bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear Representation of the Quasi-Biennial Oscillation
Authors: Lu Bei-Wei , Pandolfo Lionel , Hamilton Kevin 
Published: January 2009

AbstractA nonlinear principal component analysis (NLPCA) is applied to monthly mean zonal wind observations from January 1956 through December 2007 taken at seven pressure levels between 10 and 70 hPa in the stratosphere near the equator to represent the well-known quasi-biennial oscillation (QBO) and investigate its variability and structure. The NLPCA is conducted using a simplified two–hidden layer feed-forward neural network that alleviates the problems of nonuniqueness of solutions and data overfitting that plague nonlinear techniques of principal component analysis. The QBO is used as a test bed for the new compact model of NLPCA.The two nonlinear principal components of the dataset of the equatorial stratospheric zonal winds, determined by the compact NLPCA, offer a clear picture of the QBO. In particular, their structure shows that the QBO phase consists of a predominant 28.3-month cycle that is modulated by an 11-yr cycle as well as by longer cycles. The differences in wind variability between westerly and easterly regimes and between Northern Hemisphere winter and summer seasons and the tendency for a seasonal synchronization of the QBO phases are well captured.
Do Models and Observations Disagree on the Rainfall Response to Global Warming?
Authors: Liepert Beate G. , Previdi Michael 
Published: January 2009

Abstract
Recently analyzed satellite-derived global precipitation datasets from 1987 to 2006 indicate an increase in global-mean precipitation of 1.1%–1.4% decade−1. This trend corresponds to a hydrological sensitivity (HS) of 7% K−1 of global warming, which is close to the Clausius–Clapeyron (CC) rate expected from the increase in saturation water vapor pressure with temperature. Analysis of two available global ocean evaporation datasets confirms this observed intensification of the atmospheric water cycle. The observed hydrological sensitivity over the past 20-yr period is higher by a factor of 5 than the average HS of 1.4% K−1 simulated in state-of-the-art coupled atmosphere–ocean climate models for the twentieth and twenty-first centuries. However, the analysis shows that the interdecadal variability in HS in the models is high—in particular in the twentieth-century runs, which are forced by both increasing greenhouse gas (GHG) and tropospheric aerosol concentrations. About 12% of the 20-yr time intervals of eight twentieth-century climate simulations from the third phase of the Coupled Model Intercomparison Project (CMIP3) have an HS magnitude greater than the CC rate of 6.5% K−1. The analysis further indicates different HS characteristics for GHG and tropospheric aerosol forcing agents. Aerosol-forced HS is a factor of 2 greater, on average, and the interdecadal variability is significantly larger, with about 23% of the 20-yr sensitivities being above the CC rate. By thermodynamically constraining global precipitation changes, it is shown that such changes are linearly related to the difference in the radiative imbalance at the top of the atmosphere (TOA) and the surface (i.e., the atmospheric radiative energy imbalance). The strength of this relationship is controlled by the modified Bowen ratio (here, global sensible heat flux change divided by latent heat flux change). Hydrological sensitivity to aerosols is greater than the sensitivity to GHG because the former have a stronger effect on the shortwave transmissivity of the atmosphere, and thus produce a larger change in the atmospheric radiative energy imbalance. It is found that the observed global precipitation increase of 13 mm yr−1 decade−1 from 1987 to 2006 would require a trend of the atmospheric radiative imbalance (difference between the TOA and the surface) of 0.7 W m−2 decade−1. The recovery from the El Chichón and Mount Pinatubo volcanic aerosol injections in 1982 and 1991, the satellite-observed reductions in cloudiness during the phase of increasing ENSO events in the 1990s, and presumably the observed reduction of anthropogenic aerosol concentrations could have caused such a radiative imbalance trend over the past 20 years. Observational evidence, however, is currently inconclusive, and it will require more detailed investigations and longer satellite time series to answer this question.
Distribution and Modification of North Pacific Intermediate Water around the Subarctic Frontal Zone East of 150°E
Authors: Masujima Masachika , Yasuda Ichiro 
Published: January 2009

