bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the effectiveness of hexose transporters for transporting xylose during glucose and xylose co‐fermentation by a recombinant Saccharomyces yeast
Authors: Sedlak Miroslav , Ho Nancy W. Y.
Published: June 2004

We have developed recombinant Saccharomyces yeasts that can effectively co‐ferment glucose and xylose to ethanol. However, these yeasts still ferment glucose more efficiently than xylose. The transport of xylose could be one of the steps limiting the fermentation of xylose. In this study, we characterized the changes in the expression pattern of the hexose transporter and related genes during co‐fermentation of glucose and xylose using one of our recombinant yeasts, Saccharomyces cerevisiae 424A(LNH‐ST). The transcription of the hexose transporter and related genes was strongly influenced by the presence of glucose; HXT1, HXT2 and HXT3 were greatly activated by glucose and HXT5, HXT7 and AGT1 were significantly repressed by glucose. We also examined the effectiveness of individual transporters encoded by HXT1, HXT2, HXT4, HXT5, HXT7 and GAL2 genes for transporting xylose during co‐fermentation of glucose and xylose in a Saccharomyces hxt° mutant (RE700A). We compared these hxt° derivatives to RE700A wild‐type strain (S. cerevisiae MC996A) where all of them contained the same xylose metabolizing genes present in our xylose‐fermenting yeasts such as 424A(LNH‐ST). Our results showed that recombinant RE700A containing the cloned HXT7 or HXT5 were substantially more effective for fermenting xylose to ethanol. In addition, we found that the efficiency of transporters for intracellular accumulation of xylose was as follows: HXT7 > HXT5 > GAL2 > WT > HXT1 > HXT4 > > > RE700A. Furthermore, we provided evidence that the Saccharomyces galactose transporter system could be a highly effective xylose transporter. The information reported here should be of great importance for improving the Saccharomyces yeast transport of xylose. Copyright © 2004 John Wiley & Sons, Ltd.
Analysis of a Ty1‐less variant of Saccharomyces paradoxus: the gain and loss of Ty1 elements
Authors: Moore Sharon P. , Liti Gianni , Stefanisko Karen M. , Nyswaner Katherine M. , Chang Caroline , Louis Edward J. , Garfinkel David J.
Published: June 2004

Because Ty elements transpose through an RNA intermediate, element accumulation through retrotransposition must be regulated or offset by element loss to avoid uncontrolled genome expansion. Here we examine the fate of Ty sequences in Saccharomyces strain 337, a strain that is reported to lack Ty1 and Ty2 elements, but contains remnant solo long terminal repeats (LTRs). Although strain 337 was initially classified as Saccharomyces cerevisiae, our work indicates that this strain is more closely related to S. paradoxus. Several degenerate Ty1 and Ty2 LTRs were mapped to the same insertion sites as full‐length Ty1 and Ty2 elements in S. cerevisiae, suggesting that this strain lost Ty elements by LTR–LTR recombination. Southern analysis indicates that strain 337 also lacks Ty4 and Ty5 elements. We estimated the rates of element gain and loss in this strain by introducing a single transposition‐competent Ty1 element. The results indicate that Ty1 retrotransposition occurs at a much higher rate than elimination, suggesting that copy‐number‐dependent co‐factors or environmental conditions contribute to the loss of Ty elements in this genome. Copyright © 2004 John Wiley & Sons, Ltd.
Comparative Effectiveness of Several Agents for Preventing Postoperative Adhesions
Authors: Kutlay Jehat , Ozer Yusuf , Isık Burak , Kargici Hulagu
Published: June 2004

Postoperative adhesions (PAs) are usually clinically asymptomatic. Symptomatic cases, however, may present with chronic abdominal and pelvic pain, infertility, and intestinal obstruction; and they may require intensive, costly therapeutic modalities. Various agents have been used to prevent PAs, but the results indicate general suboptimal effectiveness. Our objective was to evaluate the comparative effectiveness of two pharmacologic agents for preventing PA: nadroparine calcium (low‐molecular‐weight heparin, or LMWH) and aprotinin, as well as a barrier agent, sodium hyaluronate/carboxymethycellulose (SCMC). Our subjects were 40 male Wistar‐Albino rats divided into four groups, each consisting of 10 rats, which underwent standard cecal abrasion preceding midline laparotomy. In the control group (group 1) 1 ml of 0.9% NaCl was administered intraperitoneally before abdominal closure. In the three preventive groups, 100 U AXa (anti factor X activity) LMWH, 1800 IU aprotinin, and SCMC were administered intraperitoneally to groups 2, 3, and 4, respectively. Relaparotomy was performed on the 14th postoperative day. Visceral and abdominal wall adhesions were scored in a blinded fashion. The adhesion scores (mean ± SD) for groups 1, 2, 3, and 4 were 2.00 ± 0.67, 0.6.00 ± 0.84, 1.10 ± 0.74, and 0.20 ± 0.42, respectively. The differences in the adhesion scores among all three preventive groups (groups 2, 3, 4) were statistically significant when compared with the control group (p < 0.001, p = 0.017, p < 0.001, respectively). Intraperitoneal SCMC and administration of LMWH were more effective than giving aprotinin.
Molecular Detection of APC, K‐ras, and p53 Mutations in the Serum of Colorectal Cancer Patients as Circulating Biomarkers
Authors: Wang Jaw‐Yuan , Hsieh Jan‐Sing , Chang Mei‐Yin , Huang Tsung‐Jen , Chen Fang‐Ming , Cheng Tian‐Lu , Alexandersen Ketil , Huang Yu‐Sheng , Tzou Wen‐Shyong , Lin Shiu‐Ru
Published: June 2004

