bluuebunny/crossref_metadata_2025 huggingface dataset:
A template search reveals mechanistic similarities and differences in β‐ketoacyl synthases (KAS) and related enzymes
Authors: Dawe Jennifer H. , Porter Craig T. , Thornton Janet M. , Tabor Alethea B.
Published: July 2003

A detailed comparison of the active sites in β‐ketoacyl synthases (KAS) and related enzymes has been made. Using three‐dimensional templates of the three catalytic residues to scan the protein structural database reveals differences in both the geometry and the catalytic role of equivalent residues in different members of the family. The template based on the catalytic cysteine and two histidines in the KAS I and II is totally specific for this family, with no false hits. However, the role of the histidines in catalysis is different between KAS I/II and thiolase on the one hand and KAS III/chalcone synthase on the other. In contrast, a template comprising only cysteine and one histidine is not specific with many hits including members of the KAS family, metal binding sites, other active sites in nonhomologous proteins, and some “random” nonactive sites. Proteins 2003;52:427–435. © 2003 Wiley‐Liss, Inc.
Deciphering a novel thioredoxin‐like fold family
Authors: Kinch Lisa N. , Baker David , Grishin Nick V.
Published: July 2003

Sequence ‐ and structure‐based searching strategies have proven useful in the identification of remote homologs and have facilitated both structural and functional predictions of many uncharacterized protein families. We implement these strategies to predict the structure of and to classify a previously uncharacterized cluster of orthologs (COG3019) in the thioredoxin‐like fold superfamily. The results of each searching method indicate that thioltransferases are the closest structural family to COG3019. We substantiate this conclusion using the ab initio structure prediction method rosetta, which generates a thioredoxin‐like fold similar to that of the glutaredoxin‐like thioltransferase (NrdH) for a COG3019 target sequence. This structural model contains the thiol‐redox functional motif CYS‐X‐X‐CYS in close proximity to other absolutely conserved COG3019 residues, defining a novel thioredoxin‐like active site that potentially binds metal ions. Finally, the rosetta‐derived model structure assists us in assembling a global multiple‐sequence alignment of COG3019 with two other thioredoxin‐like fold families, the thioltransferases and the bacterial arsenate reductases (ArsC). Proteins 2003;52:323–331. Published 2003 Wiley‐Liss, Inc.
Comparative analysis of structural properties of the C‐type‐lectin‐like domain (CTLD)
Authors: Zelensky Alex N. , Gready Jill E.
Published: July 2003

The superfamily of proteins containing the C‐type‐lectin‐like domain (CTLD) is a group of abundant extracellular metazoan proteins characterized by evolutionary flexibility and functional versatility. Several CTLDs are also found in parasitic prokaryotes and viruses. The 37 distinct currently available CTLD structures demonstrate significant structural conservation despite low or undetectable sequence similarity. Our aim in this study was to perform an extensive comparative analysis of all available CTLD structures to establish the most conserved structural features of the fold, and to test and extend the early analysis of Drickamer. By implication, these features should be those critical for maintenance of integrity of the fold. By analyzing CTLD structures superimposed by several methods, we have established groups of conserved structural positions involved in fold maintenance but not in ligand binding; these are consistent with the fold's known functional flexibility. In addition to the well‐recognized disulfide bridges, groups of conserved residues are involved in hydrophobic interactions stabilizing the core of the fold and the long loop region, and in an α2‐β1–β5 polar interaction. Evaluation of the conclusions of the structure comparison study compared with alignments of all available human, mouse and Caenorhabditis elegans CTLD sequences showed that conservation patterns are preserved throughout the whole CTLD sequence space. Our observations provide an improved understanding of CTLD structure, and will help in identification of new CTLDs and the mechanisms that drive and constrain the coevolution of the structure and function of the fold. Proteins 2003;52:466–477. © 2003 Wiley‐Liss, Inc.
An Information‐Theoretic Approach to Descriptor Selection for Database Profiling and QSAR Modeling
Authors: Godden Jeffrey W. , Bajorath Jürgen
Published: July 2003

In order to rationalize the selection of molecular descriptors for QSAR and other applications, we have adapted the Shannon entropy concept that was originally developed in digital communication theory. The approach has been extended to facilitate the large‐scale analysis of molecular descriptors and their information content in diverse compound databases. This has enabled us to identify descriptors with consistently high information content. Furthermore, it has been possible to select descriptors that are sensitive to systematic property differences in diverse compound collections (synthetic compounds, natural products, drug‐like molecules, or drugs) and, in addition, to quantify such database‐specific differences. Selection of descriptors based on information content has been proven useful for binary QSAR analysis. In this review, we describe the principles of entropy‐based descriptor selection and discuss different applications.
Neighborhood Behavior. Fuzzy Molecular Descriptors and their Influence on the Relationship between Structural Similarity and Property Similarity
Authors: Horvath Dragos , Mao Boryeu
Published: July 2003

