent with emerging deep, hydrous melting models that predict decreasing overall extent of melting despite increasing melt production. Support for hydrous melting comes from decreasing heavy REE, increasing La/Sm and La/Yb, and the systematics of decreasing FeO and increasing CaO and Al2O3 with decreasing distance to the hot spot. Overall, an enriched, deep melt component appears to coexist in the shallow mantle with a ubiquitous, depleted primitive melt component, consistent with new models for channelized melt flow connecting a deep hydrous melt regime with the dry shallow mantle. Nevertheless, an absence of low‐Fe lavas suggests that hydrous melting is strictly limited beneath the eastern GSC, becoming dominant only near the western geochemical peak where input from a hydrous “Northern” or “Wolf‐Darwin” plume component is inferred.
Some thoughts on the use of InSAR data to constrain models of surface deformation: Noise structure and data downsampling
Authors: Lohman Rowena B. , Simons Mark
Published: January 2005

Repeat‐pass Interferometric Synthetic Aperture Radar (InSAR) provides spatially dense maps of surface deformation with potentially tens of millions of data points. Here we estimate the actual covariance structure of noise in InSAR data. We compare the results for several independent interferograms with a large ensemble of GPS observations of tropospheric delay and discuss how the common approaches used during processing of InSAR data affects the inferred covariance structure. Motivated by computational concerns associated with numerical modeling of deformation sources, we then combine the data‐covariance information with the inherent resolution of an assumed source model to develop an efficient algorithm for spatially variable data resampling (or averaging). We illustrate these technical developments with two earthquake scenarios at different ends of the earthquake magnitude spectrum. For the larger events, our goal is to invert for the coseismic fault slip distribution. For smaller events, we infer the hypocenter location and moment. We compare the results of inversions using several different resampling algorithms, and we assess the importance of using the full noise covariance matrix.
A study of the freshwater discharge from the Amazon River into the tropical Atlantic using multi‐sensor data
Authors: Jo Young‐Heon , Yan Xiao‐Hai , Dzwonkowski Brian , Liu W. Timothy
Published: January 2005

We study freshwater discharge from the Amazon River into the tropical Atlantic using monthly mean multi‐sensor data from September 1997 to July 2003. In order to demonstrate freshwater discharge, we used chlorophyll concentration (Chl_a) and diffuse attenuation coefficient (DAC) measured by the Sea‐viewing Wide Field‐of‐view Sensor (SeaWiFS), and salt steric height anomaly (Δη′S) derived from Integrated Multi‐Sensor Data Analysis (IMSDA). IMSDA was obtained from estimating the long term‐time series of Δη′S by removing the thermal steric height anomaly (η′T) from altimetry data. Comparisons of long‐term time series of Δη′S, Chl_a, and DAC were made with mooring data at 8°N, 38°W, which were highly correlated. There are three‐ to five‐month lags between the Amazon River discharge and 4°N latitude estimated from latitude‐time diagram derived from SeaWiFS measurements.
Atmospheric volatile organic compound measurements during the Pittsburgh Air Quality Study: Results, interpretation, and quantification of primary and secondary contributions
Authors: Millet Dylan B. , Donahue Neil M. , Pandis Spyros N. , Polidori Andrea , Stanier Charles O. , Turpin Barbara J. , Goldstein Allen H.
Published: January 2005

