bluuebunny/crossref_metadata_2025 huggingface dataset:
A framework for adaptive execution in grids
Authors: Huedo Eduardo , Montero Ruben S. , Llorente Ignacio M.
Published: April 2004

Grids offer a dramatic increase in the number of available processing and storing resources that can be delivered to applications. However, efficient job submission and management continue being far from accessible to ordinary scientists and engineers due to their dynamic and complex nature. This paper describes a new Globus based framework that allows an easier and more efficient execution of jobs in a ‘submit and forget’ fashion. The framework automatically performs the steps involved in job submission and also watches over its efficient execution. In order to obtain a reasonable degree of performance, job execution is adapted to dynamic resource conditions and application demands. Adaptation is achieved by supporting automatic application migration following performance degradation, ‘better’ resource discovery, requirement change, owner decision or remote resource failure. The framework is currently functional on any Grid testbed based on Globus because it does not require new system software to be installed in the resources. The paper also includes practical experiences of the behavior of our framework on the TRGP and UCM‐CAB testbeds. Copyright © 2004 John Wiley & Sons, Ltd.
A taxonomy of computer‐based simulations and its mapping to parallel and distributed systems simulation tools
Authors: Sulistio Anthony , Yeo Chee Shin , Buyya Rajkumar
Published: April 2004

In recent years, extensive research has been conducted in the area of simulation to model large complex systems and understand their behavior, especially in parallel and distributed systems. At the same time, a variety of design principles and approaches for computer‐based simulation have evolved. As a result, an increasing number of simulation tools have been designed and developed. Therefore, the aim of this paper is to develop a comprehensive taxonomy for design of computer‐based simulations, and apply this taxonomy to categorize and analyze various simulation tools for parallel and distributed systems. Copyright © 2004 John Wiley & Sons, Ltd.
UbiCrawler: a scalable fully distributed Web crawler
Authors: Boldi Paolo , Codenotti Bruno , Santini Massimo , Vigna Sebastiano
Published: April 2004

We report our experience in implementing UbiCrawler, a scalable distributed Web crawler, using the Java programming language. The main features of UbiCrawler are platform independence, linear scalability, graceful degradation in the presence of faults, a very effective assignment function (based on consistent hashing) for partitioning the domain to crawl, and more in general the complete decentralization of every task. The necessity of handling very large sets of data has highlighted some limitations of the Java APIs, which prompted the authors to partially reimplement them. Copyright © 2004 John Wiley & Sons, Ltd.
Optimization of differential display polymerase chain reaction as a bioindicator for the cladoceran Daphnia magna
Authors: Diener Lara C. , Schulte Patricia M. , Dixon D. George , Greenberg Bruce M.
Published: April 2004

Research on toxicant‐responsive genes is providing new and important bioindicators for environmental biologists. Identifying genes whose expression is modulated by toxicant exposure provides important clues into the mechanisms underlying toxicity. In addition, toxicant‐responsive genes can be developed as molecular end points that are likely to be sensitive tools for environmental assessment. Differential display polymerase chain reaction (ddPCR) is a useful approach for screening and analyzing the expression of genes. A ddPCR protocol was optimized to investigate gene expression in the cladoceran Daphnia magna. The modified protocol requires submicrogram quantities of total RNA (from <10 animals) and utilizes a sensitive fluorescent tagging system. By reverse‐transcribing total RNA with arbitrary 18‐nucleotide primers and PCR‐amplifying the cDNA using the same arbitrary primers under low‐stringency conditions, reproducible and consistent ddPCR profiles were generated. Minimal variability was introduced by reaction differences or biological variability. A trial stress (starvation) was found to generate modest differences in the ddPCR profiles. This technique promises to significantly advance knowledge regarding gene expression during toxicant insult. Furthermore, this represents the first step in the development of a novel gene fingerprinting technique that can be applied to any compound and organism of interest. © 2004 Wiley Periodicals, Inc. Environ Toxicol 19: 179–190, 2004.
Estrogenicity of municipal effluents assessed in vivo and in vitro
Authors: Nakari Tarja
Published: April 2004

The estrogenic potency of municipal sewage treatment plant effluents was studied by comparing in vitro and in vivo test methods. The egg yolk protein precursor vitellogenin was used as a biological indicator of estrogenicity. The in vitro screening technique, based on the synthesis and secretion of vitellogenin from isolated rainbow trout liver cells and performed in the presence of estrogenic effluents, produced a dose–response curve. Three weeks' exposure of juvenile rainbow trout to undiluted estrogenic effluents caused a very pronounced increase in their plasma vitellogenin concentration. The response was very specific, because no effect was observed in the control fish. Moreover, the multigeneration test of zebrafish provided clear evidence of the estrogenicity of one of the effluents. The sex ratio of the offspring generations was changed to favor females. Also, the diluted effluent was sufficient to induce vitellogenin production in the exposed zebrafish males. The effective concentrations of the effluents that were tested were lower in the in vitro screening test than in the zebrafish multigeneration test. Based on the results of this study, the in vitro screening approach seems to be as least as sensitive as the in vivo approach to mixed effluents. Thus, using the in vitro approach affords advantages of both practicality and sensitivity for an initial screening of effluents for estrogenicity, but to ascertain significant effects, using the multigeneration in vivo test is recommended. © 2004 Wiley Periodicals, Inc. Environ Toxicol 19: 207–215, 2004.
Does the availability of maternal HbA1c results improve the accuracy of sonographic diagnosis of macrosomia?
Authors: Weissmann‐Brenner A. , O'Reilly‐Green C. , Ferber A. , Divon M. Y.
Published: April 2004

Objective

To determine whether measuring maternal glycosylated hemoglobin (HbA1c) can improve the accuracy of sonographic estimation of fetal macrosomia.