Abstract
Modification and distribution of North Pacific Intermediate Water (NPIW) in the area north of 30°N and east of 150°E are discussed based on an isopycnal particle tracking experiment with the velocity field estimated from a β-spiral inverse method based on climatological data, annual climatological data analysis, and isopycnal-tracking profiling float data. NPIW emanating from 149.5°E between 35.5° and 37.5°N retains its salinity minimum structure along the eastward flow of the northern subtropical gyre, and these pathways occupy the northern part of the NPIW distribution. On the other hand, NPIW from 149.5°E between 37.5° and 40.5°N loses its salinity minimum as it flows eastward to the “transition domain.” The extinction of the salinity minimum structure is caused by a salinity decrease in the upper layer (26.5–26.6 σθ) in the region at 40°–45°N, 155°–165°E where a winter mixed layer is developed to a depth of 300 m and a density of 26.7 σθ. This extinction was observed by a profiling float tracking a 26.7-σθ isopycnal density surface. Low-salinity subarctic water advected southward across the Subarctic Front by wind-induced Ekman drift from strong westerlies in winter is suggested as the source of the low-salinity mixed layer. After the extinction of the salinity minimum structure, a state without salinity minimum is maintained during transport eastward in the transition domain because the winter mixed layer in the area east of the deep mixed layer region reaches a density surface shallower than 26.5 σθ.
Coastal Wind-Driven Circulation in the Vicinity of a Bank. Part II: Modeling Flow over the Heceta Bank Complex on the Oregon Coast
Authors: Whitney Michael M. , Allen J. S. 
Published: January 2009

Abstract
This study investigates wind-driven circulation in the vicinity of the Heceta Bank complex along the Oregon shelf. Numerical experiments forced with steady winds (0.1 Pa) are conducted; upwelling and downwelling cases are compared. The asymmetric bank bathymetry is the only configurational difference from the symmetric bank runs analyzed in Part I (Whitney and Allen). Upwelling-favorable winds generate an upwelling front and southward baroclinic jet. Model results indicate the upwelling jet is centered on the 100-m isobath along the straight shelf. The jet follows this isobath offshore around the northern part of the bank but separates from sharply turning isobaths in the southern half and flows over deeper waters. The jet turns back toward the coast farther downstream. Inshore of the main jet, currents reverse and flow back onto the bank. These reversed currents turn southward again (at the bank center) and join a secondary southward coastal upwelling jet. This secondary coastal jet converges with the stronger main jet farther downstream. Upwelling is intense at the northern bank edge near the coast, where a dense water tongue is advected over the bank. Upwelling also is strong on the southern bank half where the flow turns and reverses. Other areas of the bank have reduced upwelling or even downwelling during upwelling-favorable winds. Downwelling-favorable winds drive a near-bottom density front and a northward jet. The slower downwelling jet flows along the 130-m isobath over the straight shelf. The jet departs from isobaths over the southern bank half and follows a straighter path over shallower waters. There are no reversed currents over the bank. The bank is an area of reduced downwelling. Some of the differences in the evolution of the current and density fields are linked to fundamental differences between the upwelling and downwelling regimes; these are anticipated by the symmetric bank results of Part I. Other differences arise because of the bank asymmetry and opposite flow directions over the bank.
The lowest-order depth-averaged across-stream momentum balance remains geostrophic over the bank. Advection, ageostrophic pressure gradients, wind stress, and bottom stress all are important in the depth-averaged alongstream momentum balance over the Heceta Bank complex. Both across-shelf and alongshelf density advection are important. Barotropic potential vorticity is not conserved over the bank, but the tendency for relative vorticity changes and depth changes to partially counter each other influences the different paths of the upwelling and downwelling jets. There are several regions of active upwelling and downwelling over the bank. In these areas, vertical velocities at the top of the bottom boundary layer are linked to topographic upwelling and downwelling and Ekman pumping. There is considerable spatial variability in the currents, densities, and dynamics over the Heceta Bank complex.
Model Estimates of M2 Internal Tide Generation over Mid-Atlantic Ridge Topography
Authors: Zilberman N. V. , Becker J. M. , Merrifield M. A. , Carter G. S. 
Published: January 2009