Early detection of tumor DNA in serum/plasma prior to the development of recurrence or metastases could help improve the outcome of patients with colorectal cancer (CRC) after tumor resection. Recent advances in the detection of tumor DNA in the serum/plasma has opened up numerous new areas for investigation and new possibilities for molecular diagnosis. APC and K‐ras mutations are considered to be early‐stage developments of CRCs, whereas p53 mutations are thought to be relatively late events in the tumorigenesis of CRCs. The aim of this study was to search for the presence of genetic mutations in the DNA extracted from the serum of CRC patients and healthy subjects. We simultaneously evaluate the significance of APC, K‐ras, and p53 gene mutations in cancer tissues and their paired serum samples of 104 CRC patients by polymerase chain reaction‐single strand conformation polymorphism analysis (PCR‐SSCP) followed by direct sequencing. Additionally, analysis was carried out to detect the serum carcinoembryonic antigen (CEA) levels in CRC patients. Overall, we found at least one of the gene mutations in tumor tissues from 75% (78/104) of the CRC patients. Comparison of the three molecular markers showed that the detection rates in the serum were 30.4%, 34.0%, and 34.2% for APC, K‐ras, and p53 genes, respectively. Of these patients, 46.2% (36/78) were identified as having positive serum results, whereas all healthy controls remained negative. The overall positive tumor DNA detection rates in the serum were 0% (0/7) for Dukes’ A classification, 22.4% (11/49) for Dukes’ B, 48.7% (19/39) for Dukes’ C, and 66.7% (6/9) for Dukes’ D. The detection rate increased as the tumor stage progressed (p = 0.012). Concurrently, a significant difference was observed between lymph node metastases and positive serum tumor DNA detection (p < 0.001). A significantly higher postoperative metastasis/recurrence rate in patients harboring gene mutations with serum tumor DNA than those without serum tumor DNA was also demonstrated (p < 0.001). However, no significant correlation between the postoperative metastasis/recurrence and serum CEA levels was observed (p = 0.247). These data suggest that the identification of circulating tumor DNA using the molecular detection of APC, K‐ras, and p53 gene mutations is a potential tool for early detection of postoperative recurrence/metastases. Moreover, these genes may be potential molecular markers of poor clinical outcome in CRC patients.
Source Control for Surgical Infections
Authors: Schein Moshe , Marshall John
Published: June 2004

The concept of source control encompasses all of the physical interventions, surgical and otherwise, that are used to treat infection. Although source control is one of the most important aspects of the treatment of serious infection, it has received relatively little attention. It is the topic of this overview, which draws heavily on a book we edited recently: Source Control: A Guide to the Management of Surgical Infection (Springer‐Verlag, 2002). The first section focuses on general considerations: historical perspective, scientific basis, and surgical principles of source control. The second section highlights specific considerations of source control in various situations.
17β‐Estradiol enhances neuronal differentiation of mouse embryonic stem cells
Authors: Murashov Alexander K , Pak Elena S , Hendricks Wesley A , Tatko Lisa M
Published: June 2004

Existing protocols show a variety in the percentage of neurons that can be generated from mouse embryonic stem (ES) cells. In the current study, we compared effects of various differentiating conditions, including gelatin and poly‐l‐ornithine/fibronectin coatings, and NGF and 17β‐estradiol treatments on the total yield of neurons, as well as, neurite growth and branching. Here, we show that combination of fibronectin coating with 17β‐estradiol increased number of generated neurons over 50%. Poly‐l‐ornithine/fibronectin increased the percent of neurons in all cultures, suggesting its direct influence on neurogenesis. Addition of 17β‐estradiol reduced mean neurite length in culture, but significantly increased branching. Our results indicate a substrate‐dependent regulation of estrogen‐induced ES cells differentiation into neuronal cells.
Antioxidant enzymes and redox regulating thiol proteins in malignancies of human lung
Authors: Kinnula Vuokko L , Pääkkö Paavo , Soini Ylermi
Published: June 2004

Oxidants are known to modulate cell proliferation and apoptosis, and induce synthesis of growth factors that play an important role in tumor growth and invasion. Antioxidant enzymes and thiol proteins regulating cellular redox state constitute the major cellular protection against oxidants. Consequently, they are also associated both with carcinogenesis and tumor progression. Superoxide dismutases, glutamate cysteine ligase, catalase, thioredoxins and peroxiredoxins, which are the most important of these enzymes, are expressed in lung malignancies, and especially in pleural mesothelioma. This has consequences not only for tumor behavior but also for resistance of tumor cells to cytotoxic drugs and radiation.
Enterobacter aerogenes OmpX, a cation‐selective channel mar‐ and osmo‐regulated
Authors: Dupont Myrielle , Dé Emmanuelle , Chollet Renaud , Chevalier Jacqueline , Pagès Jean-Marie
Published: June 2004

