bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative analysis of cation binding to the adenosine nucleotides using the Variable Ionic Strength method: Validation of the Debye–Hückel–Onsager theory of electrophoresis in the absence of counterion binding
Authors: Stellwagen Earle , Stellwagen Nancy C. 
Published: February 2007

AbstractThe free solution mobilities of the adenosine nucleotides 5′‐adenosine triphosphate (ATP), 5′‐adenosine diphosphate (ADP), 5′‐adenosine monophosphate (AMP), and 3′‐5′‐cyclic AMP (cAMP) have been measured in diethylmalonate buffers containing a wide variety of monovalent cations. The mobilities of all nucleotides increase gradually with the increase in intrinsic conductivity of the cation in the BGE. However, at a given conductivity, the mobilities observed for ATP, ADP, and AMP in BGEs containing alkali metal ions and other cations are lower than these observed in BGEs containing tetraalkylammonium ions. Since the mobility of cAMP is independent of the cation in the BGE, the results suggest that the relatively low mobilities observed for ATP, ADP, and AMP in BGEs containing cations other than a tetraalkylammonium ion are due to cation binding, reducing the effective net charge of the nucleotide and thereby reducing the observed mobility. To measure the binding quantitatively, the mobilities of the nucleotides were measured as a function of ionic strength. The mobilities of ATP, ADP, and AMP decrease nonlinearly with the square root of ionic strength (I1/2) in BGEs containing an alkali metal ion or Tris+. By contrast, the mobilities decrease linearly with I1/2 in BGEs containing a nonbinding quaternary ammonium ion, as expected from Debye–Hückel–Onsager (DHO) theory. The mobility of cAMP, a nonbinding analyte, decreases linearly with I1/2, regardless of the cation in the BGE. Hence, a nonlinear decrease of the mobility of an analyte with I1/2 appears to be a hallmark of counterion binding. The curved mobility profiles observed for ATP, ADP, and AMP in BGEs containing an alkali metal ion or Tris+ were analyzed by nonlinear curve fitting, using difference mobility profiles to correct for the effect of the physical properties of BGE on the observed mobilities. The calculated apparent dissociation constants range from 22 to 344 mM, depending on the particular cation–nucleotide pair. Similar values have been obtained by other investigators, using different methods. Interestingly, Tris+ and Li+ bind to the adenosine nucleotides with approximately equal affinities, suggesting that positively charged Tris+ buffer ions can compete with alkali metal ions in Tris‐buffered solutions.
Volumetric methods for evaluating energy loss and heat transfer in cavity flows
Authors: Norris Stuart , Mallinson Gordon 
Published: February 2007

AbstractMethods have been developed for calculating irreversible energy losses and rates of heat transfer from computational fluid dynamics solutions using volume integrations of energy dissipation or entropy production functions. These methods contrast with the more usual approach of performing first law energy balances over the boundaries of a flow domain. Advantages of the volumetric approach are that the estimates involve the whole flow domain and are hence based on more information than would otherwise be used, and that the energy dissipation or entropy production functions allow for detailed assessment of the mechanisms and regions of energy loss or entropy production.Volume integrations are applied to the calculation of viscous losses in a lid‐driven cavity flow, and to the viscous losses and heat transfer due to natural convection in a side‐heated cavity. In the convection problem comparison with the entropy increase across a stationary heat conducting layer leads to a novel volume integral expression for the Nusselt number. The predictions using this method compare well with traditional surface integrals and benchmark results. Copyright © 2007 John Wiley & Sons, Ltd.
On level set modelling of bi‐fluid capillary flow
Authors: Lesage Anne‐Cécile , Allain Olivier , Dervieux Alain 
Published: February 2007

AbstractWe consider the adaptation of a level set (LS) method for the simulation of capillary flows on unstructured meshes. The advection step is first analysed. In order not to lose accuracy, this step should be one order more accurate than the discretization of the velocity. We then compare different ways in choosing the LS velocity and in re‐initializing the LS function between advection phases without losing too much accuracy. Applications to Rayleigh flows and to reorientation with contact angle are presented. Copyright © 2007 John Wiley & Sons, Ltd.
Numbering techniques for preconditioners in iterative solvers for compressible flows
Authors: Pollul B. , Reusken A. 
Published: February 2007

AbstractWe consider Newton–Krylov methods for solving discretized compressible Euler equations. A good preconditioner in the Krylov subspace method is crucial for the efficiency of the solver. In this paper we consider a point‐block Gauss–Seidel method as preconditioner. We describe and compare renumbering strategies that aim at improving the quality of this preconditioner. A variant of reordering methods known from multigrid for convection‐dominated elliptic problems is introduced. This reordering algorithm is essentially black‐box and significantly improves the robustness and efficiency of the point‐block Gauss–Seidel preconditioner. Results of numerical experiments using the QUADFLOW solver and the PETSc library are given. Copyright © 2007 John Wiley & Sons, Ltd.
The impact of execution delay on the profitability of put‐call‐futures trading strategies—Evidence from Taiwan
Authors: Chiou Jong‐Rong , Hsieh Wen‐Liang Gideon , Lin Yuan‐Yi 
Published: February 2007