Methods

Sonographic estimation of fetal weight (EFW) and maternal HbA1c were obtained in term, non‐diabetic patients within 1 week before delivery. Neonatal birth weights were recorded at delivery and compared with both sonographic estimations and HbA1c. Macrosomia was defined as birth weight of ≥4000 g. The absolute error of the sonographic EFW was calculated. Receiver–operating characteristics (ROC) curve analysis was used to evaluate sonographic EFW and HbA1c as predictors of birth weight ≥4000 g. Variables were tested using regression analysis and student's t‐test.

Results

One hundred and sixty two patients were evaluated between July and December 2002. Twenty‐eight patients (17.3%) delivered macrosomic infants. Sonographic EFW ≥4000 g predicted macrosomia with sensitivity, specificity and positive and negative predictive values of 66.6%, 88.8%, 54.5% and 93.0%, respectively. Its overall accuracy was 85.5%. The area under the ROC curve of sonographic EFW in the prediction of macrosomia was 0.9 (P < 0.001). HbA1c levels in women delivering macrosomic and non‐macrosomic neonates were 5.3 ± 0.7% and 5.2 ± 0.5%, respectively (P = 0.27). The area under the ROC curve of HbA1c in the prediction of macrosomia was 0.53 (P = 0.27).

Conclusions

Maternal HbA1c is not a useful test in the prediction of birth weight. It therefore cannot be used to improve the accuracy of sonographic EFW. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Quasi‐brittle to ductile transition in impact‐modified PVC
Authors: Yu J. , Summers J. , Hiltner A. , Baer E.
Published: April 2004

The toughness of impact‐modified poly(vinyl chloride) (PVC) compounds was examined by using a modified Charpy test. Increasing impact speed resulted in a quasi‐brittle to ductile transition in all PVC compounds. In the quasi‐brittle region, a PVC of 56,000 Mw fractured through a craze‐like damage zone that could be described by a modified Dugdale model. Furthermore, the same molecular‐weight PVC modified with either 10 pph (parts per hundred parts by weight) of chlorinated polyethylene (CPE) or 10 pph of methylmethacrylate‐butadiene‐styrene (MBS) impact modifier also conformed to the Dugdale model with the craze‐like damage zone. The CPE effectively improved the impact performance of PVC by shifting the quasi‐brittle to ductile transition to a higher loading rate. Compared to CPE, MBS was a better impact modifier, and its use resulted in a higher quasi‐brittle to ductile transition loading rate in the same PVC matrix. Fracture initiation toughness of all the materials was described by the Hayes‐Williams modification of the Dugdale model. The intrinsic brittle fracture energy obtained by extrapolation to zero craze length was determined only by the PVC matrix and was independent of the impact modifier. However, the kinetics of craze growth, and hence the response to rapid loading, depended on the impact modifier. Increasing the molecular weight of the PVC resin resulted in a more complex damage zone that was not amendable to the Dugdale analysis. J. Vinyl Addit. Technol. 10:11–16, 2004. © 2004 Society of Plastics Engineers.
Polybutadiene‐modified clay and its polystyrene nanocomposites
Authors: Su Shengpei , Jiang David D. , Wilkie Charles A.
Published: April 2004

Vinylbenzyl chloride was allowed to react with a low‐molecular‐weight oligomer of butadiene in order to give a material that could then be used to alkylate an amine to form an ammonium salt. This ammonium salt was ion‐exchanged onto a clay to give a new organically modified clay, which was used to prepare polystyrene‐clay nanocomposites by solution and bulk polymerization and by melt blending. The nanocomposites were characterized by using X‐ray diffraction, transmission electron microscopy, thermogravimetric analysis, cone calorimetry, and the evaluation of mechanical properties. These systems show good nanodispersion and improvement in thermal and mechanical properties. J. Vinyl Addit. Technol. 10:44–51, 2004. © 2004 Society of Plastics Engineers.
Safe and Permissible Limits of Hepatectomy in Obstructive Jaundice Patients
Authors: Takahashi Tetsuya , Togo Shinji , Tanaka Kuniya , Endo Itaru , Fujii Yoshiro , Shimada Hiroshi
Published: April 2004