The ompX gene of Enterobacter aerogenes was cloned. Its overexpression induced a decrease in the major porin Omp36 production and consequently a β‐lactam resistance was noted. Purified outer membrane protein X (OmpX) was reconstituted into artificial membranes and formed ion channels with a conductance of 20 pS in 1 M NaCl and a cationic selectivity. Both MarA expression and high osmolarity induced a noticeable increase of the OmpX synthesis in the E. aerogenes ATCC 13048 strain. In addition, OmpX synthesis increased under conditions in which the expression of the E. aerogenes major non‐specific porins, Omp36 and Omp35, decreased.
Collagen fibres of the spontaneously ruptured human tendons display decreased thickness and crimp angle
Authors: Järvinen Tero A. H. , Järvinen Teppo L. N. , Kannus Pekka , Józsa László , Järvinen Markku
Published: June 2004

Purpose. To study collagen fibre thickness and crimp formation in healthy and ruptured human tendons.

Methods. The thickness, crimp angle and wavelength of the collagen fibres were analyzed by interference and polarization microscopy and the samples were studied by transmission and scanning electron microscopy in four different healthy human tendons (Achilles, Quadriceps, Biceps brachii and Extensor pollicis longus) and in 66 spontaneously ruptured tendons.

Results. In the normal (healthy) tendons, the diameter and crimp angle of the collagen fibres varied greatly between the four different tendons, the thickest fibres with the largest crimp angle being in the Achilles and Quadriceps tendons, whereas the Biceps brachii and Extensor pollicis longus, tendons that bear lighter strains but carry functions of high specificity, were found to have substantially smaller collagen fibres with lower crimp angle. Ruptured tendons had significantly smaller collagen fibre diameter than the normal tendons, the fibre diameter being −36% in comparison to their healthy counterparts in the Achilles tendons (P < 0.0001), −24% in the Quadriceps tendons (P < 0.0001), −37% in the Biceps brachii (P < 0.0001) and −14% in the Extensor pollicis longus (P = 0.10), respectively. Similarly, the crimp angle of the collagen fibres was also found to be lower in the ruptured tendons than in healthy, normal tendons. Further, the collagen fibres in the ruptured human tendons showed great variation in the crimp angle between the adjacent fibres and in the successive crimps of the same fibre.

Conclusion. Our results show that spontaneously ruptured tendons display focal regions with decreased collagen fibre thickness, decreased crimp angle and disrupted crimp continuity, microscopic alterations that possibly result in reduced strength of the tendons being less resistant to tensile forces, and thus, place them at increased risk of ruptures. © 2004 Orthopaedic Research Society. Published y Elsevier Ltd. All rights reserved.
The Bidding Game: Competitive Funding Regimes and the Political Targeting of Urban Programme Schemes
Authors: JOHN PETER , WARD HUGH , DOWDING KEITH
Published: June 2004

Public bodies adopt procedures for the competitive bidding for funds in the belief that they improve public welfare, while critics regard such practices as a waste of resources and open to political manipulation. We test the operation of a competitive bidding regime through Tobit models of data drawn from successful and unsuccessful bids in four years of the Single Regeneration Budget programme in England. We derive hypotheses from a model of competitive bidding, the official evaluation of the programme and the pork-barrel literature. Our data and statistical models show that successive rounds did not greatly improve the quality of the bids, did not systematically reward needy communities and diverted resources to ministers' parliamentary seats in some regions.
Off-line classification of Polish vowel spectra using artificial neural networks
Authors: Jassem Wiktor , Grygiel Waldemar
Published: June 2004

The mid-frequencies and bandwidths of formants 1–5 were measured at targets, at plus 0.01 s and at minus 0.01 s off the targets of vowels in a 100-word list read by five male and five female speakers, for a total of 3390 10-variable spectrum specifications. Each of the six Polish vowel phonemes was represented approximately the same number of times. The 3390* 10 original-data matrix was processed by probabilistic neural networks to produce a classification of the spectra with respect to (a) vowel phoneme, (b) identity of the speaker, and (c) speaker gender. For (a) and (b), networks with added input information from another independent variable were also used, as well as matrices of the numerical data appropriately normalized. Mean scores for classification with respect to phonemes in a multi-speaker design in the testing sets were around 95%, and mean speaker-dependent scores for the phonemes varied between 86% and 100%, with two speakers scoring 100% correct. The individual voices were identified between 95% and 96% of the time, and classifications of the spectra for speaker gender were practically 100% correct.
Tamil
Authors: Keane Elinor
Published: June 2004

Tamil is a Dravidian language spoken by 53 million speakers in India, according to census figures from 1991, predominantly in the state of Tamil Nadu. There are also sizeable communities of Tamil speakers elsewhere, including Sri Lanka, Malaysia and Singapore, in all of which it has the status of a national language. Tamil is diglossic, the formal or ‘literary’ variety still largely conforming to standards set in the thirteenth century by the Tamil grammarian Pavanandi. It is used in almost all written media, and also for certain high-register functions. In all other situations colloquial Tamil is used and is characterized by considerable regional and social variation.
A fission track thermochronological study of King George and Livingston islands, South Shetland Islands (West Antarctica)
Authors: SELL I. , POUPEAU G. , GONZÁLEZ-CASADO J.M. , LÓPEZ-MARTÍNEZ J.
Published: June 2004