The similarity principle, stating that molecules of similar structure behave similarly, is an important concept in medicinal chemistry. A properly characterized and well‐understood neighborhood behavior of the structural space versus the activity space is fundamental for the application of the similarity principle in computational chemistry. In this work we focus on the utilization of a fuzzy pharmacophore description of molecular similarity and specifically on the influence of fuzzy pharmacophore pattern matching on the neighborhood behavior (NB) of the similarity scoring scheme. NB is defined as a structure‐activity relationship between the intermolecular distances/dissimilarities in the pharmacophore fingerprint structure space and the corresponding activity differences, formally seen as intermolecular distances in the activity spaces. The latter are defined on hand of a wide variety of datasets on pharmacological and physico‐chemical properties and property profiles. We also investigate the clustering behavior (CB), where the structure‐activity relationship is described in terms of distance‐derived associations of compounds into clusters via classical hierarchical clustering procedures. The neighborhood behavior and the cluster behavior provide alternative and complementary criteria for evaluating the pertinence of a molecular similarity metric.
Genetic Neural Networks for Functional Approximation
Authors: Chiu Ting‐Lan , So Sung‐Sau
Published: July 2003

Quantitative structure‐activity relationship (QSAR) analysis is a commonly used ligand‐based molecular design method for the lead optimization process in the pharmaceutical industry. Typically, development of a QSAR model goes through the following stages: descriptor generation, function approximation (including feature selection and model construction), and model validation. This article highlights a promising genetic neural network (GNN) method for function approximation in QSAR and reviews its underlying theoretical concepts, techniques, and recent applications.
ChemSpaceShuttle: A tool for data mining in drug discovery by classification, projection, and 3D visualization
Authors: Givehchi Alireza , Dietrich Axel , Wrede Paul , Schneider Gisbert
Published: July 2003

The ChemSpaceShuttle toolbox provides a graphical interface allowing for ligand‐based design of focused compound libraries by means of linear and non‐linear projection techniques and clustering algorithms. The software implements a non‐linear encoder network and non‐linear partial least squares for the projection of high‐dimensional descriptor vectors into a three dimensional space for visualisation. Compound clustering by a self‐organising map (SOM) is incorporated. Visualization can facilitate the selection of compounds with desired properties from large compound libraries. Two sample applications are presented: similarity‐based compound selection for focused library design, and classification of drugs and nondrugs. A version of ChemSpaceShuttle is freely available at URL: http://gecco.org.chemie.uni‐frankfurt.de/gecco.html.
Threat and trauma: An overview
Authors: Macy Robert D. , Barry Susanna , Noam Gil G.
Published: July 2003

Common responses after exposure to threat include reexperiencing the event, intrusive thoughts and images, hyperarousal, avoidance and numbing, a sense of a foreshortened future, and shattered assumptions about control and safety.
Community‐based trauma response for youth
Authors: Macy Robert D.
Published: July 2003

The “golden rule” of youth trauma response is that those most affected by the trauma or threat event must be afforded an ongoing opportunity to play a central role in the resolution of and recovery from the trauma and its aftermath.
Healing in familiar settings: Support for children and youth in the classroom and community
Authors: Macy Robert D. , Johnson Macy Dicki , Gross Steven I. , Brighton Pamela
Published: July 2003

The Classroom‐Based Intervention emphasizes a specific theme each week to allow children to construct safe places to express their stories and develop coping strategies in a group environment.
A culture of threat: Right‐wing extremism and negative identity formation in German youth
Authors: Edelstein Wolfgang
Published: July 2003

The specific case of Eastern Germany is illustrative of a more general framework for how identity formation, family processes, and humiliation, alienation, and deprivation are linked to local conditions or situational contexts.
Capacity building in trauma therapy and trauma research in Bosnia‐Herzegovina
Authors: Röper Gisela , Gavranidou Maria
Published: July 2003

When Bosnia‐Herzegovina was thrown into war in the summer of 1991, one and a half million people lost their homes and were in flight. It was clear from the beginning that the extent of trauma would be enormous and evident for generations to come.
Threat in the life of Iraqi children
Authors: Dyregrov Atle , Raundalen Magne
Published: July 2003

Given the magnitude of the possible exposure and duration of distress evidenced by Iraqi children, there is strong reason to expect that this, in combination with malnutrition and reduced school attendance, will dramatically reduce their learning potential.
Time frames
Authors: Harris William W.
Published: July 2003

Response to the events of 9/11 evidenced the need for greater local and national capacity to meet the needs of children and families before, during, and after future attacks
Electrical conductivity images of Quaternary faults and Tertiary detachments in the California Basin and Range
Authors: Park Stephen K. , Wernicke Brian
Published: July 2003

Comparison of an electrical resistivity section derived from magnetotelluric (MT) data to a geologic section extending eastward from the Sierra Nevada near latitude 36°20′N shows that the crust is dominated by steeply dipping conductive features that correlate with active strike‐slip faults. While there is a subhorizontal conductor at a depth ∼20 km beneath some of the profile, it is broken by vertical structures associated with the active strike‐slip faults. The continuous subhorizontal anomalies in the lower crust typically observed in extensional regions are therefore absent in the resistivity section. The present‐day strike‐slip tectonic regime as indicated by geodetic data in this part of the Basin and Range is not producing features that could be inferred to indicate subhorizontal shear zones resulting from lateral crustal flow during extension. Because the Miocene tectonic regime resulted in the formation of metamorphic core complexes and thus was accompanied by such flow, the present regime appears to represent a fundamental transition in the mode of crustal deformation in the region. A serendipitous result of our study was the identification on resistivity sections of carbonate aquifers in the upper crust. Comparison of resistivities from the MT section to measured fluid resistivities from springs and boreholes suggests that the aquifers must be heterogeneous, with more saline brines occupying the deepest portions of the carbonates.
Mesozoic and Cenozoic tectonic evolution of the Shiquanhe area of western Tibet
Authors: Kapp Paul , Murphy Michael A. , Yin An , Harrison T. Mark , Ding Lin , Guo Jinghu
Published: July 2003