The safe and permissible limits of hepatectomy in obstructive jaundice patients and the usefulness of preoperative portal embolization (PE) for increasing the limit for safe hepatectomy were examined. We classified 416 patients with hepatectomy performed over 9 years under the following headings: normal liver function (n = 242); chronic hepatitis (n = 71); liver cirrhosis (n = 64); and liver after relief of obstructive jaundice (n = 39). Hepatectomy was done after the total bilirubin level was reduced below 3 mg/dl by preoperative biliary drainage. Factors influencing the maximum total bilirubin level measured within 2 weeks after hepatectomy were investigated, and this level was taken to reflect the degree of surgical stress. PE was carried out in 18 patients with obstructive jaundice. The maximum total bilirubin, expressed as a logarithm, was significantly correlated with the percent of liver resected in all groups. Hepatectomy followed by a maximum total bilirubin of less than 8.5 mg/dl was accepted as safe, and hepatectomy followed by a bilirubin level of 14.4 mg/dl was deemed the maximum permissible resection. On the basis of these results, the safe and permissible limits of hepatectomy in patients with obstructive jaundice were 48.7% and 71.6%, respectively. PE decreased the maximum total bilirubin from 8.5 mg/dl to 3.9 mg/dl when 48.7% of the liver (a safe proportion in all cases) was resected; PE increased the safe limit of hepatectomy from 48.7% to 67.4% when a maximum posthepatectomy total bilirubin level of 8.5 mg/dl was accepted as safe.
Effect of Glutamine and Bile Acid on Hepatocyte Apoptosis after Bile Duct Ligation in the Rat
Authors: Sheen‐Chen Shyr‐Ming , Hung Kuo‐Sheng , Ho Hsin‐Tsung , Chen Wei‐Jen , Eng Hock‐Liew
Published: April 2004

Apoptosis is an important process in a wide variety of biologic systems. Cholestasis, or impaired bile formation, occurs in a wide variety of human liver diseases. Retention and accumulation of toxic hydrophobic bile salts in hepatocytes may cause hepatocyte toxicity by inducing apoptosis. In addition, the translocation of bacteria and endotoxin, well documented in patients with obstructive jaundice, contribute to the induction of hepatocyte apoptosis. We hypothesized that oral bile acid replacement, glutamine administration, or both can attenuate or abolish hepatocyte apoptosis. Male Sprague‐Dawley rats weighing 250 to 300 g were randomized to four groups (10 in each group). Group 1 underwent a sham operation and was simultaneously treated with normal saline. Group 2 underwent common bile duct (CBD) ligation and was simultaneously treated with normal saline. Group 3 underwent CBD ligation and was simultaneously treated with oral glutamine. Group 4 underwent CBD ligation and was simultaneously treated with oral bile acid replacement. After 3 days (n = 5) and 7 days (n = 5), liver tissues were harvested for histopathologic analysis and apoptosis measurements. When compared with the sham operation group, significantly increased hepatocyte apoptosis and ductular proliferation occurred after CBD ligation for either 3 or 7 days. After administration of either glutamine or bile acid, the increased hepatocyte apoptosis and ductular proliferation after CBD ligation for 3 days were significantly diminished. However, both failed to diminish the changes after CBD ligation for 7 days. Significantly increased hepatocyte apoptosis and ductular proliferation occurred after CBD ligation. The administration of either glutamine or bile acid effectively diminished the hepatocyte apoptosis and ductular proliferation after CBD ligation for 3 days, whereas both failed to show the same effect after CBD ligation for 7 days.
Improved Biomechanical Resistance Using an Expanded Polytetrafluoroethylene Composite‐Structure Prosthesis
Authors: Bellón Juan M. , Rodríguez Marta , Serrano Natalia , San‐Martín Antonio Carrera , Buján Julia
Published: April 2004

We designed a composite‐structure (laminar‐reticular) prosthesis using expanded polytetrafluoroethylene (ePTFE) as the biomaterial in an attempt to improve the biomechanical resistance of the same biomaterial in the form of a single lamina. Defects (7 × 5 cm) were created in the abdominal wall of male white New Zealand rabbits (n = 24). The defects, which comprised all the wall layers except the skin, were then repaired with one of two types of ePTFE prosthesis. One was a latest generation laminar prosthesis (DualMesh, or Gore‐Tex) and the other was a composite of in‐house design (CV‐4 mesh composite) made by suturing a mesh woven out of ePTFE thread to an ePTFE lamina. After sacrificing the animals at 14 or 90 days after surgery, implant specimens were subjected to morphologic analysis (light microscopy and scanning electron microscopy); and adhesion formation, neoperitoneal thickness, and biomechanical strength were evaluated. No significant differences were recorded between the two prosthesis regarding the consistency of adhesions or the area occupied by adhesions (DM 0.17 ± 0.06; CV‐4 mesh composite 0.18 ± 0.08 cm2) (p > 0.05). Notably, improved tissue integration was achieved using the composite prosthesis; its reticular side became infiltrated by dense connective tissue that enveloped the mesh filaments. In contrast, the DM prosthesis became encapsulated by host tissue. The neoperitoneum induced by both prostheses was homogeneous and orderly, with a layer of typical mesothelial cells lining its inner surface. The thickness of the neoperitoneum was similar (p > 0.05) for the two implants (385.0 ± 3.4 vs. 390 ± 3.1 μm), although significantly higher (p < 0.05) mechanical resistance values were recorded for the composite prosthesis (26.75 ± 3.71 vs. 14.11 ± 3.71 N). Our findings suggest that the use of a reticular and a laminar ePTFE layer in the same prosthesis leads to better repair and biomechanical behavior compared to the use of a single‐structure laminar implant.
Exploratory Celiotomy in 1474 ad: Brief Case Report
Authors: Donovan Arthur J.
Published: April 2004

In 1474 ad a prisoner in Paris underwent an exploratory celiotomy to ascertain the cause of abdominal “colic.” The patient recovered.
X‐ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold
Authors: Ericsson Ulrika B. , Nordlund Pär , Hallberg B.Martin
Published: April 2004