This paper reports the dating of apatite fission tracks in eleven rock samples from the South Shetland Archipelago, an island arc located to the north-west of the Antarctic Peninsula. Apatites from Livingston Island were dated as belonging to the Oligocene (25.8 Ma: metasediments, Miers Bluff Formation, Hurd Peninsula) through to the Miocene (18.8 Ma: tonalites, Barnard Point). Those from King George Island were slightly older, belonging to the Early Oligocene (32.5 Ma: granodiorites, Barton Peninsula). Towards the back-arc basin (Bransfield Basin), the apatite appears to be younger. This allows an opening rate of approximately 1.1 km Ma−1 (during the Miocene–Oligocene interval) to be calculated for Bransfield Basin. Optimization of the apatite data suggests cooling to 100 ± 10°C was coeval with the end of the main magmatic event in the South Shetland Arc (Oligocene), and indicates slightly different tectonic-exhumation histories for the different tectonic blocks.
Accumulation of dehydrin transcripts and proteins in response to abiotic stresses in Deschampsia antarctica
Authors: OLAVE-CONCHA NÉLIDA , RUIZ-LARA SIMÓN , MUÑOZ XIMENA , BRAVO LEÓN A. , CORCUERA LUIS J.
Published: June 2004

Deschampsia antarctica Desv. is one of two vascular plants from the Maritime Antarctic. It is usually exposed to cold, salt, and desiccating winds. We hypothesize that D. antarctica has genes that encode dehydrin proteins and their expression is regulated by low temperature, salt or osmotic stress. To test this hypothesis a fragment of a dehydrin gene from D. antarctica was identified and used as a probe to study dehydrin expression under low temperature, salt, and osmotic stress, and exogenous ABA (abscisic acid) treatments. An anti-dehydrin antibody was also used to study dehydrin protein accumulation under the same treatments. Southern analysis of genomic DNA treated with different endonucleases showed more than four bands recognized by the probe, suggesting that D. antarctica has several dehydrin genes. Northern analysis showed two putative dehydrin transcripts of 1.0 kb accumulated only under exogenous ABA and 1.6 kb under osmotic and salt treatments, suggesting that D. antarctica would have ABA-dependent and - independent pathways for regulation of dehydrin expression. Western analysis showed seven dehydrin proteins (58, 57, 55, 53, 48, 30 and 27 kDa) under the different stress treatments. Cold-accumulated dehydrin proteins were immunolocalized, showing that they are associated with vascular and epidermal tissue, which are preferential ice nucleation zones.
On the analysis of a non-isothermal model for superconductivity
Authors: PHILLIPS DAN , SHIN EUNJEE
Published: June 2004

We analyze a model for non-isothermal superconductivity, derived independently by G. Maugin, and K. Miya and S. A. Zhou. The model is described by a parabolic system based on the Time-Dependent Ginzburg–Landau (TDGL) equation, the Maxwell equations, and an energy equation such that the Clausius–Duhem inequality holds. The principal unknown fields are the complex valued Ginzburg–Landau order parameter $\psi$, the magnetic vector potential $A$, and the temperature $T$. A significant feature for this model is that it accounts for the interchange of thermal and electro-magnetic energies through Joule heating. The sensitivity of superconducting materials to thermal variations is a major obstacle to their applications. In practice one sees that time varying currents and magnetic fields generate thermal energy, producing ‘hot spots’ and increasing the temperature. This can result in suppressing superconductivity, i.e. $\psi$ tending to $0$. Our principal result is that we exhibit this phenomenon. We prove that if the electro-magnetic energy of the superconductor is sufficiently large at time $t\,{=}\,0$ then $T$ will rise beyond the critical temperature, $T_c$, and $\psi\to 0$ as $t\to\infty$. Earlier analytic work investigating electro-dynamic effects in superconductivity centered on an isothermal model consisting of the TDGL equation and Maxwell equations. This setting takes into account just electro-magnetic effects and produces markedly different evolutions.
The evolution of financial institutions in the Ottoman Empire, 1600–1914
Authors: PAMUK ŞEVKET
Published: June 2004

For most of its 600-year existence, the economic institutions and policies of the Ottoman Empire were shaped to a large degree by the priorities and interests of a central bureaucracy. The influence of landowners, merchants and moneychangers remained limited. The central bureaucracy managed to contain the many challenges it faced with pragmatism, flexibility and negotiation. This study examines long-term changes in Ottoman fiscal, monetary and financial institutions from this perspective of pragmatism, flexibility and adaptiveness. Ottoman institutions of private and public finance retained their Islamic lineage until the end of the seventeenth century. European financial institutions began to grow in influence during the eighteenth century. With the onset of the Ottoman reform movement and greater economic interaction with Europe during the nineteenth century, institutional change accelerated. Ultimately, however, Ottoman pragmatism and flexibility remained selective and was utilised for the defence of a traditional order led by the central bureaucracy. Many of the key institutions of the traditional order such as state ownership of land, urban guilds and restrictions on private capital accumulation remained intact until the nineteenth century.
Sound morphology and the articulation of structure in electroacoustic music
Authors: YOUNG JOHN
Published: June 2004

A catalyst for the thinking in this paper is the way in which the concentrated direct audition of materials central to the process of electroacoustic composition can, in conjunction with powerful tools for the deconstruction and synthesis of sounds, influence the nature of musical relationships that are formed.
Seasonal variation of a coastal jet in the Long Island Sound outflow region based on HF radar and Doppler current observations
Authors: Ullman D. S. , Codiga D. L.
Published: June 2004

