bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of Mesoscale Eddies on the Main Subtropical Thermocline
Authors: Henning Cara C. , Vallis Geoffrey K. 
Published: December 2004

AbstractThe effects of mesoscale eddies on the main subtropical thermocline are explored using a simply configured wind- and buoyancy-driven primitive equation numerical model in conjunction with transformed Eulerian mean diagnostics and simple scaling ideas and closure schemes. If eddies are suppressed by a modest but nonnegligible horizontal diffusion and vertical diffusion is kept realistically small, the model thermocline exhibits a familiar two-regime structure with an upper, advectively dominated ventilated thermocline and a lower, advective– diffusive internal thermocline, and together these compose the main thermocline. If the horizontal resolution is sufficiently high and the horizontal diffusivity is sufficiently low, then a vigorous mesoscale eddy field emerges. In the mixed layer and upper-mode-water regions, the divergent eddy fluxes are manifestly across isopycnals and so have a diabatic effect. Beneath the mixed layer, the mean structure of the upper (i.e., ventilated) thermocline is still found to be dominated by mean advective terms, except in the “mode water” region and close to the western boundary current. The eddies are particularly strong in the mode-water region, and the low-potential-vorticity pool of the noneddying case is partially eroded away as the eddies try to flatten the isopycnals and reduce available potential energy. The intensity of the eddies decays with depth more slowly than does the mean flow, leading to a three-way balance among eddy flux convergence, mean flow advection, and diffusion in the internal thermocline. Eddies subduct water along isopycnals from the surface into the internal thermocline, replenishing its water masses and maintaining its thickness. Just as in the noneddying case, the dynamics of the internal thermocline can be usefully expressed as an advective–diffusive balance, but where advection is now by the residual (eddy-induced plus Eulerian mean) circulation. The eddy-induced advection partially balances the mean upwelling through the base of the thermocline, and this leads to a slightly thicker thermocline than in the noneddying case. The results suggest that as the diffusivity goes to zero, the residual circulation will go to zero but the thickness of the internal thermocline may remain finite, provided eddy activity persists.
Nonuniform Upwelling in a Shallow-Water Model of the Antarctic Bottom Water in the Brazil Basin*
Authors: Marchal Olivier , Nycander Jonas 
Published: December 2004

Abstract
A numerical model based on the shallow-water equations is developed to represent the flow of Antarctic Bottom Water (AABW) in the Brazil Basin (southwest Atlantic Ocean). The aim is twofold. First, an attempt is made to identify in a model that includes both simplified dynamics and realistic bathymetry (at 1/6° resolution) the impacts of the elevated diapycnal mixing rates near the Mid-Atlantic Ridge (MAR) documented by dissipation data of the Deep Basin Experiment (DBE). To this end, different assumptions regarding the distribution of the velocity across the AABW layer interface (w) are considered. Second, the extent to which the shallow-water model can replicate observations relative to AABW circulation in the basin, in particular the trajectory and velocity of neutrally buoyant floats released in the AABW during the DBE, is examined. The model flows are characterized by small Rossby numbers, except in the northward-flowing western boundary current where kinetic energy is largely concentrated. To interpret the flows, model streamlines are compared with isopleths of linear potential vorticity f/h0 of the shallow-water theory (f is the planetary vorticity and h0 is the layer thickness in the absence of motion). The f/h0 contours are oriented northwest–southeast in the western part of the basin and southwest–northeast in the eastern part, reflecting the bowl-shaped topography of the Southern Hemisphere basin. With a spatially uniform (positive) w, the ubiquitous vortex stretching produces a flow to the southeast, consistent with the Stommel–Arons theory. This flow occurs in most of the basin interior, even in the east where f/h0 contours converge to the northeastern end of the basin. With strongly positive w near the ridge and zero or slightly negative w elsewhere, the flow follows more closely f/h0 contours in the western interior and intersects them near the ridge. The confinement of the diapycnal mass flux near the MAR drastically reduces the southward flow in the interior or even reverses its direction, leading to a circulation quite distinct from that of the Stommel– Arons theory. The model results compare favorably to some (but not all) hydrographic estimates of AABW circulation patterns and rates. On the other hand, the model streamlines and velocities show important differences with, respectively, the trajectory and the velocity of the floats launched in the AABW layer. The prescription of vanishing w in the interior does not systematically improve the fit of the model streamlines to the float trajectories, and the model velocities simulated with spatially uniform w or spatially variable w are on average smaller by one order of magnitude than the float velocities. A variety of mechanisms, which are not included in the numerical experiments, may explain the differences between the model results and the float data.
The Response of Buoyant Coastal Plumes to Upwelling-Favorable Winds*
Authors: Lentz Steven 
Published: December 2004