Abstract
The conversion of barotropic to baroclinic M2 tidal energy is examined for a section of the Mid-Atlantic Ridge in the Brazil Basin using a primitive equation model. Model runs are made with different horizontal smoothing (1.5, 6, and 15 km) applied to a 192 km × 183 km section of multibeam bathymetry to characterize the influence of topographic resolution on the model conversion rates. In all model simulations, barotropic to baroclinic conversion is highest over near- and supercritical slopes on the flanks of abyssal hills and discordant zones. From these generation sites, internal tides propagate upward and downward as tidal beams. The most energetic internal tide mode generated is mode 2, consistent with the dominant length scales of the topographic slope spectrum (50 km). The topographic smoothing significantly affects the model conversion amplitudes, with the domain-averaged conversion rate from the 1.5-km run (15.1 mW m−2) 4% and 19% higher than for the 6-km (14.5 mW m−2) and 15-km runs (12.2 mW m−2), respectively. Analytical models for internal tide generation by subcritical topography predict conversion rates with modal dependence and spatial patterns qualitatively similar to the Princeton Ocean Model (POM) and also show a decrease in conversion with smoother topography. The POM conversion rates are approximately 20% higher than the analytical estimates for all model grids, which is attributed to spatial variations in the barotropic flow and near-bottom stratification over generation sites, which are incorporated in the model but not in the analytical estimates.
Activin-A attenuates several human natural killer cell functions
Authors: Robson Neil C. , Wei Heng , McAlpine Tristan , Kirkpatrick Naomi , Cebon Jonathan , Maraskovsky Eugene 
Published: January 2009

AbstractDendritic-cell (DC) and natural killer (NK)–cell interactions are critical in sculpting the adaptive immune response. However, the mechanisms by which DCs down-regulate NK-cell functions are not well understood. NK-cell function is inhibited by transforming growth factor beta (TGF-β), but DCs do not appear to produce TGF-β. We have previously shown that activated human DCs produce large amounts of activin-A, a TGF-β superfamily member, which autoregulates DC function. The present report shows that NKcells express type I and II activin receptors and that activin-A triggers NK-cell Smad 2/3 signaling. Furthermore, activin-A directly regulates NK cell functions by (1) down-regulating the T-box transcription factor T-bet and interferon gamma (IFN-γ) but not perforin or granzyme mRNA; (2) suppressing NK-cell IFN-γ production as potently as TGF-β; and (3) suppressing NK-cell CD25 expression and proliferation and sculpting NK-cell cytokine and chemokine profiles. Interestingly, unlike TGF-β, activin-A weakly down-regulates the NK-cell natural cytotoxicity receptors (NCRs) NKp30 and NKG2D but does not attenuate their cytotoxic function. These findings provide the first evidence for a novel immune regulatory role of activin-A during DC-mediated NK-cell regulation, highlighting the potential of antagonizing activin-A signaling in vivo to enhance NK cell–mediated immune functions and adaptive immunity.
Analytical approximations for the amplitude and period of a relaxation oscillator
Authors: Kut Carmen , Golkhou Vahid , Bader Joel S 
Published: January 2009

Abstract

Background
Analysis and design of complex systems benefit from mathematically tractable models, which are often derived by approximating a nonlinear system with an effective equivalent linear system. Biological oscillators with coupled positive and negative feedback loops, termed hysteresis or relaxation oscillators, are an important class of nonlinear systems and have been the subject of comprehensive computational studies. Analytical approximations have identified criteria for sustained oscillations, but have not linked the observed period and phase to compact formulas involving underlying molecular parameters.

Results
We present, to our knowledge, the first analytical expressions for the period and amplitude of a classic model for the animal circadian clock oscillator. These compact expressions are in good agreement with numerical solutions of corresponding continuous ODEs and for stochastic simulations executed at literature parameter values. The formulas are shown to be useful by permitting quick comparisons relative to a negative-feedback represillator oscillator for noise (10× less sensitive to protein decay rates), efficiency (2× more efficient), and dynamic range (30 to 60 decibel increase). The dynamic range is enhanced at its lower end by a new concentration scale defined by the crossing point of the activator and repressor, rather than from a steady-state expression level.

Conclusion
Analytical expressions for oscillator dynamics provide a physical understanding for the observations from numerical simulations and suggest additional properties not readily apparent or as yet unexplored. The methods described here may be applied to other nonlinear oscillator designs and biological circuits.
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae
Authors: Christensen Tobias S , Oliveira Ana Paula , Nielsen Jens 
Published: January 2009

Abstract

Background
In the yeast Saccharomyces cerevisiae, the presence of high levels of glucose leads to an array of down-regulatory effects known as glucose repression. This process is complex due to the presence of feedback loops and crosstalk between different pathways, complicating the use of intuitive approaches to analyze the system.