Surface current (HF radar) and velocity profile observations, obtained as part of the Front‐Resolving Observational Network with Telemetry (FRONT) project over an approximately 2‐year period, are used to describe the seasonal variability of a coastal jet in the Long Island Sound outflow region. The jet is observed in an area of the continental shelf where surface thermal fronts are frequently detected during both summer and winter. The current jet is coincident with a band of high summer frontal probability, and apparently arises from the interaction between Long Island Sound outflow and larger‐scale alongshore currents on the shelf. The jet reaches peak strength in summer (transport of ∼0.07 Sv) and is weak or non‐existent in winter. Flow is strongest near the surface and weakens with depth, with only moderate seasonal variations in the vertical shear. The relatively long data set of currents combined with historical hydrographic measurements and buoy wind observations is analyzed to examine the seasonal variability of the terms in the depth‐averaged momentum balance. The depth‐averaged pressure gradient is partitioned into a steric component, evaluated from the hydrography, and a non‐steric component that is estimated as the residual of the computed terms in the momentum equation. The depth‐averaged momentum balance is found to be approximately geostrophic in the across‐shore direction. The seasonal variability in the jet arises due to the shifting balance between buoyancy‐driven flow that is always downshelf but intensifies somewhat in summer and wind‐driven flow which dominates in winter when wind stress becomes strongly upwelling favorable.
Methane dynamics in the Weddell Sea determined via stable isotope ratios and CFC‐11
Authors: Heeschen Katja U. , Keir Robin S. , Rehder Gregor , Klatt Olaf , Suess Erwin
Published: June 2004

The physical, chemical/biological processes that control the methane dynamics in the Weddell Sea are revealed by the distributions of methane (CH4), its stable carbon isotope ratio, δ13C‐CH4, and the conservative transient tracer, chlorofluorocarbon‐11 (CFC‐11, CCl3F). In general, a nearly linear correlation between CH4 and CFC‐11 concentrations was observed. Air‐sea exchange is the major source of methane to this region, and the distribution of methane is controlled mainly by mixing between surface water and methane‐poor Warm Deep Water. A significant influence of methane oxidation over the predominant two end‐member mixing was only found in the Weddell Sea Bottom Water (WSBW) of the deep central Weddell Basin, where the turnover time of methane appears to be about 20 years. Mixing also controls most of the δ13C‐CH4 distribution, but lighter than expected carbon isotopic ratios occur in the deep WSBW of the basin. From box model simulations, it appears that this “anomaly” is due to methane oxidation with a low kinetic isotope fractionation of about 1.004. The surface waters in the Weddell Sea and the Antarctic Circumpolar Current showed a general methane undersaturation of 6 to 25% with respect to the atmospheric mixing ratio. From this undersaturation and model‐derived air‐sea exchange rates, we estimate a net uptake of CH4 of roughly −0.5 μmol m−2 d−1 during austral autumn.
Impact of elevated atmospheric CO2 on forest floor respiration in a temperate pine forest
Authors: Suwa Makoto , Katul Gabriel G. , Oren Ram , Andrews Jeff , Pippen Jeff , Mace Anthony , Schlesinger William H.
Published: June 2004

The effects of elevated atmospheric CO2 (CO2e) on soil respiration were evaluated using inverse models and static chamber measurements collected over 4.5 years in a maturing loblolly pine forest. The chamber measurements of forest floor CO2 efflux showed that the flux enhancement increased progressively, reaching 1.4 after 3 years, but declined thereafter to 1.10 at the end of the study. The subsurface CO2 concentration measurements show that the difference in mean annual concentration gradient between ambient and enriched plots initially increased, and then stabilized after 2 years of enrichment. However, concomitant soil moisture increases in the enriched plots reduced the soil diffusivity, especially over the last 2 years. These two observations, in combination with inverse model calculations, suggest a decline in subsurface CO2 production over the last 2 years. Enhancement in photosynthesis has declined after 4.5 years of enrichment (remaining ∼40% higher than ambient photosynthesis), and the increase in production and respiration alone cannot account for the excess carbon uptake. Thus this modeling approach would suggest that non‐gaseous carbon is accumulating belowground. However, we have not been able to measure significant changes in soil organic carbon or fine root biomass. These results, in the context of other forest floor flux studies and the carbon budget at the site, suggest a lack of closure in the carbon budget under elevated atmospheric CO2.
Modeling estimates of the global emission of dimethylsulfide under enhanced greenhouse conditions
Authors: Gabric A. J. , Simó R. , Cropp R. A. , Hirst A. C. , Dachs J.
Published: June 2004