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine in structural RNA. The pseudouridine synthase TruD, that modifies U13 in tRNA, belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life. We report here the crystal structure of Escherichia coli TruD at 2.0 Å resolution. The structure reveals an overall V‐shaped molecule with an RNA‐binding cleft formed between two domains: a catalytic domain and an insertion domain. The catalytic domain has a fold similar to that of the catalytic domains of previously characterised pseudouridine synthases, whereas the insertion domain displays a novel fold.
Secreted Klotho protein in sera and CSF: implication for post‐translational cleavage in release of Klotho protein from cell membrane
Authors: Imura Akihiro , Iwano Akiko , Tohyama Osamu , Tsuji Yoshihito , Nozaki Kazuhiko , Hashimoto Nobuo , Fujimori Toshihiko , Nabeshima Yo-Ichi
Published: April 2004

Klotho mutant mice exhibit a set of phenotypes resembling human ageing. Although the function of Klotho remains unclear, mediation of its pleiotropic functions by putative humoral factor(s) has been presumed. Newly established antibodies against Klotho allowed the detection of secreted Klotho, a candidate for the putative humoral factor, in sera and cerebrospinal fluid. Surprisingly the secreted Klotho was 130 kDa, in contrast to the 70 kDa predicted form from klotho gene transcripts. The secreted as well as the membrane‐bound Klotho proteins were suggested to form oligomerized complex. These results delineate post‐translation processing of Klotho and possible regulatory mechanisms for secretion of Klotho in vivo.
Different stabilities and denaturation pathways for structurally related aromatic amino acid hydroxylases
Authors: Kleppe Rune , Haavik Jan
Published: April 2004

We have compared the urea stability of the human aromatic amino acid hydroxylases (AAAHs), key enzymes involved in neurotransmitter biosynthesis and amino acid homeostasis. Tyrosine‐, tryptophan‐ and phenylalanine hydroxylase (TH, TPH and PAH, respectively) were transiently activated at low urea concentrations and rapidly inactivated in >3 M urea. The denaturation of TH occurred through two cooperative transitions, with denaturation midpoints of 1.41 ± 0.06 and 5.13 ± 0.05 M urea, respectively. Partially denatured human TH (hTH) retained more of its secondary structure than human PAH (hPAH), and was found to exist as tetramers, whereas hPAH dissociated into dimers. Furthermore, the urea‐induced aggregation of hPAH was 100‐fold higher than for hTH. These results suggest that the denatured state properties of the AAAHs contribute significantly to the stability of these enzymes and their tolerance towards missense mutations.
Neuronal traits are required for glucose‐induced insulin secretion
Authors: Abderrahmani Amar , Niederhauser Guy , Plaisance Valérie , Haefliger Jacques-Antoine , Regazzi Romano , Waeber Gérard
Published: April 2004

The transcriptional repressor RE1 silencer transcription factor (REST) is an important factor that restricts some neuronal traits to neurons. Since these traits are also present in pancreatic β‐cells, we evaluated their role by generating a model of insulin‐secreting cells that express REST. The presence of REST led to a decrease in expression of its known target genes, whereas insulin expression and its cellular content were conserved. As a consequence of REST expression, the capacity to secrete insulin in response to mitochondrial fuels, a particularity of mature β‐cells, was impaired. These data provide evidence that REST target genes are required for an appropriate glucose‐induced insulin secretion.
Image reconstruction for a partially immersed perfectly conducting cylinder using the steady state genetic algorithm
Authors: Li Ching‐Lieh , Chen Shao‐Hon , Yang Chih‐Ming , Chiu Chien‐Ching
Published: April 2004

This paper presents a computational approach to the imaging of a partially immersed perfectly conducting cylinder by the steady state genetic algorithm. A conducting cylinder of unknown shape scatters the incident transverse magnetic (TM) wave in free space while the scattered field is recorded in free space. Based on the boundary condition and the measured scattered field, a set of nonlinear integral equations is derived and the imaging problem is reformulated into an optimization problem. An improved steady state genetic algorithm is employed to search for the global extreme solution. Numerical results demonstrate that, even when the initial guess is far away from the exact one, good reconstruction can be obtained. Numerical results also show that the reconstructed image in the free space area is better than that in the medium area.
Relationships between the stable isotopic signatures of living and fossil foraminifera in Monterey Bay, California
Authors: Martin Jonathan B. , Day Shelley A. , Rathburn Anthony E. , Perez M. Elena , Mahn Chris , Gieskes Joris
Published: April 2004