Results
We established a logical model of yeast glucose repression, formalized as a hypergraph. The model was constructed based on verified regulatory interactions and it includes 50 gene transcripts, 22 proteins, 5 metabolites and 118 hyperedges. We computed the logical steady states of all nodes in the network in order to simulate wildtype and deletion mutant responses to different sugar availabilities. Evaluation of the model predictive power was achieved by comparing changes in the logical state of gene nodes with transcriptome data. Overall, we observed 71% true predictions, and analyzed sources of errors and discrepancies for the remaining.

Conclusion
Though the binary nature of logical (Boolean) models entails inherent limitations, our model constitutes a primary tool for storing regulatory knowledge, searching for incoherencies in hypotheses and evaluating the effect of deleting regulatory elements involved in glucose repression.
A 70-year-old male having advanced prostate cancer presenting with hypercalcemia and diffuse osteoblastic bone metastases: a case report
Authors: Liao Wan-Hsiu , Lin Sheng-Hsiang , Wu Tsu-Tuan 
Published: January 2009

Abstract

Background
Bony metastases were occasionally the initial presentations of malignancy. Overlooking of bony changes on radiographs in cancer patients with non-specific clinical symptoms may lead to delayed diagnosis.

Case presentation
We presented a 70-year-old male having hypercalcemia and diffuse osteoblastic bone metastases on routine plain films. Finally, prostate cancer was diagnosed with a prostate needle biopsy.

Conclusion
Although the modern radionuclide bone scanning is useful in diagnosis, osteoblastic bone changes are occasionally seen in plain films, which are frequently overlooked. To avoid delayed diagnosis, bony structures should be carefully examined in all plain-film radiographs.
Designable DNA Functions toward New Nanobiotechnology
Authors: Sugimoto Naoki 
Published: January 2009

Abstract
DNA has many properties that cannot be attained with other molecules. The ability of DNA to form base pairing and its structural polymorphism allow the formation of distinct secondary and tertiary structures and may have further catalytic or aptamer function. It is also of great advantage that the base pairing of a short oligonucleotide sequence can be well predicted and designed with the thermodynamic parameters of Watson–Crick base pairs, mismatch pairs, and noncanonical base pairs based on the nearest-neighbor model. We have investigated the thermodynamics of various types of oligonucleotide structures, and obtained the nearest-neighbor parameters for Watson–Crick base pair formations and fundamental information regarding the nucleotide interactions. The data of the DNA interaction energy were also applied for molecular design of a DNA logic gate and DNA nanowire. I will further discuss the importance of quantitative data of DNA interaction energy toward the rational design of artificial DNAs carried out by our laboratory, such as base pair-mimic nucleosides and DNA containing bipyridine units, useful as nanobiodevices and nanobiomaterial.
Thermodynamics of the Bis(η6-t-butylphenyl)chromium Fulleride [Cr{η6-(t-BuPh)}2]•+C60•−
Authors: Ruchenin Vitaly A , Markin Alexey V , Smirnova Natalia N , Markin Gennady V , Shevelev Yurii A , Cherkasov Vladimir K , Kuropatov Vyatcheslav A , Ketkov Sergey Y , Lopatin Mikhail A , Domrachev Georgy A 
Published: January 2009

Abstract
In this work, the temperature dependence of heat capacity $C_{\text{p,m}}^{o}$ = f(T) of crystalline bis(η6-t-butylphenyl)chromium fulleride between T = 6 and 360 K was measured for the first time by precision adiabatic vacuum calorimetry. Also, for the first time, the temperature dependence of EPR signal parameters of bis(η6-t-butylphenyl)chromium fulleride in the range from 118 to 298 K was investigated by electron paramagnetic resonance. In the interval 170–210 K the reversible endothermic transformation was detected and its thermodynamic characteristics were estimated. This transformation was caused by dedimerization of fullerene fragments during heating. Based on the experimental data, the standard (p° = 0.1 MPa) thermodynamic functions, namely, the heat capacity, enthalpy, entropy, and Gibbs function of heating were calculated for dimeric fulleride in the interval from T → 0 to 170 K as well as for monomeric [Cr{η6-(t-BuPh)}2]•+C60•− complex between 210 and 360 K. The standard thermodynamic properties of tested fulleride and previously studied C60 fullerite and neutral dimer (C60)2 were compared.
Kinetic Study on the Interactions of Cyclodextrins with Organic Phosphates and Thiophosphates
Authors: Nagata Takuya , Yamamoto Kenta , Yoshikiyo Keisuke , Matsui Yoshihisa , Yamamoto Tatsuyuki 
Published: January 2009