Primary and secondary contributions to ambient levels of volatile organic compounds (VOCs) and aerosol organic carbon (OC) are determined using measurements at the Pittsburgh Air Quality Study (PAQS) during January–February and July–August 2002. Primary emission ratios for gas and aerosol species are defined by correlation with species of known origin, and contributions from primary and secondary/biogenic sources and from the regional background are then determined. Primary anthropogenic contributions to ambient levels of acetone, methylethylketone, and acetaldehyde were found to be 12–23% in winter and 2–10% in summer. Secondary production plus biogenic emissions accounted for 12–27% of the total mixing ratios for these compounds in winter and 26–34% in summer, with background concentrations accounting for the remainder. Using the same method, we determined that on average 16% of aerosol OC was secondary in origin during winter versus 37% during summer. Factor analysis of the VOC and aerosol data is used to define the dominant source types in the region for both seasons. Local automotive emissions were the strongest contributor to changes in atmospheric VOC concentrations; however, they did not significantly impact the aerosol species included in the factor analysis. We conclude that longer‐range transport and industrial emissions were more important sources of aerosol during the study period. The VOC data are also used to characterize the photochemical state of the atmosphere in the region. The total measured OH loss rate was dominated by nonmethane hydrocarbons and CO (76% of the total) in winter and by isoprene, its oxidation products, and oxygenated VOCs (79% of the total) in summer, when production of secondary organic aerosol was highest.
Time‐ and size‐resolved chemical composition of submicron particles in Pittsburgh: Implications for aerosol sources and processes
Authors: Zhang Qi , Canagaratna Manjula R. , Jayne John T. , Worsnop Douglas R. , Jimenez Jose‐Luis
Published: January 2005

An Aerodyne aerosol mass spectrometer (AMS) was deployed at the Pittsburgh Environmental Protection Agency Supersite from 7 to 22 September 2002 as part of the Pittsburgh Air Quality Study (PAQS). The main objectives of this deployment were to characterize the concentrations, size distributions, and temporal variations of nonrefractory (NR) chemical species in submicron particles (approximately PM1) and to further develop and evaluate the AMS. Reasonably good agreement was observed on particle concentrations, composition, and size distributions between the AMS data and measurements from collocated instruments (given the difference between the PM1 and PM2.5 size cuts), including TEOM, semicontinuous sulfate, 2‐hour‐ and 24‐hour‐averaged organic carbon, SMPS, 4‐hour‐averaged ammonium, and micro‐orifice uniform deposit impactor. Total NR‐PM1 mass concentration in Pittsburgh accumulates over periods of several days punctuated with rapid cleaning due to rain or air mass changes. Sulfate and organics are the major NR‐PM1 components while the concentrations of nitrate and chloride are generally low. Significant amounts of ammonium, which most of the time are consistent with sulfate present as ammonium sulfate, are also present in particles. However, there are periods when the aerosols are relatively acidic and more than 50% of sulfate is estimated to be in the form of ammonium bisulfate. No major enhancement of the organic concentration is observed during these acidic periods, which suggests that acid‐catalyzed SOA formation was not an important process during this study. Size distributions of particulate sulfate, ammonium, organics, and nitrate vary on timescales of hours to days, showing unimodal, bimodal and even trimodal characteristics. The accumulation mode (peaking around 350–600 nm in vacuum aerodynamic diameter for the mass distributions) and the ultrafine mode (<100 nm) are observed most frequently. The accumulation mode is dominated by sulfate that appears to be internally mixed with oxidized organics, while combustion‐emitted organics are often the main component of the ultrafine particles (except during nucleation events). The ultrafine‐mode organic aerosols are mainly associated with combustion sources (likely traffic).
Characterization of east Asian dust outbreaks in the spring of 2001 using ground‐based and satellite data
Authors: Darmenova Kremena , Sokolik Irina N. , Darmenov Anton
Published: January 2005