Fossil foraminifera are critical to paleoceanographic reconstructions including estimates of past episodes of methane venting. These reconstructions rely on benthic foraminifera incorporating and retaining unaltered the ambient isotopic compositions of pore fluids and bottom waters. Comparisons are made here of isotopic compositions of abundant live and fossil foraminifera (Uvigerina peregrina, Epistominella pacifica, Bulimina mexicana, and Globobulimina pacifica) collected in Monterey Bay, CA from two cold seeps (Clam Flats and Extrovert Cliffs) and from sediments ∼5 m outside of the Clam Flats seep. Clam Flats has steep δ13CDIC gradients (to <−45‰), but DIC at Extrovert Cliffs is less enriched in 12C (to approximately −22‰). Oxygen isotope values of fossil foraminifera at Clam Flats are ∼1.5‰ enriched in 18O over the living foraminifera, as well as those of both live and fossil foraminifera at Extrovert Cliffs, suggesting they may have lived during the last glacial maximum. Statistical comparisons (Student's t and Kolmogorov‐Smirnov tests) of δ13C and δ18O values indicate that live and fossil foraminifera come from different populations at both Clam Flats and Extrovert Cliffs. At Clam Flats, the difference appears to result from alteration enriching some fossil foraminifera in 12C over live foraminifera. At Extrovert Cliffs, the fossil foraminifera are enriched in 13C over the live foraminifera, suggesting they lived prior to the onset of venting and thus that venting began recently. The short time of venting at Extrovert Cliffs may be responsible for the less alteration there compared with Clam Flats. These results indicate that preservation of foraminifera is likely to be poor within long‐lived cold seeps, but that foraminifera living in the surrounding sediment may incorporate and preserve broad basin‐wide changes in isotopic compositions of the ambient water.
Evolution of Navajo eclogites and hydration of the mantle wedge below the Colorado Plateau, southwestern United States
Authors: Smith Douglas , Connelly James N. , Manser Kathryn , Moser Desmond E. , Housh Todd B. , McDowell Fred W. , Mack Lawrence E.
Published: April 2004

Eclogite and pyroxenite xenoliths from ultramafic diatremes of the Navajo province on the Colorado Plateau have been analyzed to investigate hydration of continental mantle and effects of low‐angle subduction on the mantle wedge. Xenoliths have been characterized by petrographic and electron probe analysis and by Sm‐Nd, Rb‐Sr, K‐Ar, and O isotopic analysis of mineral separates from one eclogite and by U‐Pb isotopic analysis of zircons from three samples. K‐Ar analysis of phengite establishes eruption of a Garnet Ridge, Arizona, diatreme at 30 Ma. Sm‐Nd and Rb‐Sr analyses of clinopyroxene and garnet from that eclogite document recrystallization shortly preceding eruption. Three zircon fractions have been analyzed from that eclogite and from two others representing the nearby Moses Rock and Mule Ear diatremes. Seven of nine small multigrain fractions scatter about a poorly fit discordia between ca. 35 Ma and 1515 Ma (fractions range from overlapping concordia at the lower intercept to a 207Pb/206Pb age of ca. 1220 Ma). The discordant fractions establish a mid‐Proterozoic zircon component in each eclogite, inconsistent with an origin from basalt of the Farallon plate. The pressure recorded by one of these eclogites (3.3 GPa) exceeds that of an eclogite previously attributed to the Farallon plate. Nonetheless, each of the eclogites contains a fraction of nearly concordant zircons with ages in the range 35 to 41 Ma, and one rock also contains a fraction that is nearly concordant at 70 Ma. These concordant ages are interpreted to record episodic zircon growth during recrystallization of Proterozoic mantle. The concordant zircon ages are consistent with published data that establish recrystallization of Navajo eclogites from 81 to 33 Ma, a time interval similar to that of the Laramide orogeny. The eclogite‐facies recrystallization and growth of new zircon are attributed to the catalytic effects of water introduced into the mantle from the Farallon slab. Water penetrated fracture zones extending for at least tens of kilometers into the mantle wedge above the Farallon slab during low‐angle subduction. Magmatism in the San Juan volcanic field to the northeast of the diatremes may be related to similar hydration.
Convection dynamics and driving mechanism of a small substorm during dominantly IMF By+, Bz+ conditions
Authors: Liang Jun , Sofko G. J. , Donovan E. F. , Watanabe M. , Greenwald R. A.
Published: April 2004

Ground‐based optical, magnetic and radar measurements detected a small substorm on October 9, 2000. Solar wind observations on GEOTAIL revealed a prolonged dominant Bz+ and steady By+ interplanetary magnetic field (IMF) prior to the substorm onset, except for a southward excursion at 0645–0655 UT, and a “square‐wave” IMF Bx‐By structure at 0727–0735 UT. We find that the IMF southward excursion led to the dayside convection enhancement and energy transport into the magnetosphere. When the dayside convection decreased, two pseudobreakups occurred as the consequence of the release of magnetospheric energy into the ionosphere. The substorm onset was associated with the IMF Bx‐By structure in “directly driven” fashion. There was also a Stage‐2 expansion which was internally driven within the magnetotail.
Global and multi‐scale features of solar wind‐magnetosphere coupling: From modeling to forecasting
Authors: Ukhorskiy A. Y. , Sitnov M. I. , Sharma A. S. , Papadopoulos K.
Published: April 2004

The Earth's magnetosphere is a spatially extended nonlinear system driven far from equilibrium by the turbulent solar wind. During substorms it exhibits both global and multi‐scale features which reconciliation has been a long standing issue. This paper presents a data‐derived model of the solar wind‐magnetosphere coupling that combines a nonlinear dynamical description of the global features with a statistical description of the multi‐scale aspects. This approach yields deterministic predictions of the global component of magnetospheric dynamics and probabilistic predictions of its multi‐scale features.
Three separate ion populations observed simultaneously in the plasma sheet boundary layer in the distant geomagnetic tail
Authors: Saito Yoshifumi , Mukai Toshifumi , Terasawa Toshio , Machida Shinobu
Published: April 2004