In the Shiquanhe area of far‐western Tibet, mid‐Cretaceous strata lie unconformable on ophiolitic melange and Jurassic flysch associated with the Bangong‐Nujiang suture zone. On the basis of our mapping and geochronologic studies, we suggest that these Cretaceous strata were shortened by >57% over a north south distance of 50 km during Late Cretaceous‐early Tertiary time. The Late Cretaceous Narangjiapo thrust placed Permian strata >20 km over ophiolitic melange and Cretaceous strata. North of the Narangjiapo thrust, >40 km of shortening was accommodated by the Late Cretaceous‐early Tertiary south directed Jaggang thrust system that involves Jurassic flysch and Cretaceous strata, and roots into a decollement within ophiolitic melange. The most recent shortening was accommodated to the south of the Narangjiapo thrust, along the north dipping Shiquanhe thrust. The Shiquanhe thrust cuts flat‐lying 22.6 ± 0.3 Ma volcanic rocks and underlying folded, Tertiary nonmarine strata in its footwall and was likely active during slip along the Oligocene Gangdese thrust system of southern Tibet. Ophiolitic melange and structurally overlying Jurassic flysch near Shiquanhe are interpreted to represent remnants of a subduction‐accretion complex and forearc basin, respectively, that were obducted southward onto the margin of the Lhasa terrane during Late Jurassic‐Early Cretaceous closure of the Bangong‐Nujiang Ocean. Subsequent imbrication of the obducted sheet could have produced the two east‐west trending belts of ophiolitic melanges, separated by ∼100 km, in western Tibet. Late Cretaceous‐early Tertiary thin‐skinned shortening may have been accommodated in the deeper crust by northward underthrusting and duplexing of Lhasa terrane rocks beneath the obducted ophiolitic melange and the Qiangtang terrane to the north.
Proterozoic history of the Borborema province (NE Brazil): Correlations with neighboring cratons and Pan‐African belts and implications for the evolution of western Gondwana
Authors: Neves Sérgio Pacheco
Published: July 2003

Geological and geochronological correlations between Borborema province (NE Brazil) and neighboring cratons and Brasiliano/Pan‐African belts indicate that the Amazonian, West African, and São Francisco/Congo cratons and the basement of the Araguaia, Borborema, Nigerian, and Cameroon provinces were part of the Atlantica supercontinent. This continent was established at the end of the Transamazonian/Eburnean cycle (∼2.0 Ga) and, apart from ubiquitous taphrogenesis in the 1.8–1.7 Ga interval, remained largely unaffected for the following 1 Ga. Around 1 Ga an important magmatic event in Borborema province correlates with rifting episodes and anorogenic magmatism in the São Francisco, Congo, and Amazonian cratons. These events are interpreted as failed attempts to break up Atlantica, which at this time may have been part of the larger Rodinia supercontinent. Renewed extensional conditions in Borborema province during the middle and late Neoproterozoic are attributed to far‐field stresses transmitted to the interior of Atlantica by outwardly dipping subduction zones that encircled its northern (present day coordinates) portion. The rarity of petrotectonic assemblages typical of subduction zone environments indicates that extension did not evolve enough to form large oceans basins and thus that the Borborema province essentially includes reworked intracontinental domains. Regional deformation and metamorphism, starting at 650–640 Ma, and shear zone development, beginning at 590–595 Ma, were continuously developed through time and were synchronous throughout most of the Borborema, Araguaia, Cameroon, and Nigerian provinces. Postorogenic conditions were reached 540–530 Myr ago, while active deformation was still occurring in other belts that accreted around Atlantica to form western Gondwana.
Extreme chemical variability as a consequence of channelized melt transport
Authors: Spiegelman Marc , Kelemen Peter B.
Published: July 2003

The spatial and temporal variability of chemical signals in lavas, residues, and melt inclusions provides important constraints on source heterogeneity, the efficiency of convection, and melt transport processes in the mantle. The past decade has seen an impressive increase in the number, precision, and spatial resolution of chemical analyses. However, as resolution has increased, the picture of variation that emerges has become increasingly difficult to understand. For example, mid‐ocean ridge basalts can display large variations in trace element concentration on scales from 1000 km of ridge to melt inclusions in 500 micron crystals. These observations suggest that melt transport processes do not readily homogenize partially molten regions. While some of the observed variability is due to source variations, a large proportion could be the consequence of magma transport in channelized systems. We present results of numerical models that calculate the trace element signatures of high‐porosity dissolution channels produced by reactive fluid flow. These models were originally developed to explain the organization of melt transport networks, based on observations of “replacive dunites” found in ophiolites. Channelized flow can produce orders of magnitude variation in the concentrations of highly incompatible elements, even for idealized systems with a homogeneous source, constant bulk partition coefficients, and equilibrium transport. Most importantly, the full range of variability may be found in each channel because channelization can transpose the chemical variability produced by melting throughout the melting column into horizontal variability across the width of the channel. The centers of channels contain trace element–enriched melts from depth, while the edges of the channels transport highly depleted melts extracted from the interchannel regions at shallower levels. As dunite channels may be spaced on scales of 1–100 m in the mantle, this mechanism allows highly variable melt compositions to be delivered to the Moho on small length scales. The chemical variation produced in the models is consistent with that seen in melt inclusion suites, lavas, and residual mantle peridotites dredged from the ridges and sampled in ophiolites.
Spatio‐temporal structure of storm‐time chorus
Authors: Santolík O. , Gurnett D. A. , Pickett J. S. , Parrot M. , Cornilleau‐Wehrlin N.
Published: July 2003