Abstract
To better understand the response of a buoyant coastal plume to wind-induced upwelling, a two-dimensional theory is developed that includes entrainment. The primary assumption is that competition between wind-driven vertical mixing and lateral buoyancy forcing in the region where the isopycnals slope upward to intersect the surface results in continual entrainment at the offshore edge of the plume. The theory provides estimates of the buoyant plume characteristics and offshore displacement as a function of time t, given the wind stress, the characteristics of the buoyant plume prior to the onset of the wind forcing, and a critical value for the bulk Richardson number (Ric). The theory predicts that, for t̂ ≡ t/ts, the plume density anomaly decreases as (1 + t̂)−1, the thickness increases as (1 + t̂)1/3, the width increases as (1 + t̂)2/3, and the plume average entrainment rate decreases as (1 + t̂)−2/3. Here ts = 2Ao/(RicUE) is the time for entrainment to double the cross-sectional area of the plume Ao at the onset of the wind forcing, where UE is the Ekman transport. The theory reproduces results from 20 numerical model runs by Fong and Geyer, including their estimates of the plume-average entrainment rate (correlations greater than 0.98 and regression coefficients approximately 1 for plume characteristics and 1.7 for the entrainment rate). The theory, modified to allow for time-variable wind stress, also reproduces the observed response of the buoyant coastal plume from Chesapeake Bay during an 11-day period of upwelling winds in August 1994.
Mammalian defensins: structures and mechanism of antibiotic activity
Authors: Sahl Hans-Georg , Pag Ulrike , Bonness Sonja , Wagner Sandra , Antcheva Nikolinka , Tossi Alessandro 
Published: December 2004

AbstractAntibiotic peptides are important effector molecules in host-parasite interactions throughout the living world. In vertebrates, they function in first-line host defense by antagonizing a wide range of microbes including bacteria, fungi, and enveloped viruses. The antibiotic activity is thought to be based on their cationic, amphipathic nature, which enables the peptides to impair vital membrane functions. Molecular details for such activities have been elaborated with model membranes; however, there is increasing evidence that these models may not reflect the complex processes involved in the killing of microbes. For example, the overall killing activity of the bacterial peptide antibiotic nisin is composed of independent activities such as the formation of target-mediated pores, inhibition of cell-wall biosynthesis, formation of nontargeted pores, and induction of autolysis. We studied the molecular modes of action of human defense peptides and tried to determine whether they impair membrane functions primarily and whether additional antibiotic activities may be found. We compared killing kinetics, solute efflux kinetics, membrane-depolarization assays, and macromolecular biosynthesis assays and used several strains of Gram-positive cocci as test strains. We found that membrane depolarization contributes to rapid killing of a significant fraction of target cells within a bacterial culture. However, substantial subpopulations appear to survive the primary effects on the membrane. Depending on individual strains and species and peptide concentrations, such subpopulations may resume growth or be killed through additional activities of the peptides. Such activities can include the activation of cell-wall lytic enzymes, which appears of particular importance for killing of staphylococcal strains.
Diagnostic FISH probes for del(17)(p11.2p11.2) associated with Smith–Magenis syndrome should contain the RAI1 gene
Authors: Vlangos Christopher N. , Wilson Meredith , Blancato Jan , Smith Ann C.M. , Elsea Sarah H. 
Published: December 2004