The detailed structure of ion velocity space distributions in the plasma sheet boundary layer (PSBL) in the distant geomagnetic tail has been investigated. Three separate, tailward‐streaming ion populations have been observed simultaneously in PSBL crossings in which the inner edge of the PSBL was identified as a slow mode shock: cold, low‐energy, ions presumably of ionospheric origin that fill much of the tail lobes, and two more energetic populations. The more energetic of these latter populations, which was concentrated in the outer (lobe) layers of the PSBL, had a “kidney bean” shape. The less energetic population had a well‐defined low‐energy cutoff that decreased with increasing penetration into the PSBL from the lobe. The sources of these two populations may be cold lobe ions accelerated in the current sheet near the distant neutral line and plasma sheet ions that leak across the shock, respectively.
Mineral maps of the Moon
Authors: Lucey Paul G.
Published: April 2004

Global maps of the distribution of plagioclase, orthopyroxene, clinopyroxene and olivine on the Moon were derived from radiative transfer analysis of 400,000 Clementine UVVIS spectra. Plagioclase inversely correlates with iron while clinopyroxene positively correlates with iron showing these are the major carriers of aluminum and iron respectively. The distribution of olivine in the maria agrees with previous studies; in the highlands the abundance of olivine is low but ubiquitous at a few percent, except within the South Pole‐Aitken basin where it is only present in very small exposures. In the very anorthositic farside highlands, olivine is often the sole mafic mineral. The abundance of orthopyroxene is generally low, excepting elevated abundances in the nearside highlands and in areas near and within South Pole‐Aitken basin. Mare units with elevated abundances of orthopyroxene are found in some mare and cryptomare deposits distant from the sample return sites.
Dynamic deformation of Seguam Island, Aleutian Islands, Alaska, 1993–2000: Implications for magmatic and hydrothermal processes
Authors: Price Evelyn J.
Published: April 2004

The most recent volcanic eruption on Seguam Island was detected in December 1992 and lasted until July or August of 1993. A series of radar interferograms, generated from imagery collected by the European Space Agency's ERS‐1 and ERS‐2 satellites, are used here to map the spatial and temporal evolution of the deformation field from June of 1993 to September of 2000. This evolution consists of a coeruptive period of uplift surrounding the eruption; two posteruptive subsidence signals, centered within each of the two calderas on the island, each of which lasted for 4 years after the end of the eruption; and then uplift beneath the caldera on the eastern side of the island and the surrounding region from mid 1999 through the end of the time series in September 2000. The locations and magnitudes of the sources of the deformation are inferred from the interferometric synthetic aperture radar displacement data using an elastic half‐space Earth model with multiple Mogi point sources and a Levenburg‐Marquardt nonlinear inversion technique. This inference reveals that the sources of subsidence are located within the upper 2 km of the Earth's crust, while the sources of uplift are located below 2.5 km. The locations of dilatational sources are consistent with a model of the volcanic system where ascending magma accumulates below a density or structural boundary near 2.5–3 km depth. The subsidence signals are most likely associated with cooling of shallow magmatic bodies emplaced during the 1992–1993 eruption. However, the possibility that they indicate a combination of magma cooling and depressurization of a hydrothermal system cannot be ruled out using the geodetic data alone. Implications for the long‐term evolution of the volcanic edifice are discussed.
Synoptics of dust intrusion days from the African continent into the Atlantic Ocean
Authors: Barkan J. , Kutiel H. , Alpert P. , Kishcha P.
Published: April 2004

The phenomenon of dust intrusion from north Africa into the Atlantic Ocean was examined on daily bases for the month of July from 1983 to 1988 (184 cases). Composite patterns of wind flows and geopotential heights for the intrusion versus no‐intrusion cases as well as the difference between them (intrusion minus no intrusion), in the area (60°W–25°E, 0°–60°N), were analyzed. For both intrusion and no‐intrusion days a closed high pressure, centered at approximately (45°W, 32°N), was found, with a ridge northeastward. East of the ridge was a trough located to the west of the European and the north African coast. Further east was a closed high in the western Sahara with a ridge northeastward. Each of the maps presenting the difference between the two aforementioned variables shows two highs: one over western Europe and the other, quite strong, west of the African coast on the 24°N–25°N latitudes. Between them, centered about (15°W, 37°N), there is a low‐pressure area. As a result of the higher pressure at the African anticyclone in the intrusion cases, an easterly‐northeasterly flow dominates at the latitudes 18°N–22°N, which presumably causes the dust intrusion from the continent into the Atlantic. Correlation between the Total Ozone Mapping Spectrometer aerosol index on the one hand and the wind magnitude and the u and v components on the other hand was also analyzed for the entire data set. Correlation coefficients of r = 0.52, r = −0.46, and r = −0.27 were found. Analysis of two extreme intrusion and no‐intrusion cases in July 1983 demonstrates the synoptic situation that allows the Saharan dust to reach England and NW Europe.
Azimuthal anisotropy of longwave and infrared window radiances from the Clouds and the Earth's Radiant Energy System on the Tropical Rainfall Measuring Mission and Terra satellites
Authors: Minnis Patrick , Gambheer Arvind V. , Doelling David R.
Published: April 2004