We discuss chorus emissions measured by the four Cluster spacecraft at close separations during a geomagnetically disturbed period on 18 April 2002. We analyze the lower band of chorus below one half of the electron cyclotron frequency, measured at a radial distance of 4.4 Earth's radii, within a 2000 km long source region located close to the equator. The characteristic wave vector directions in this region are nearly parallel to the field lines and the multipoint measurement demonstrates the dynamic character of the chorus source region, changing the Poynting flux direction at time scales shorter than a few seconds. The electric field waveforms of the chorus wave packets (forming separate chorus elements on power spectrograms) show a fine structure consisting of subpackets with a maximum amplitude above 30 mV/m. To study this fine structure we have used a sine‐wave parametric model with a variable amplitude. The subpackets typically start with an exponential growth phase, and after reaching the saturation amplitude they often show an exponential decay phase. The duration of subpackets is variable from a few milliseconds to a few tens of milliseconds, and they appear in the waveform randomly, with no clear periodicity. The obtained growth rate (ratio of the imaginary part to the real part of the wave frequency) is highly variable from case to case with values obtained between a few thousandths and a few hundredths. The same chorus wave packets simultaneously observed on the different closely separated spacecraft appear to have a different internal subpacket structure. The characteristic scale of the subpackets can thus be lower than tens of kilometers in the plane perpendicular to the field line, or hundreds of kilometers parallel to the field line (corresponding to a characteristic time scale of few milliseconds during the propagation of the entire wave packet). Using delays of time‐frequency curves obtained on different spacecraft, we have found the same propagation direction as obtained from the simultaneous Poynting flux calculations. The delays roughly correspond to the whistler‐mode group velocity estimated from the cold plasma theory. We have also observed delays corresponding to antiparallel propagation directions for two neighboring chorus wave packets, less than 0.1 s apart.
On the eddy‐Kuroshio interaction: Meander formation process
Authors: Waseda Takuji , Mitsudera Humio , Taguchi Bunmei , Yoshikawa Yasushi
Published: July 2003

The Kuroshio flows along the southern coast of Japan during its non‐large‐meandering state, then separates from the coast near the Kii Peninsula and attaches at the north of the Izu Ridge. The amplitude of the offshore displacement of the Kuroshio changes as a result of mesoscale perturbations. Satellite SSH and SST observations (TOPEX/Poseidon: T/P and NOAA AVHRR) have suggested that the short‐term Kuroshio meander formation is triggered by anticyclonic eddies originating in the Kuroshio Extension. To simulate such an event, a numerical experiment using a high‐resolution regional GCM was conducted by initializing the eddy with the observed T/P sea level anomaly. An anticyclonic eddy was injected to the south of the Kuroshio (140°E, 30°N) by means of sequential data assimilation of the T/P data of October 1992 for 30 days. The volume transport of the model Kuroshio was kept constant at 25 Sv, a condition which would not cause large meander of the Kuroshio. The simulation successfully reproduced the four phases of the interaction: (1) westward propagation of the eddy; (2) advection of the eddy by the Kuroshio; (3) meander formation; and (4) detachment of the eddy from the Kuroshio and their repetition. The analyses revealed that the inshore high potential vorticity (PV) water is generated at the sharp coastal topography (the Kii peninsula). The cyclonic eddies shed will eventually coalesce with the existing inshore cyclonic circulation and the meander grows. During the growth of the meander, the necessary barotropic kinetic energy is produced through the shallowing of the thermocline of the anticyclonic eddy as it elongates and splits. The growth of the meander ceases when the split anticyclonic eddies merge, the thermocline deepens, and the eddy detaches itself from the Kuroshio as a result of its own westward thrust. Simultaneously, the accumulated high PV inshore is released to the Kuroshio Extension region as cyclonic eddies. This study provides evidence for the active role of the anticyclonic eddy in causing the variability of the Kuroshio path and suggests a mechanism of rapid discharge/recharge of the available potential energy of the eddy and production/release of high PV inshore Kuroshio to cause the short‐term Kuroshio meander.
Haze layer characterization and associated meteorological controls along the eastern coastal region of southern Africa
Authors: Stein Deborah C. , Swap Robert J. , Greco Steven , Piketh Stuart J. , Macko Stephen A. , Doddridge Bruce G. , Elias Thierry , Bruintjes Roelof T.
Published: July 2003