We have used a marine food‐web model, an atmosphere‐ocean general circulation model (GCM), and an empirical dimethylsulfide (DMS) algorithm to predict the DMS seawater concentration and the DMS sea‐to‐air flux in 10° latitude bands from 70°N to 70°S under contemporary and enhanced greenhouse conditions. The DMS empirical algorithm utilizes the food‐web model predictions of surface chlorophyll and the GCM's simulation of oceanic mixed layer depth. The food‐web model was first calibrated to contemporary climate conditions using satellite‐derived chlorophyll data and meteorological forcings. For the climate change simulations, the meteorological forcings were derived from a transient simulation of the CSIRO Mark 2 GCM, using the IPCC/IS92a radiative forcing scenario to the period of equivalent CO2 tripling (2080). The globally integrated DMS flux perturbation is predicted to be +14%; however, we found strong latitudinal variation in the perturbation. The greatest perturbation to DMS flux is simulated at high latitudes in both hemispheres, with little change predicted in the tropics and sub‐tropics. The largest change in annual integrated flux (+106%) is simulated in the Southern Hemisphere between 50°S and 60°S. At this latitude, the DMS flux perturbation is most influenced by the GCM‐simulated changes in the mixed layer depth. The results indicate that future increases in stratification in the polar oceans will play a critical role in the DMS cycle and climate change.
Effects of depth‐ and CO2‐dependent C:N ratios of particulate organic matter (POM) on the marine carbon cycle
Authors: Schneider Birgit , Engel Anja , Schlitzer Reiner
Published: June 2004

According to a recent study, C:N ratios of sinking particulate organic matter (POM) in the ocean appear to be higher than Redfield (7.1 instead of 6.6) and depth dependent (increase +0.2/km). Here we investigate the effects of vertically variable C:N element ratios on marine carbon fluxes and the air‐sea exchange of CO2 using a global ocean carbon cycle model (AAMOCC). For a steady‐state ocean, the results show that models using the constant classical Redfield ratio underestimate both, total inventory and vertical gradients of dissolved inorganic carbon (DIC). While the amount of additional DIC (+150 Gt C) is negligible compared to the high marine carbon inventory, the C:N depth dependence can reduce the ambient atmospheric pCO2 by 20 ppm, permanently. Moreover, the simulation of a future scenario, estimating a possible effect of CO2‐dependent C:N ratios of POM on the marine carbon cycle, has shown that even a moderate rise in the C:N element ratio of sinking POM, which is on the order of magnitude of natural variability, yields a considerably higher oceanic uptake of anthropogenic CO2 on timescales of decades to centuries. The assumption is based on a predicted increase in the production of highly carbon enriched transparent exopolymer particles (TEP) caused by rising atmospheric CO2 concentrations and enhanced nutrient limitation. However, counteracting a predicted decrease of the physical (solubility) CO2 pump as a consequence of global change, the effect in our scenario will alleviate further rising atmospheric CO2 concentrations rather than compensate a reduced physical uptake.
A theoretical analysis of steady state δ13C profiles of soil organic matter
Authors: Poage Michael A. , Feng Xiahong
Published: June 2004

Soil organic matter (SOM) is the largest reservoir of terrestrial carbon and plays an important role in the global carbon cycle. Carbon isotope systematics of SOM have been widely used to constrain the dynamics of this important carbon reservoir though interpretation of carbon isotope data remains controversial. It has been widely observed that the 13C/12C ratio of SOM increases systematically with soil depth though there is little consensus as to which of several mechanisms may be responsible for this pattern. Here we present a process‐based theoretical model of steady state δ13CSOM versus depth profiles, which is coupled with a carbon concentration model. We show that widely observed δ13CSOM versus depth profiles can be modeled using a reasonable range of model parameters. More importantly, we show that coupling carbon isotope data with carbon concentrations in soils allows for tighter constraints on model parameters that have biological and environmental significance.
Methane and nitrous oxide emissions from a paddy field with Japanese conventional water management and fertilizer application
Authors: Nishimura Seiichi , Sawamoto Takuji , Akiyama Hiroko , Sudo Shigeto , Yagi Kazuyuki
Published: June 2004

The seasonal courses of methane (CH4) and nitrous oxide (N2O) fluxes were simultaneously monitored in a paddy field using a closed chamber system with automated gas sampling and analyzing equipment. Water management and fertilizer application practices followed Japanese conventional ones. CH4 flux gradually increased after the first flood irrigation of the field and reached ∼150 mg CH4 m−2 d−1 at the beginning of July. After the first summer drainage, however, CH4 flux dropped rapidly to almost zero within a few days. CH4 flux then gradually increased again according to intermittent flood irrigations, but was much less than that before the first drainage. Immediately after the first flood irrigation, N2O flux rapidly increased, although its temporal peak lasted only within a few days. During the subsequent continuously and intermittently flooded periods, N2O flux remained at almost zero until the final drainage, except for slight and temporal peaks just after the top‐dress application of supplemental fertilizer. About 1 week after the final drainage in autumn, N2O flux gradually increased, and the most significant high peak of N2O flux was observed after the harvest of rice plants, which lasted for about 2 weeks. The amounts of cumulative CH4 and N2O emissions throughout the whole year of 2002 were 3128 mg CH4 m−2 and 60.2 mg N m−2, respectively. Both the amounts of cumulative CH4 and N2O emissions during the rice cultivation period were low compared with those reported in previous studies. These results suggest the advantage of Japanese conventional water management and fertilizer application for reducing the combined effect for global warming by CH4 and N2O emissions from paddy fields, since the practices of drainage and intermittent flood irrigation in summer markedly lessen CH4 emission in the latter half of the rice cultivation period with little enhancement of N2O emission.
Aircraft engine soot as contrail nuclei
Authors: Popovicheva O. B. , Persiantseva N. M. , Lukhovitskaya E. E. , Shonija N. K. , Zubareva N. A. , Demirdjian B. , Ferry D. , Suzanne J.
Published: June 2004