Shadowing by vegetation, landforms, or clouds can reduce the surface temperature relative to unshadowed portions of the same land area. This shading effect can cause azimuthal variation of the outgoing infrared radiance that is currently not taken into account in remote sensing and Earth radiation budget analyses. In this paper, multiangle longwave (LW) (5–200 μm) and window (WN) (8–12 μm) radiances taken by the Clouds and the Earth's Radiant Energy System (CERES) rotating azimuth plane scanner on the Tropical Rainfall Measuring Mission (TRMM) and Terra satellites are used to determine the azimuthal anisotropy of LW and WN fields over all solar zenith angles and surface types in clear and cloudy conditions. The azimuthal component of the anisotropy is isolated by constructing limb‐darkening models for each category of surface type and topography in each solar zenith angle (SZA) bin. The viewing zenith angle dependence of WN and LW radiances in clear scenes depends on the SZA, possibly because of changes in the boundary layer temperature structure during the day. The observed mean radiances, in general, are greater when viewing the sunlit hemisphere (backscattering) than when viewing the shaded (forward scattering) hemisphere. This forward‐back contrast increases with increasing terrain roughness and is stronger for surfaces with open vegetation such as shrubs and grass than for contiguous vegetation like forests. The anisotropy is less well defined for barren deserts. Maximum anisotropy occurs for SZAs between 48° and 70°. This paper provides the first evidence that clouds also induce longwave azimuthal anisotropy. Strong forward‐back radiance contrast is evident for partly, mostly, and overcast scenes for SZA < 48°. The contrast disappears for overcast scenes and decreases for partly and mostly cloudy scenes at higher SZAs. The TRMM sampling is limited and causes some biases at particular angle sets but overall provides a reasonable depiction of the anisotropy at all SZAs. Terra yields a more accurate anisotropy characterization but only for SZAs between 48° and 70°. A simple model constructed from the TRMM results for clear scenes reduces clear‐sky temperature prediction RMS errors by 38% or more while minimizing the biases associated with azimuthal anisotropy. The model should yield similar or better reductions in the errors associated with retrievals of skin temperature or LW fluxes, especially those from geostationary satellites. In addition, future analyses of combined TRMM, Terra, and Aqua CERES data will likely provide more accurate correction models that could further reduce errors in surface skin temperature and radiative flux for both clear and cloudy scenes.
Lumped element models of double negative metamaterial‐based transmission lines
Authors: Ziolkowski Richard W. , Cheng Ching‐Ying
Published: April 2004

Realizations of double negative (DNG) metamaterials using lumped element representations of lossless and lossy transmission lines are reported. Double negative media are artificial materials in which the permittivity and permeability are both negative. Analytical and numerical results for a variety of transmission line network representations explain how they can exhibit low‐pass, high‐pass, and band‐pass dispersion characteristics when a DNG medium is produced in a specified frequency region of interest. Detailed dispersion properties of these various configurations are given. Comparisons with previous formulations are provided. It is shown conclusively that the DNG metamaterials occur only when the overall equivalent transmission line per‐unit‐length impedance is capacitive and the overall equivalent transmission line per‐unit‐length admittance is inductive. A convenient categorization of the possible DNG medium designs in transmission line constructs or more complex 2‐D or 3‐D inclusion based structures thus is provided.
The boundaries of the distribution of somatic hypermutation of rearranged immunoglobulin variable genes
Authors: Blanden Robert V , Franklin Andrew , Steele Edward J
Published: April 2004

Available evidence about the mechanisms and distribution of somatic hypermutation (SHM) of rearranged immunoglobulin (IgV) genes is reviewed with particular emphasis on the 5′ boundary. In heavy (H) chain genes, the 5′ boundary of SHM is the transcription start site; in contrast to κ light (L) chain genes, it is located in the leader (L) intron. DNA‐based models of SHM cannot account for this difference. However, an updated reverse transcriptase (RT)‐based model invoking error‐prone RT activity of DNA polymerase η copying IgV pre‐mRNA templates to produce cDNA of the transcribed strand (TS) of IgV DNA, which then replaces the corresponding section of the original TS, can explain the difference. This explanation incorporates recent knowledge of pre‐mRNA processing, in particular, binding of the splicing‐associated protein termed U2AF to a pyrimidine‐rich tract in the L intron of pre‐mRNA of κ L chains that may block RT progression further upstream to the end of the pre‐mRNA template (transcription start site). Reasons why this block may not occur in H chains and other aspects of the updated RT‐model are discussed.
Some Scaling Principles for the Immune System
Authors: Wiegel Frederik W , Perelson Alan S
Published: April 2004

Using recent progress in biological scaling, we explore the way in which the immune system of an animal scales with its mass (M). It is shown that the number of cells in a single clone of B cells should scale asMand that the B‐cell repertoire scales asln(cM), wherecis a constant. The time that a B cell needs to circulate once through the organism is shown to scale asM1/4ln(cM). It is suggested that the scaling of other cell populations in the immune system could be derived from these scaling relations for B cells.
CD4+ T cells cross‐compete for MHC class II‐restricted peptide antigen complexes on the surface of antigen presenting cells
Authors: Hayball John D , Robinson Bruce W S , Lake Richard A
Published: April 2004