Episodes of regionally extensive haze were observed over southern African during the dry season intensive of the Southern African Regional Science Initiative (SAFARI 2000). Several case studies of southern African haze layers were examined and characterized in terms of physical structure as they exited off of the eastern coastal region of southern Africa. In situ observations of aerosols and trace gases and their physical and chemical characteristics were collected on board South African Weather Service Aerocommander research aircraft. Haze structure, based on these measurements, is examined as it varies with synoptic type. Despite strong differences in the observed ENSO regime between SAFARI 2000 and that observed during the Southern African Fire‐Atmosphere Research Initiative (SAFARI‐92) and their respective aerosol accumulation mechanisms (col Rrgions/weak anticyclones versus strong anticyclones), a surprising degree of consistency in the observed vertical structure of the lower troposphere was found in southern Africa.
Neogene carbonate burial in the Pacific Ocean
Authors: Lyle Mitchell
Published: July 2003

I have compiled CaCO3 mass accumulation rates (MARs) for the period 0–25 Ma for 144 Deep Sea Drilling Project and Ocean Drilling Program drill sites in the Pacific in order to investigate the history of CaCO3 burial in the world's largest ocean basin. This is the first synthesis of data since the beginning of the Ocean Drilling Program. Sedimentation rates, CaCO3 contents, and bulk density were estimated for 0.5 Myr time intervals from 0 to 14 Ma and for 1 Myr time intervals from 14 to 25 Ma using mostly data from Initial Reports volumes. There is surprisingly little coherence between CaCO3 MAR time series from different Pacific regions, although regional patterns exist. A transition from high to low CaCO3 MAR from 23–20 Ma is the only event common to the entire Pacific Ocean. This event is found worldwide. The most likely cause of lowered pelagic carbonate burial is a rising sea‐level trend in the early Miocene. The central and eastern equatorial Pacific is the only region with adequate drill site coverage to study carbonate compensation depth (CCD) changes in detail for the entire Neogene. The latitude‐dependent decrease in CaCO3 production away from the equator is an important defining factor of the regional CCD, which shallows away from the equatorial region. Examination of latitudinal transects across the equatorial region is a useful way to separate the effects of changes in carbonate production (“productivity”) from changes in bottom water chemistry (“dissolution”) upon carbonate burial.
Modeling the water masses of the Atlantic Ocean at the Last Glacial Maximum
Authors: Paul André , Schäfer‐Neth Christian
Published: July 2003

We produced gridded monthly sea‐surface boundary conditions for the Atlantic Ocean at the Last Glacial Maximum (LGM) based on the sea‐surface temperature reconstruction of the GLAMAP project. We used an ocean general circulation model (OGCM), subject to these sea‐surface boundary conditions and a corresponding wind stress field from an atmospheric general circulation model, to study the differences in the distribution of the main water masses between the LGM and the present. Our global OGCM is characterized by high vertical resolution, low vertical diffusion, and isopycnal mixing and hence allows for a realistic representation of the hydrology and circulation of the modern Atlantic Ocean. According to a series of LGM experiments with an increasing sea‐surface salinity anomaly in the Weddell Sea, the ventilated thermocline was colder than today by 2–3°C in the North Atlantic Ocean and, in the experiment with the largest anomaly (1.0 beyond the global anomaly), by 4–5°C in the South Atlantic Ocean. Its depth was reduced by 50 m on average, most notably in the tropics. In the North Atlantic Ocean the outcrop locations of the thermocline isopycnal surfaces migrated southward by 5°–10°, and the ventilation increased. In the South Atlantic Ocean the mixed layer and thermocline water masses were dominated by cold water originating from Drake Passage, and the import of warm water from the Indian Ocean was reduced to about 4 Sv or 40% of its modern value. Antarctic Intermediate Water was colder by 3–4°C and could be traced as far as 10°N. The meridional overturning rates of North Atlantic Deep Water (NADW) and Antarctic Bottom Water (AABW) in the Atlantic Ocean were similar to those of the present‐day experiment (9–10 Sv and 4 Sv, respectively). However, NADW cooled by 2.5°C and AABW by 1°C. AABW was near the freezing point of seawater at the surface and the saltiest water mass in the Atlantic Ocean, even saltier than NADW. We show that the differences between the LGM and the present‐day experiments can be traced back to the changes in the subpolar and interhemispheric sea‐surface density gradients.
Paleoproductivity, nutrient burial, climate change and the carbon cycle in the western equatorial Atlantic across the Eocene/Oligocene boundary
Authors: Nilsen E. B. , Anderson L. D. , Delaney M. L.
Published: July 2003

Paleoproductivity, nutrient burial, and carbon cycling were investigated across the Eocene/Oligocene (E/O) boundary (begin to end; 36.9–32.7 Ma at ∼40 kyr resolution, timescale of Shackleton et al. [1999]) at Ocean Drilling Program Site 925 on the Ceara Rise in the western equatorial Atlantic (3040 m present water depth; 748.26–850.70 mbsf). Downcore bulk sediment records of biogenic barium, total reactive phosphorus, biogenic silica, and calcium carbonate are interpreted to represent export production, net nutrient burial, biogenic opal production, and inorganic carbon burial, respectively. The global positive excursion in δ13C subsequent to the E/O boundary is recorded at Site 925. Export production appears to have been externally forced by orbital parameters at eccentricity frequencies during the study interval, based on spectral analysis of the biogenic barium and reactive phosphorus records. Biogenic silica production or preservation increased after the Eocene/Oligocene boundary to a higher baseline, although overall productivity and nutrient burial did not increase, based on barium and reactive phosphorus records. Thus, although absolute production did not increase at this site, a shift in relative abundance of siliceous versus carbonate productivity may have resulted in a change in relative organic carbon burial. This may have contributed to the positive excursion in global oceanic δ13C subsequent to the Eocene/Oligocene boundary, although the silica maximum persists after the carbon isotope excursion ends.
Solar electron bursts at very low energies: Evidence for acceleration in the high corona?
Authors: Gosling J. T. , Skoug R. M. , McComas D. J.
Published: July 2003