AbstractSmith–Magenis syndrome (SMS) is a mental retardation syndrome with distinctive behavioral characteristics, dysmorphic features, and congenital anomalies usually associated with an interstitial deletion of chromosome 17p11.2. While high quality G‐banding will identify most SMS patients, fluorescent in situ hybridization (FISH) is the recommended test for confirmation of an SMS diagnosis. Recently, haploinsufficiency of the RAI1 gene due to deletion or mutation was determined to be the likely cause of SMS. All diagnostic FISH probes available commercially contain the FLII gene and are approximately 580 kb centromeric to RAI1. We present two patients with SMS who have interstitial deletions at 17p11.2 but are not deleted for currently available commercial FISH probes that include FLII; both patients have deletions that are demonstrated with probes containing the RAI1 gene. We recommend that for diagnostic accuracy, all future FISH tests for SMS be performed with probes containing the RAI1 gene, as some atypical deletions in the region critical to the SMS phenotype will otherwise be missed. © 2004 Wiley‐Liss, Inc.
Simultaneous determination of tryptophan and kynurenine in serum by HPLC with UV and ﬂuorescence detection
Authors: Vignau J. , Jacquemont M.‐C. , Lefort A. , Imbenotte M. , Lhermitte M. 
Published: December 2004

AbstractTryptophan metabolism is disturbed in mental depression, and the induction of indoleamine 2,3‐dioxygenase increases kynurenine production. In order to determine this disturbance in patients with chronic hepatitis C and receiving interferon‐based immunotherapy, a new and speciﬁc HPLC protocol was elaborated. For tryptophan, the assay was linear from 6.25 to 100 µmol L−1, and the limits of detection (LOD) and quantitation (LOQ) for the method were 0.7 and 8.0 µmol L−1. For kynurenine, the linearity of calibration was from 0.0625 to 6.25 µmol L−1, with LOD and LOQ of 2 and 3 nmol L−1. Reproducibility and repeatability were satisfactory. The method allowed study of human blood serum. Copyright © 2004 John Wiley & Sons, Ltd.
Levels of transforming growth factor beta 1 in south Indian type 2 diabetic subjects
Authors: Viswanathan Vijay , Snehalatha C. , Nair Mamtha B. , Kumutha R. , Ramachandran A. 
Published: December 2004

AbstractBackground and AimsThe prosclerotic cytokine TGFβ has been implicated as an important downstream mediator in the progression of the renal pathological changes occurring in diabetic patients. This study was undertaken to determine (1) whether serum levels of zTGFβ1 was elevated in South Indian type 2 diabetic subjects and (2) whether treatment with oral hypoglycaemic agents/insulin and angiotensin‐converting enzyme inhibitors (ACEI) and/or angiotensin receptor blockers (ARB) influenced TGFβ1 levels in diabetic subjects.MethodsAmong the 131 study subjects, 101 were consecutive type 2 diabetic patients and the other 30 subjects were non‐diabetic, normoglycaemic (NGT, M : F 15 : 15) healthy subjects who had undergone an Oral Glucose Tolerance Test (OGTT) during medical checkup. TGFβ1 was determined using solid‐phase sandwich enzyme‐linked immunosorbent assay.ResultsMean serum TGFβ1 levels were significantly elevated (p < 0.0001) in the type 2 diabetic subjects (30 ± 13.1 ng/mL) when compared with the non‐diabetic subjects (19 ± 8.3 ng/mL). Diabetic subjects who were being treated with a combination of OHA and insulin (n = 53;25.6 ± 11.5 ng/mL) had significantly (p = 0.0009) lower levels of TGFβ1 when compared with those who were being treated with OHA alone (n = 48;34.1 ± 13.4 ng/mL). Nearly 36% of the diabetic subjects were being treated with ACEI/ARB, and they had significantly (p = 0.01) lower levels of TGFβ1 (n = 36;25.4 ± 12.6 ng/mL) when compared with those who were not being treated with ACEI/ARB (n = 65;32 ± 12.9 ng/mL).ConclusionThe present study demonstrated significantly elevated TGFβ1 levels in South Indian type 2 diabetic patients when compared with the non‐diabetic subjects. Insulin and ACEI/ARB treatment appears to have a protective effect by lowering TGFβ1 concentrations in these subjects. Copyright © 2004 John Wiley & Sons, Ltd.
A quantum chemical method for rapid optimization of protein structures
Authors: Wada Mitsuhito , Sakurai Minoru 
Published: December 2004