CD4+ T cells are activated upon recognition of peptide antigen in the context of MHC class II molecules, expressed by specialized APC. In this study, we show that CD4+ T cells cross‐compete for antigenic complexes on the surface of APC, inhibiting activation of other potentially reactive T cells of the same and differing specificities. T cells with either a higher affinity receptor for antigen or which have undergone prior activation compete more efficiently than low affinity or resting T cells. This implies that T‐cell avidity for the APC is primarily responsible for the competitive advantage. We also provide evidence that the mechanism for competition is steric hindrance of the surface of the APC, rather than T‐cell‐mediated sequestration or internalization of antigenic complexes. This is because removal of competing T cells restores the antigenic potential of the APC, and APC fixation does not abrogate competition. Demonstration that competition for access to APC can also occur in vivo suggests that this process may represent a physiologically important mechanism for influencing the quality and quantity of CD4+ T‐cell responses.
Gene expression signatures in lymphoid tumours
Authors: Kees Ursula R
Published: April 2004

Lymphoid tumours comprise the acute and chronic leukaemias, the broad spectrum of lymphomas, including Hodgkin's disease, and multiple myeloma. The subdivision of the acute leukaemias according to the proliferating type of white blood cells has had a major impact on the care of these patients. More recently, specific chromosomal translocations have been used to identify patients who may benefit from more intensive therapies. The novel high‐throughput genomic technologies, such as microarrays, provide new avenues for the molecular diagnosis of the haematological malignancies. Rapid advances in genome sequencing and gene expression profiling provide unprecedented opportunities to identify specific genes involved in complex biological processes, including tumorigenesis. The features of microarray technology and the variety of experimental approaches to elucidate lymphoid malignancies are discussed. Microarray technology has the potential to lead to more accurate prognostic assessment for patients and is expected to ultimately allow the clinician to select therapies optimally suited to each patient.
Living with the ups and downs of the two signal model
Authors: Bretscher Peter
Published: April 2004

I am delighted to have been asked to join in the celebrations of Bob Blanden's scientific life. Though I have never formally collaborated with Bob, it has been a pleasure to interact with him on many occasions, and so it was particularly touching to be invited. I have always had a special regard for Bob as a gentleman scientist.
Memories of virus‐specific CD8+ T cells
Authors: Doherty Peter C , Turner Stephen J
Published: April 2004

This brief review focuses on the way that our understanding of virus‐specific CD8+ T‐cell‐mediated immunity evolved, giving particular attention to the early impact of the program at the Australian National University. The story developed through a sequence of distinct eras, each of which can be defined in the context of the technologies available at that time. The progress has been enormous, but there is a great deal still to be learned. A particular challenge is to use what we know for human benefit.
Compound Brushing Explained
Authors: Chen Hong
Published: April 2004

This paper proposes a conceptual model called compound brushing for modeling the brushing techniques used in dynamic data visualization. In this approach, brushing techniques are modeled as higraphs with five types of basic entities: data, selection, device, renderer, and transformation. Using this model, a flexible visual programming tool is designed not only to configure and control various common types of brushing techniques currently used in dynamic data visualization but also to investigate new brushing techniques.
Paraquat resistance in a population of Lolium rigidum
Authors: Yu Qin , Cairns Andrew , Powles Stephen B.
Published: April 2004

The first case of field-evolved paraquat resistance in a population of Lolium rigidum Gaud. (from the Western Cape, South Africa) was confirmed and the mechanism of resistance investigated. The LD50 for the resistant population (R) was 404 g ha–1, some 14 times greater than for the herbicide-susceptible (S) population (30 g ha–1). In addition, the R population was found to be more resistant to paraquat when kept at low temperature (15°C) than when kept at 30°C after paraquat treatment. The R population is normally affected by herbicides with other modes of action. No differences were found in the interaction of paraquat with Photosystem I in thylakoids isolated from the R and the S populations. Constitutive levels of the antioxidative enzymes superoxide dismutase (SOD) and ascorbate peroxidase (APX) did not differ significantly between the two populations and these enzymes responded similarly to paraquat treatment. When [14C] paraquat was applied as droplets to intact plant leaves, similar leaf uptake of [14C] paraquat occurred in the R and S populations. However, quantification data and phosphor imaging revealed restricted translocation of [14C] paraquat to untreated leaves in the R compared to S population. The results of this study with this resistant L. rigidum population from South Africa resemble those found in R biotypes of Hordeum spp. from Australia. The resistance is suggested to be primarily due to sequestration of paraquat, limiting its translocation within the plants. The exact site and mechanism of paraquat sequestration remains to be determined.
RNA interference microarrays: High-throughput loss-of-function genetics in mammalian cells
Authors: Silva Jose M. , Mizuno Hana , Brady Amy , Lucito Robert , Hannon Gregory J.
Published: April 2004

RNA interference (RNAi) is a biological process in which a doubles-tranded RNA directs the silencing of target genes in a sequence-specific manner. Exogenously delivered or endogenously encoded double-stranded RNAs can enter the RNAi pathway and guide the suppression of transgenes and cellular genes. This technique has emerged as a powerful tool for reverse genetic studies aimed toward the elucidation of gene function in numerous biological models. Two approaches, the use of small interfering RNAs and short hairpin RNAs (shRNAs), have been developed to permit the application of RNAi technology in mammalian cells. Here we describe the use of a shRNA-based live-cell microarray that allows simple, low-cost, high-throughput screening of phenotypes caused by the silencing of specific endogenous genes. This approach is a variation of “reverse transfection” in which mammalian cells are cultured on a microarray slide spotted with different shRNAs in a transfection carrier. Individual cell clusters become transfected with a defined shRNA that directs the inhibition of a particular gene of interest, potentially producing a specific phenotype. We have validated this approach by targeting genes involved in cytokinesis and proteasome-mediated proteolysis.