More than 280 impulsive solar electron bursts, largely associated with type III radio bursts, have been observed by the solar wind experiment on ACE at energies below 1.4 keV. Here we illustrate some of the characteristics of these events with detailed observations of a particularly intense and long‐lasting (>19 hours) event that extended smoothly as a power law in energy down to at least 142 eV. Such low‐energy extensions of burst spectra may be evidence that the electrons in these bursts are accelerated at altitudes considerably greater than 1 solar radius above the photosphere. If so, then other characteristics of these events make it appear unlikely that the bursts result from shock acceleration. An alternate possibility is that acceleration actually occurs relatively low in the corona, as would be inferred from observations of type III bursts, and is followed by a more gradual release of electrons to the heliosphere.
Edge Preserving Smoothing for Oblique Images
Authors: Liu Yike , Luo Yi , Deng Zhuoyi
Published: July 2003

Recently, edge preserving smoohting (EPS) method has been introduced to exploration geophysics from remote sensing for reducing noise while preserving discotinuities in seismic datasets. It has been approved to be very helpful for highlighting and analysising faults, channels and fractures in seismic interpretation and placing optimal well locations. In this paper, we extended the basic EPS method to oblique “images” (curves, surfaces and seismic events in 3D seismic cubes) which were assumed to be horizontal in the original EPS. In this study, we tried two (the dip‐steering and least‐square fitting) approaches, and found that the latter one produced more satisfactory results than the former one did. With this extention, EPS can improve the effectness and widen the applications of the basic EPS in geophysics.
Seasonal predictability of wintertime storminess over the North Atlantic
Authors: Qian Budong , Saunders Mark A.
Published: July 2003

Interannual variability in winter storminess over the North Atlantic and Europe causes significant risk and uncertainty. Attempts to seasonally predict winter storminess levels have identified little skill to date. However, recent statistical studies of observational data indicate the presence of marginal but useful skill in predicting the winter North Atlantic Oscillation (NAO). This predictability arises from a significant (p < 0.01) link between northern hemisphere summer snow extent and the coming winter NAO state. We apply this link to assess the seasonal predictability in winter storminess 1972/3–2000/1 at a given point. The correlation skill for predicting, by early September, the numbers of winter gale days and storm force days in the main North Atlantic winter storm track region is between 0.5 and 0.6. Our finding suggests the seasonal predictability of North Atlantic winter storminess may be higher and extend to longer leads than thought previously.
Short wave versus long wave radiative forcing by Indian Ocean aerosols: Role of sea‐surface winds
Authors: Satheesh S. K. , Lubin D.
Published: July 2003

Recent observations over the Indian Ocean have demonstrated aerosol short wave absorption as high as 20 to 25 W m−2. The aerosol net radiative forcing reduces substantially while considering the broad spectrum including the long wave region (due to large infrared forcing which is opposite in sign). At high winds, presence of large amounts of sea‐salt aerosols (absorbing in infrared) enhances the infrared forcing; hence reduces the net radiative forcing. In this paper, we examine the role of sea‐surface winds (which enhance sea‐salt aerosols) on long wave aerosol forcing. Even at moderate winds (6–10 m s−1), the short wave forcing reduces by ∼45% due to the dominance of sea‐salt aerosols. At high winds (>10 m s−1), a major fraction of the long wave forcing is contributed by sea‐salt (more than 70%). Our studies show that neglecting aerosol long wave radiative forcing can cause large errors in climate models.
Martian climatic events on timescales of centuries: Evidence from feature morphology in the residual south polar ice cap
Authors: Byrne Shane , Ingersoll Andrew P.
Published: July 2003

Flat‐floored, quasi‐circular depressions on the southern residual cap of Mars have been observed to expand rapidly. Analysis of the size distribution combined with modeling of the growth process yields information about the ages of these features. We report on properties of a population of these features within a selected study area. We find a narrow size distribution that indicates a common formation time and a finite period during which new features were forming. Some change in environmental conditions occurred during this period, which we date at several Martian decades to centuries ago depending on modeled growth rates. We report on THEMIS data that reveals the nature of larger features outside our study area. Underlying water ice is exposed on the flat floors of these depressions near the outer walls. These features may record more than one growth phase, indicating that conditions conducive to growth may switch on and off with characteristic timescales of Martian centuries.
The use of ocean reanalysis products to initialize ENSO predictions
Authors: Tang Youmin , Kleeman Richard , Moore Andrew M. , Weaver Anthony , Vialard Jérôme
Published: July 2003