AbstractA quantum chemical method for rapid optimization of protein structures is proposed. In this method, a protein structure is treated as an assembly of amino acid units, and the geometry optimization of each unit is performed with taking the effect of its surrounding environment into account. The optimized geometry of a whole protein is obtained by repeated application of such a local optimization procedure over the entire part of the protein. Here, we implemented this method in the MOPAC program and performed geometry optimization for three different sizes of proteins. Consequently, these results demonstrate that the total energies of the proteins are much efficiently minimized compared with the use of conventional optimization methods, including the MOZYME algorithm (a representative linear‐scaling method) with the BFGS routine. The proposed method is superior to the conventional methods in both CPU time and memory requirements. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 160–168, 2005
NfCR1, the first non‐LTR retrotransposon characterized in the Australian lungfish genome, Neoceratodus forsteri, shows similarities to CR1‐like elements
Authors: Sirijovski Nickolche , Woolnough Catherine , Rock Jennifer , Joss Jean M. P. 
Published: December 2004

AbstractThe genomes of lungfish, together with those of some urodele amphibians, are the largest of all vertebrate genomes. It has been assumed that the bulk of the DNA making up these large genomes has been derived from repeat elements, like the noncoding DNA of those genomes that have been sequenced (e.g., human). In an attempt to characterize repeat sequences in the lungfish genome, we have isolated, by restriction enzyme digestion of genomic DNA, sequences of a repeat element in Neoceratodus forsteri, the most primitive of the living lungfishes. The fragments sequenced from the EcoRI and BglII digests were used to perform genome walking PCR in order to obtain the full sequence of the repeat element. This element shares homology with the non‐LTR (LINE) element, Chicken Repeat 1 (CR1), described for several vertebrates and some invertebrates; we have called it N. forsteri CR1 (NfCR1). NfCR1 shares all the domains of other CR1 elements but it also has several unique features that suggest it may no longer be active in the lungfish genome. It occurs in both full‐length and 5′‐truncated versions and in its present “inactive” form represents ∼0.05% of the lungfish genome. J. Exp. Zool. (Mol. Dev. Evol.) 304B:1–10, 2005. © 2005 Wiley‐Liss, Inc.
Effect of metal cationization on the tandem mass spectra of glycosyl dithioacetals
Authors: Madhusudanan K. P. , Kumar Brijesh , Tiwari Pallavi , Madhusudan Soni Kamlesh , Misra A. K. 
Published: December 2004

AbstractThe effect of metal cationization on the tandem mass spectra of glycosyl dithioacetals of glucose, mannose, galactose, rhamnose, arabinose and xylose was studied by electrospray ionization mass spectrometry under ammonium and metal (Li, Na, Ag and Cu) ion cationization conditions. The ammonium‐cationized glycosyl dithioacetals fragment by loss of ammonia followed by either two molecules of EtSH or one molecule of EtSH and one molecule of H2O. Lithium cationization leads to additional eliminations such as EtSEt and EtSSEt and CC cleavages. Elimination of EtSH is not observed under sodium cationization. Silver cationization, on the other hand, leads to additional fragmentations involving the elimination of silver as AgOH and AgSEt. Copper cationization results in adducts where copper has undergone a change of oxidation state from II to I. Li+, Ag+ and Cu+ cationization seem to favour cyclization resulting in elimination of EtSH. However, the mechanisms seem to be differently affected by different metal ions. Li+ and Ag+ cationization appear to be non‐specific and favour cyclization involving C2‐, C4‐ and C5‐hydroxyl hydrogens, whereas Cu+ cationization seems to favour cyclization involving C4‐hydroxyl hydrogen. Copyright © 2004 John Wiley & Sons, Ltd.
Amino acid cluster formation studied by electrospray ionization mass spectrometry
Authors: Nemes Péter , Schlosser Gitta , Vékey Károly 
Published: December 2004