The physico‐chemical properties of aircraft engine soot are characterized with respect to their ability to act as CCN. Comparison with laboratory‐generated kerosene soot shows a significant influence of combustion conditions on the morphology, microstructure, chemical composition, surface nature, and hygroscopicity of soot. Engine soot particles separate into two components based on composition and structural heterogeneities: a main soot fraction and a fraction of impurities containing an appreciable amount of metal and sulfur. The high concentration of soluble sulfates, of inorganics and of organics in the fraction that contains impurities, explains the engine soot hygroscopicity and its ability to act as CCN at threshold conditions for contrail formation. Laboratory–generated kerosene soot is not able to reproduce the hygroscopicity of engine soot, but we show that it is a good surrogate for the insoluble black carbon fraction of aircraft soot in the upper troposphere.
Observed tidal currents outside Block Island Sound: Offshore decay and effects of estuarine outflow
Authors: Codiga Daniel L. , Rear Laura V.
Published: June 2004

An array of moored profiling current meters on the inner continental shelf 15–65 m deep is used to investigate tidal currents outside the Block Island Sound and Long Island Sound estuarine system. The M2 constituent dominates due to near‐resonant semi‐diurnal estuarine response. Vertical‐mean M2 currents rotate clockwise in time in ellipses elongated toward the estuary mouth with little sensitivity to complex local bathymetry; semi‐major axes decay sharply offshore (55 to 20 cm/s over 10 km) in agreement with the nearly inverse‐square radius dependence of a kinematic theory. Estimated tidal volume exchange out of Block Island Sound to the south is 2.9 × 105 m3/s. Observed vertical structure of M2 ellipses in the deepest 10–20 m (amplitude decay, ellipse flattening, major axis turning clockwise, phase advance) is generally captured well by optimally fit frictional solutions despite the fact that they omit bathymetry and include stratification only indirectly through its influence on eddy viscosity. In the upper water column, vertical structure varies seasonally: Mid‐depth ellipses enlarge in spring; near‐surface ellipses are larger (smaller) than optimal‐fit solutions in fall/winter (spring). Observed seasonal‐average estuarine outflow includes surface‐intensified Coriolis‐deflected mean flow that strengthens and spreads farther offshore in spring. Richardson numbers based on moored hydrographic profiler records suggest spring stratification suppresses deep eddy viscosities, which in frictional solutions can explain mid‐depth ellipse enlargement. An inviscid theory for mean‐flow modifications due to ambient vorticity of estuarine outflow currents is shown to be the most plausible explanation for observed seasonal changes in near‐surface tidal ellipses.
Mantle 3He distribution and deep circulation in the Indian Ocean
Authors: Srinivasan Ashwanth , Top Zafer , Schlosser Peter , Hohmann Roland , Iskandarani Mohamed , Olson Donald B. , Lupton John E. , Jenkins William J.
Published: June 2004

The World Ocean Circulation Experiment Indian Ocean helium isotope data are mapped and features of intermediate and deep circulation are inferred and discussed. The 3He added to the deep Indian Ocean originates from (1) a strong source on the mid‐ocean ridge at about 19°S/65°E, (2) a source located in the Gulf of Aden in the northwestern Indian Ocean, (3) sources located in the convergent margins in the northeastern Indian Ocean, and (4) water imported from the Indonesian Seas. The main circulation features inferred from the 3He distribution include (1) deep (2000–3000 m) eastward flow in the central Indian Ocean, which overflows into the West Australian Basin through saddles in the Ninetyeast Ridge, (2) a deep (2000–3000 m) southwestward flow in the western Indian Ocean, and (3) influx of Banda Sea Intermediate Waters associated with the deep core (1000–1500 m) of the through flow from the Pacific Ocean. The large‐scale 3He distribution is consonant with the known pathways of deep and bottom water circulation in the Indian Ocean.
A model for low‐temperature biogeochemistry of sulfur, carbon, and iron on Europa
Authors: Zolotov Mikhail Y. , Shock Everett L.
Published: June 2004

Galileo spacecraft data obtained from Jupiter's ice‐covered satellite Europa suggest the existence of a subsurface water ocean. The formation of this ocean is a direct consequence of early igneous and hydrothermal processes that may have facilitated oxidation through H2 and CH4 escape. These processes could have led to a moderately alkaline sulfate‐carbonate ocean and a moderately oxidized magnetite‐bearing silicate mantle. When the ocean formed, low‐temperature chemical disequilibria involving oceanic sulfate, bicarbonate, and ferrous minerals in underlying rocks could have provided multiple energy sources for chemotrophic organisms. Potential metabolic processes include oxidation of ferrous iron, sulfides, native sulfur, methane, hydrogen, and organic compounds, as well as reduction of water, sulfate, bicarbonate and carbonate ions (methanogenesis and acetogenesis), native sulfur, and ferric iron. If they occurred, these reactions would have provided close coupling for biogeochemical cycles of S, C, and Fe in the ocean. Periodic supplies of fresh rocks and/or aqueous fluids at the oceanic floor could drive these cycles throughout the satellite's history, including the present epoch. Signs of chemical disequilibria in the ocean would indicate chemical sources of energy for metabolism but should not be considered as indicators of life. In turn, observational signs of low‐temperature redox equilibration among sulfur and carbon species would be suggestive of ancient life.
Optimal extraction from a renewable groundwater aquifer with stochastic recharge
Authors: Zeitouni N.
Published: June 2004