With a three‐dimensional variational (3D‐Var) assimilation scheme and a hybrid coupled model, we have explored the possibility of initializing ENSO prediction models by assimilating NCEP (National Centers of Environment Prediction) reanalysis subsurface temperatures. Our results show that, compared to predictions without assimilation, the reanalysis product can effectively improve prediction of both Niño3 sea surface temperature anomalies (SSTA) at all lead times up to 12 months (in particular for lead times over 4–6 months) and of El Niño episodes. The oceanic analysis from the assimilation with the reanalysis product can be as good as those generated by directly assimilating subsurface in situ temperature observations.
Characterization of two new HLA‐B alleles by sequence‐based typing: HLA‐B*0817 and HLA‐B*1311
Authors: Longhi E. , Frison S. , Espaolas de Arias A. , Bianchi P. , Ferrioli G. , Poli F. , Scalamogna M.
Published: July 2003

Abstract:  In this brief communication we report the characterization of two new HLA‐B variants officially named HLA‐B*0817 and HLA‐B*1311. The HLA‐B*0817 allele was identified in a Caucasoid male candidate for renal transplantation in the North Italy Transplant program. The nucleotidic sequence of exons 2, 3 and 4 of this novel allele is identical to that of HLA‐B*0804 except for three point mutations in exon 2: from A to G at position 259, from C to G at position 261 and from G to A at position 302. These mutations are responsible for two aminoacidic substitutions [Asn (r) Glu, codon 63, and Ser (r) Asn, codon 77]. HLA‐B*1311 was found in a volunteer donor belonging to National Marrow Donor Program®. This new variant is identical to that of HLA‐B*1301 except for three nucleotide substitutions at positions 353, 355 and 369 leading to two aminoacidic variations from Ile to Thr at codon 94 and from Ile to Leu at codon 95 and a silent mutation at codon 99.
Expression of HLA class I/II antigens and T cell immune response in human neuroendocrine tumors of the pancreas
Authors: Ryschich E. , Autschbach F. , Eisold S. , Klar E. , Buchler M.W. , Schmidt J.
Published: July 2003

Abstract:  Peptide presentation by HLA class I and II antigens regulates specific antigen recognition by T cells. The present study aimed to investigate T cell infiltration and its relation to HLA antigen expression in pancreatic neuroendocrine tumors. Fresh tissue samples were collected from five insulinomas and six other neuroendocrine tumors (one gastrinoma, one glucagonoma, two carcinoid, and two neuroendocrine carcinomas). Normal pancreatic and splenic tissue samples were used as controls. Investigation of infiltrating lymphocyte populations, as well as staining of HLA class I and II antigens, were performed by standard immunohistochemistry. The majority of investigated tumors demonstrated an intratumoral infiltration by CD3+, CD4+ and CD8+ T cells that was significantly higher than in normal pancreatic islets. Only a minority of tumor‐infiltrating T cells showed the CD45RO+ phenotype. The expression of HLA class I antigen was altered in 10 of 11 tumors. A loss of beta−2microglobulin represented the most frequent type of alteration to HLA class I expression, although the total loss of HLA class I was found in only one case of neuroendocrine carcinoma. HLA class II molecules were expressed by endothelial and lymphoid cells and not by tumor cells. In conclusion most neuroendocrine pancreatic tumors induce a T cell mediated immune response resulting in an intratumoral infiltration with CD3+, CD4+ and CD8+ T cells. Loss of beta‐2microglobulin is a frequent alteration in these tumors, which may influence the normal function of the HLA class I antigen complex. In contrast to malignant tumors of the exocrine pancreas, expression of HLA class II was absent in neuendocrine pancreatic tumor cells.
A Gambian TNF haplotype matches the European HLA‐A1,B8,DR3 and Chinese HLA‐A33,B58,DR3 haplotypes
Authors: Price P. , Bolitho P. , Jaye A. , Glasson M. , Yindom L‐M. , Sirugo G. , Chase D. , McDermid J. , Whittle H.
Published: July 2003

Abstract:  Caucasians carry TNFA‐308*2 in the 8.1 ancestral haplotype (AH) (HLA‐A1,B8,DR3). In Gambians, TNFA‐308*2 occurs without HLA‐B8 or ‐DR3, suggesting an independent effect of TNFA‐308 on disease. Hence we sought a segment of the 8.1 AH in Gambians. BAT1 (intron 10)*2 was selected as a specific marker of the haplotype and was found with TNFA‐308*2 in Gambians. Samples homozygous at TNFA‐308 and BAT1 (intron 10) demonstrated identity between the African TNFA‐308*2 haplotype, the 8.1AH and the Asian diabetogenic 58.1AH (HLA‐A33,B58,DR3) across a region spanning BAT1, ATP6G, IKBL, LTA, TNFA, LTB, LST‐1 and AIF‐1. Conservation of this block in geographically distinct populations suggests a common evolutionary origin and challenges current views of the role of TNFA‐308*2 in disease.
Comparative study of 0.1% olopatadine hydrochloride and 0.5% ketorolac tromethamine in the treatment of seasonal allergic conjunctivitis
Authors: Yaylali Volkan , Demirlenk Ibrahim , Tatlipinar Sinan , Özbay Davut , Esme Arif , Yildirim Cem , Özden Serap
Published: July 2003

Purpose:  To compare the therapeutic effects of two ophthalmic solutions (0.1% olopatadine hydrochloride and 0.5% ketorolac tromethamine) with different pharmacological mechanisms on the clinical signs and Symptoms of seasonal allergic conjunctivitis (SAC).