AbstractThe association properties of natural and non‐natural amino acids were studied in detail using electrospray ionization mass spectrometry. The results show a highly diverse cluster formation behavior of amino acids. There are differences regarding the degree of clustering (average cluster size), the presence or absence of one or several ‘magic’ clusters of special stability and the influence of chirality on cluster stability. Cluster formation does not show a good correlation with simple physico‐chemical properties (such as solubility), indicating that it is a specific process and not only a simple aggregation during evaporation/ionization. A systematic study of cluster formation of serine derivatives reveals that all functional groups play a prominent role in the binding of the magic octamer. The results support the idea of the zwitterionic character of the octamer. Electrospray ionization of the side‐chain acetylated serine shows the formation of a very stable tetramer with a strong preference for homochirality. The results suggest that Ser8 is made up of two tetramer subunits, held together by hydrogen bonds of the side‐chain. Copyright © 2004 John Wiley & Sons, Ltd.
Lactate transport and transporters: General principles and functional roles in brain cells
Authors: Hertz Leif , Dienel Gerald A. 
Published: December 2004

AbstractLactate is transported across cell membranes by diffusional, saturable cotransport with protons, mediated by monocarboxylate transporters (MCTs). This transport is bidirectional and in the absence of a transcellular H+ gradient, it can increase the intracellular concentration of lactate up to but not beyond the extracellular level (or vice versa). If extra‐ and intracellular pH differ, however, the equilibrium level is determined by the gradients of both lactate anions and protons. Rates of lactate uptake are determined most often by measuring uptake of labeled lactate, e.g., [U‐14C]lactate. In the case of lactate and other compounds that are metabolized, errors are introduced easily because continuing inwardly directed diffusional net transport of label can be achieved by intracellular metabolism, reducing the intracellular level of the nonmetabolized lactate and thus maintaining a concentration gradient between extra‐ and intracellular concentrations of the nonmetabolized compound (metabolism‐driven uptake). For measurement of facilitated diffusion kinetics, it is essential that the period during which the uptake is measured is short enough that little or no metabolism‐driven uptake contributes to the measured uptake (or that first‐order regression analysis is carried out to obtain initial uptake rates from nonlinear traces). To achieve initial uptake rates, incubation periods well below 1 min are generally required. Lactate uptake is fast in astrocytes, which express powerful, low‐affinity MCTs, i.e., MCT1 and MCT4. Due to the low affinity of these transporters, they respond to increased lactate gradients with enhanced transporter activity. The predominant MCT in neurons is the high‐affinity MCT2, which can only increase its activity to a limited extent in the face of an increased lactate gradient. This is reflected by a high‐affinity lactate uptake, although most investigators also have demonstrated a component of lactate uptake with lower affinity. In both neurons and astrocytes, however, facilitated diffusion is fast enough that under most conditions lactate fluxes will be determined mainly by the rate of metabolism‐driven uptake, and MCT‐mediated transport only will be rate‐limiting after establishment of large transmembrane gradients. © 2004 Wiley‐Liss, Inc.
Inclusion Complex Formation between α‐Cyclodextrin and Biodegradable Aliphatic Polyesters
Authors: Shin Kyung‐moo , Dong Tungalag , He Yong , Taguchi Yoichi , Oishi Akihiro , Nishida Haruo , Inoue Yoshio 
Published: December 2004

AbstractSummary: Inclusion complexes (ICs) between α‐cyclodextrin (α‐CD) and three kinds of biodegradable aliphatic polyesters with different sequence lengths of the monomeric repeating units poly(3‐hydroxypropionate) [P(3HP)], poly(4‐hydroxybutyrate) [P(4HB)] and poly(ε‐caprolactone)(PCL) were prepared by mixing a solution of α‐CD with that of the polymer, followed by stirring. The ICs were obtained as insoluble precipitates and characterized by FT‐IR, WAXD and DSC. All measurements showed that the polymer chains of all three kinds of polyester were included into the α‐CD cavity and formed ICs with different stoichiometries. WAXD patterns and thermal analysis indicated that these ICs possessed a channel structure and the crystallization of the polyester chains was suppressed upon inclusion into the α‐CD cavity.Expansion of the FT‐IR spectra of α‐CD‐PCL IC. Ex: experimental result; Cr: crystalline component; Am: amorphous component; Hb: hydrogen‐bonded component; OH: hydroxyl component (water).magnified imageExpansion of the FT‐IR spectra of α‐CD‐PCL IC. Ex: experimental result; Cr: crystalline component; Am: amorphous component; Hb: hydrogen‐bonded component; OH: hydroxyl component (water).