This study presents a detailed examination of east Asian dust events during March–April of 2001, by combining satellite multisensor observation (Total Ozone Mapping Spectrometer (TOMS), Moderate‐Resolution Imaging Spectroradiometer (MODIS), and Sea‐Viewing Wide Field‐of‐View Sensor (SeaWiFS)) meteorological data from weather stations in China and Mongolia and the Pennsylania State University/National Center for Atmospheric Research Mesoscale Modeling System (MM5) driven by the National Centers for Environmental Prediction Reanalysis data. The main goal is to determine the extent to which the routine surface meteorological observations (including visibility) and satellite data can be used to characterize the spatiotemporal distribution of dust plumes at a range of scales. We also examine the potential of meteorological time series for constraining the dust emission schemes used in aerosol transport models. Thirty‐five dust events were identified in the source region during March and April of 2001 and characterized on a case‐by‐case basis. The midrange transport routes were reconstructed on the basis of visibility observations and observed and MM5‐predicted winds with further validation against satellite data. We demonstrate that the combination of visibility data, TOMS aerosol index, MODIS aerosol optical depth over the land, and a qualitative analysis of MODIS and SeaWiFS imagery enables us to constrain the regions of origin of dust outbreaks and midrange transport, though various limitations of individual data sets were revealed in detecting dust over the land. Only two long‐range transport episodes were found. The transport routes and coverage of these dust episodes were reconstructed by using MODIS aerosol optical depth and TOMS aerosol index. Our analysis reveals that over the oceans the presence of persistent clouds poses a main problem in identifying the regions affected by dust transport, so only partial reconstruction of dust transport routes reaching the west coast of the United States was possible.
Model simulations of dust sources and transport in the global atmosphere: Effects of soil erodibility and wind speed variability
Authors: Grini Alf , Myhre Gunnar , Zender Charles S. , Isaksen Ivar S. A.
Published: January 2005

Global atmospheric dust is simulated using the Dust Entrainment and Deposition (DEAD) model in combination with the global‐scale Oslo chemical transport model CTM2 using meteorological data for 1996. Dust sources are calculated using both mean wind speeds with model resolution T63 and subgrid wind speeds. Different data sets are used to describe soil erodibility. We explain how the different assumptions about dust production affect atmospheric dust burden and deposition. Some aspects of the annual dust cycle, such as the east Asian dust emissions, are largely dependent on the data used to determine soil erodibility. Other aspects, such as the timing of the maximum in the African plume at Northern Hemisphere summer, are well modeled with all data sets applied here. We show that the daily variation in optical depth at Cape Verde on the west coast of Africa is well simulated when we assume that erodibility is correlated with surface reflectivity from Moderate‐Resolution Imaging Spetroradiometer (MODIS) satellite data. Using a subgrid probability density function of wind speed to drive the dust sources facilitates dust emissions in areas with low wind speeds. Dust concentrations in remote areas are sensitive to the parameterization of wet deposition. Our results point out the need for a detailed soil erodibility data set for global dust modeling, and they suggest that surface reflectivity is potentially valuable for producing or evaluating such data sets.
A simple method to relate microwave radiances to upper tropospheric humidity
Authors: Buehler S. A. , John V. O.
Published: January 2005

A brightness temperature (BT) transformation method can be applied to microwave data to retrieve Jacobian weighted upper tropospheric relative humidity (UTH) in a broad layer centered roughly between 6 and 8 km altitude. The UTH bias is below 4% RH, and the relative UTH bias below 20%. The UTH standard deviation is between 2 and 6.5% RH in absolute numbers, or between 10 and 27% in relative numbers. The standard deviation is dominated by the regression noise, resulting from vertical structure not accounted for by the simple transformation relation. The UTH standard deviation due to radiometric noise alone has a relative standard deviation of approximately 7% for a radiometric noise level of 1 K. The retrieval performance was shown to be of almost constant quality for all viewing angles and latitudes, except for problems at high latitudes due to surface effects. A validation of AMSU UTH against radiosonde UTH shows reasonable agreement if known systematic differences between AMSU and radiosonde are taken into account. When the method is applied to supersaturation studies, regression noise and radiometric noise could lead to an apparent supersaturation even if there were no supersaturation. For a radiometer noise level of 1 K the drop‐off slope of the apparent supersaturation is 0.17% RH−1, for a noise level of 2 K the slope is 0.12% RH−1. The main conclusion from this study is that the BT transformation method is very well suited for microwave data. Its particular strength is in climatological applications where the simplicity and the a priori independence are key advantages.