Methods:  Forty patients with the signs and symptoms of SAC (i.e. hyperaemia, itching, mucus discharge, tearing) were included in this placebo‐controlled, randomized, parallel group, single centre study. In group 1 (20 patients) one eye of each patient was treated with olopatadine and the other with placebo. In group 2 (20 patients) one eye of each patient was treated with ketorolac solution and the other with placebo. The principal signs and symptoms of SAC (hyperaemia and itching) were evaluated at 30 mins and at 2, 7 and 15 days.

Results:  In group 1, both parameters improved significantly in eyes treated with olopatadine compared with those receiving placebo at all control examinations (all p < 0.05). Similarly, eyes treated with ketorolac showed significant reductions in signs and symptoms compared with those receiving placebo (all p < 0.05). When the clinical parameters of eyes treated with olopatadine were compared with those treated with ketorolac, the mean score of hyperaemia was found to be lower in the olopatadine group, but the difference was not statistically significant (all p > 0.05). However, the itching score was significantly lower in the olopatadine group from the second day through to the end of the study (p < 0.05).

Conclusions:  Both olopatadine and ketorolac ophthalmic solutions were found to be effective in alleviating the clinical signs and symptoms of SAC compared to placebo. However, olopatadine reduces ocular itching significantly more than ketorolac.
Familial uveal melanoma: a report on two families and a review of the literature
Authors: Kodjikian Laurent , Nguyen Khôi , Lumbroso Livia , Gauthier‐Villars Marion , Chauvel Pierre , Plauchu Henri , Sterkers Margaret , Devouassoux Mojgan , Grange Jean‐Daniel
Published: July 2003

Purpose:  A total of 69 families affected by uveal melanoma have been reported in the literature. This report describes two additional families. In addition to presenting these cases, which constitute exceptions, the paper reviews the literature.

Material and Methods:  Two families, each with two affected members, were analysed in this retrospective study. The pedigree of each family has been pieced together.

Results:  Considering the low incidence of familial uveal melanoma in the general population, it seems unlikely that inherited genetic factors are responsible for the condition; this question remains difficult to resolve.

Discussion:  The characteristics of each family history are described and compared with the literature data. The mode of possible inheritance is discussed. Both the histopathology and anatomical location are studied, after which we discuss the body of evidence to establish whether there is an inherited cancer predisposition syndrome in patients with familial uveal melanoma.

Conclusion:  The statistical likelihood of such an uncommon tumour occurring independently in two or more family members leads us to believe that some cases of familial uveal melanoma may go unrecognized, and that reports on too few families have been published worldwide to prove the existence of a single mendelien gene. However, appropriate tissue samples, such as blood and tumour samples, should be obtained and conserved for present or future cytogenetic and molecular genetic studies.
Bilateral combined retinal and choroidal detachment in antineutrophil cytoplasmic antibody‐positive scleritis
Authors: Non Matthews B , Stavrou Panagiota
Published: July 2003

Purpose:  To describe a rare complication of scleritis in a patient with positive serum antineutrophil cytoplasmic antibodies (ANCA).

Methods:  We present a case report of a patient who developed bilateral retinal and choroidal detachment associated with ANCA‐positive scleritis.

Results:  Oral steroids alone were insufficient to maintain sustained remission of ocular inflammation. Clinical relapse of the scleritis was associated with ANCA titres becoming positive again. A combination of cyclophosphamide and steroids was successful in achieving control of the intraocular inflammation over a follow‐up period of 18 months.

Conclusion:  Bilateral combined retinal and choroidal detachment is a potentially blinding complication of ANCA‐positive scleritis. Monitoring of ANCA titres is useful in the management of the disease.
A comparison of Nd:YAG capsulotomy rate in two different intraocular lenses: AcrySof and Stabibag
Authors: Stordahl Per Bjørn , Drolsum Liv
Published: July 2003

Purpose:  To evaluate the incidence of posterior capsule opacification after implantation of two different intraocular lenses (IOLs), AcrySof® and Stabibag®, by comparing the neodymium:YAG (Nd:YAG) laser capsulotomy rates.

Methods:  The medical records of 596 patients (705 eyes) who underwent phacoemulsification and posterior chamber IOL implantation using either AcrySof (n = 335) or Stabibag (n = 370) IOLs during a 1‐year (1999) period were reviewed. Eyes with secondary cataract, combined procedures or operative complications, such as capsule tears, were excluded from the study. The subjects' age, sex, surgeon (two surgeons), and time for Nd:YAG laser capsulotomy were recorded.

Results:  The mean follow‐up was 23 months in both IOL groups. There were no statistically significant differences within the two IOL groups regarding sex distribution or surgeon. The mean age in the AcrySof group was 77.0 years compared to 79.2 years in the Stabibag group (p = 0.001). Nd:YAG laser capsulotomy was performed in 7.6% of patients in the Stabibag group compared to 2.7% in the AcrySof group (i.e. at a significantly higher rate) (p = 0.004). Survival analyses demonstrated that age and type of IOL were the only independent predictors of the incidence of capsulotomy.

Conclusions:  This study shows that the frequency of eyes with posterior capsule opacification needing capsulotomy was significantly higher in eyes with Stabibag IOLs compared to eyes with AcrySof IOLs.