Abstract
α-Cyclodextrin (α-CD) and 6-O-α-d-glucopyranosyl-β-cyclodextrin (G1-β-CD) affected the rates of phenol release from a few dimethyl(nitrophenyl) phosphates and the corresponding thiophosphates in aqueous alkaline solutions. Curve-fitting analysis of changes in the rate constants with CD concentrations showed that both α-CD and G1-β-CD form not only 1:1 but also 2:1 (host:guest) complexes with the phosphates and thiophosphates. In 1:1 complexes, phenol release from the phosphates was mostly accelerated, and that from the thiophosphates was decelerated. In 2:1 complexes, the reactions both of the phosphates and thiophosphates were strongly retarded. Binding constants and rate constants determined showed significant host and substrate specificities.
Benzothiazole-2-thiolato-Bridged Heterometallic Complexes and Their I2-Doped Products: Preparation, Characterization, and Conducting Properties
Authors: Singh Nanhai , Prasad Akhilesh , Sinha Rohit K 
Published: January 2009

Abstract
A series of new heterometallic complexes of the type [MM′(bzta)4] [M = Co2+, Pd2+, or 2Cu+; M′ = Ni2+; M = Fe3+ or Co3+; M′ = Cu+; bzta− = benzothiazole-2-thiolate (C6H4NSCS−)] and their I2-doped products have been synthesized. These have been characterized by elemental analyses, magnetic susceptibility measurement, IR and UV–visible spectroscopies, and solid-state electrical conductivity techniques. A significant observation is the ligand benzothiazole-2-thiolate mediated reduction of Cu2+ to Cu+ and subsequent oxidation of Co2+/Fe2+ to Co3+/Fe3+ in aqueous medium for some of the bimetallic complexes. Room-temperature solid-state electrical conductivities, σrt, ≈10−12 S m−1 and the increase in conductivity with increase in temperature in the 300–420 K range with activation energies, Ea = 0.20–0.68 eV show semiconducting properties of [CoNi(bzta)4], [NiPd(bzta)4], and [FeCu(bzta)4]. The σrt of I2-doped products of the complexes are increased 10–102 fold and show the behavior of semiconductors over the given temperature range.
Hydrophobic Ionic Liquids Composed of Perfluoroalkyltrifluoroborates for Ionic Liquid–Water Two-Phase Systems
Authors: Nishi Naoya , Suzuki Akihito , Kakiuchi Takashi 
Published: January 2009

Abstract
Ionic liquids (ILs) composed of perfluoroalkyltrifluoroborate ions (CnF2n+1BF3−, n = 2, 3, 4, and 6) and highly hydrophobic cations are found to have properties suitable to the applications of ILs in IL–water (W) two-phase systems because of their high stability against hydrolysis, high hydrophobicity, and low melting points. The rate of hydrolysis of CnF2n+1BF3− is four orders of magnitude slower than that of BF4−. The ion-transfer voltammograms for the transfer of CnF2n+1BF3− across the interface between nitrobenzene and W show that these CnF2n+1BF3− have hydrophobicity comparable to or higher than those of PF6− and bis(trifluoromethylsulfonyl)imide depending on n. The physicochemical properties (density, viscosity, conductivity, and solubility of ILs in W) of CnF2n+1BF3−-based ILs are measured for the ILs having melting points lower than room temperature. The hydrophobicity of the CnF2n+1BF3− ions is well correlated with the solubility of the ILs in W and also with the width of the polarized potential window at the IL|W interface.
Blast Counts in Bone Marrow Aspirate Smears
Authors: Vollmer Robin T. 
Published: January 2009

Abstract
Counts of cells or other phenomena observed through a microscope are numeric observations and, as such, are subject to mathematical and statistical analyses. For example, the Poisson probability function provides the probability of observing a particular number of blasts in a bone marrow aspirate, given an underlying true fraction of blasts present and a particular number of cells evaluated. Furthermore, using the Poisson function, Bayes theorem can provide the probabilities of specific categories of refractory anemia, given a number of observed blasts in a specific total of cells evaluated. Herein, I introduce and demonstrate these mathematical functions for the analysis of counts of blasts in marrow aspirates and explore the uncertainty that naturally arises when counts of blasts are near cut points used to separate the categories of refractory anemia without excess blasts, refractory anemia with excess blasts, and acute leukemia.