This work considers the management of an aquifer with stochastic recharge and finite boundaries. For a class of such models we show that there is a positive threshold of the water stock that the manager should aim at keeping. Thus, under the optimal extraction regime at a time when the water stock is lower than this threshold, there should be no pumping from the aquifer, while at times when the water stock is greater than the threshold, all water in excess of the threshold level should be pumped. The threshold level happens to coincide with the aquifer boundary for sufficiently high unit cost of pumping, in which case, only the runoff water of excess recharge should be collected.
Potential for groundwater management: Gisser‐Sanchez effect reconsidered
Authors: Koundouri Phoebe
Published: June 2004

This paper revisits Gisser‐Sanchez's effect, a paradoxical empirical result that persists in the groundwater literature since 1980, when it was first identified by Gisser and Sanchez. In essence, Gisser‐Sanchez's effect (GSE) states that the numerical magnitude of benefits of optimally managing groundwater is insignificant. This paper critically reviews both the theoretical and empirical attempts to address GSE. It highlights the fact that in the theoretical literature the single most important cause for the presence of GSE is the prevalence of very steep marginal groundwater use benefit curves, which imply that groundwater usage is not very sensitive to price changes. However there exist circumstances that its effects can be eliminated. Thus the case for different theoretical investigations is put forward. Moreover, this paper also points at various misconceptions, inaccuracies, and omissions of the current state of the literature that could potentially resolve part of the existing puzzle.
Water pricing: Analysis of differential impacts on heterogeneous farmers
Authors: Gómez‐Limón José A. , Riesgo Laura
Published: June 2004

European water policy requires all EU Member States to implement volumetric water pricing at rates that roughly cover the total costs of providing water services. The objective of this paper is to develop a methodology that will enable us to analyze the differential impact that a water pricing policy for irrigation would have on heterogeneous farmers of an irrigated area. For this purpose, multiattribute utility theory (MAUT) mathematical programming models were used. The methodology is implemented on a representative area in the Duero Valley in Spain. Our results show the usefulness of differential analysis in evaluating the impact of a water pricing policy. From them we observe significant differences in the evolution of agricultural incomes and estimate the cost recovery by the state, the demand for farm labor, and the consumption of agrochemicals resulting from the rise in water price between the various groups of farmers established within the analyzed irrigated area.
An explicit unconditionally stable numerical solution of the advection problem in irrotational flow fields
Authors: Bascià Alessandra , Tucciarelli Tullio
Published: June 2004

A new methodology for the Eulerian numerical solution of the advection problem is proposed. The methodology is based on the conservation of both the zero‐ and the first‐order spatial moments inside each element of the computational domain and leads to the solution of several small systems of ordinary differential equations. Since the systems are solved sequentially (one element after the other), the method can be classified as explicit. The proposed methodology has the following properties: (1) it guarantees local and global mass conservation, (2) it is unconditionally stable, and (3) it applies second‐order approximation of the concentration and its fluxes inside each element. Limitation of the procedure to irrotational flow fields, for the 2‐D and 3‐D cases, is discussed. The results of three 1‐D and 2‐D literature tests are compared with those obtained using other techniques. A new 2‐D test, with radially symmetric flow, is also carried out.
Density and electric field fluctuations associated with the gradient drift instability in the high‐latitude ionosphere
Authors: Gondarenko N. A. , Guzdar P. N.
Published: June 2004

The magnitudes of the density and electric field fluctuations and their spectral characteristics were studied with a three‐dimensional nonlinear model of the structuring in high‐latitude patches caused by the primary gradient drift instability. The simulations were compared with the simultaneous density and electric field spectra obtained from noon‐midnight and dawn‐dusk orbits of the Dynamic Explorer 2 (DE 2) satellite [Basu et al., 1990]. The magnitudes of the simulated density and electric field fluctuations were found to be in very good agreement with the measured data. In the directions parallel and perpendicular to convection, the similarities in the spectral slope distributions of both simulated and observed density and electric field fluctuations were demonstrated. These findings together with our earlier results [Gondarenko and Guzdar, 1999, 2001, 2003; Gondarenko et al., 2003] provide a significant evidence for coexistence of the primary gradient drift instability and subsequent secondary Kelvin‐Helmholtz and tertiary shear‐flow instabilities.
Evidence of high ice supersaturation in cirrus clouds using ARM Raman lidar measurements
Authors: Comstock Jennifer M. , Ackerman Thomas P. , Turner David D.
Published: June 2004

Water vapor amounts in the upper troposphere are crucial to understanding the radiative feedback of cirrus clouds on the Earth's climate. We use a unique, year‐long dataset of water vapor mixing ratio inferred from ground‐based Raman lidar measurements to study the role of ice supersaturation in ice nucleation processes. We find that ice supersaturation occurs 31% of the time in over 300,000 data points. We also examine the distribution of ice supersaturation with height and find that in the uppermost portion of a cloud layer, the air is ice supersaturated 43% of the time. These measurements show that large ice supersaturation is common in cirrus clouds, which supports the theory of ice forming homogeneously. Given the continuous nature of these Raman lidar measurements, our results have important implications for studying ice nucleation processes using cloud microphysical models.