AbstractThis study examines the impact of execution delay on the profitability of put‐call‐futures quasi‐arbitrage strategies using trade and quote data in the Taiwanese market. Assuming order execution at the next immediate price following a mispricing signal, the execution of individual components is traced and a substantial delay resulting from the late execution of an option is reported. A fill‐or‐kill strategy that directly restricts such a delay is unsatisfactory because unwinding already acquired positions involves added transaction costs. Ex ante performance is significantly improved for combined strategies that execute the less liquid asset first, while shortening the time before acquisition of the first position. © 2007 Wiley Periodicals, Inc. Jrl Fut Mark 27:361–385, 2007
On inverse carrying charges and spatial arbitrage
Authors: Larson Donald F. 
Published: February 2007

AbstractA dynamic trader problem under uncertain demand is presented and spatial and temporal arbitrage conditions derived from first‐order conditions. A time‐varying storage premium that explains backwardation and inverse carrying charges independent of risk‐aversion, stockouts, or convenience is developed. Random‐returns and cost‐of‐carry models are expressed as special conditions of the derived model. An applied composite‐error model is estimated using data from the London Metal Exchange's copper contract. Predictions of the model are tested against well‐known alternatives. © 2007 Wiley Periodicals, Inc. Jrl Fut Mark 27:305–336, 2007
Tissue type plasminogen activator induced in rat dorsal horn astrocytes contributes to mechanical hypersensitivity following dorsal root injury
Authors: Kozai Toyoko , Yamanaka Hiroki , Dai Yi , Obata Koichi , Kobayashi Kimiko , Mashimo Takashi , Noguchi Koichi 
Published: February 2007

AbstractDorsal root injury is known to induce alteration of the extracellular environment in the spinal cord and synaptic reorganization with degradation of injured primary afferent and sprouting of spared terminal. These changes affect behavioral sensitivity and sometimes lead to neuropathic pain. We have hypothesized that changes in extracellular proteolysis in the dorsal horn is involved in neuroplastic changes in the dorsal horn after nerve injury. Tissue type plasminogen activator (tPA) is a well‐known extracellular serine protease and is involved in the modification of the extracellular matrix, which leads to neuroplastic changes such as long‐term potentiation in the hippocampus. In the present study, we found a marked induction of tPA in activated astrocytes following L4/5 root injury and a resultant increase of proteolytic enzymatic activity in the dorsal horn. We also examined the involvement of tPA activity on mechanical hypersensitivity using a root ligation model which has been used for investigating radiculopathy pain behavior. Intrathecal and continuous administration of tPA inhibitor, tPA‐STOP, suppressed root ligation‐induced mechanical allodynia in a dose‐dependent manner during an early stage of injury (0–4 days). In contrast, the delayed administration of tPA‐STOP during the chronic stage of injury (10 days) did not affect pain behavior. These data suggest an important contribution of astrocytes in the dorsal horn to the pathophysiology of radiculopathy pain, and astrocyte‐derived tPA and the proteolytic activity in the dorsal horn may be one of the essential factors involved in pain following root injury. © 2007 Wiley‐Liss, Inc.
Murine model of Alexander disease: Analysis of GFAP aggregate formation and its pathological significance
Authors: Tanaka Kenji F. , Takebayashi Hirohide , Yamazaki Yoshihiko , Ono Katsuhiko , Naruse Masae , Iwasato Takuji , Itohara Shigeyoshi , Kato Hiroshi , Ikenaka Kazuhiro 
Published: February 2007

AbstractAlexander disease is caused by a coding mutation in the glial fibrillary acidic protein (GFAP) gene. The pathological hallmark is the formation of cytoplasmic inclusions within astrocytes known as Rosenthal fibers (RFs), which primarily consist of GFAP and several heat shock proteins. The presence of mutant GFAP would appear to be involved in RF formation; however, overproduction of wild type human GFAP in mouse brain also results in RF formation. Here, we investigated the in vivo conditions leading to formation of RF‐like aggregates. We used transgenic mice (mouse GFAP promoter‐human GFAP cDNA with R239H mutation) in which the dosage of the GFAP transgene could be manipulated within the same genetic locus. We found that the presence of mutant GFAP per se was insufficient for aggregate formation. Instead, a 30% increase in GFAP content over that in wild type was also required. GFAP aggregates upregulated endogenous GFAP and nestin gene expression, and intermediate filament structure revealed by immunostaining was fragmented under these conditions. However, overall morphology of astrocytes, including their fine processes, was unaffected. In this transgenic animal model, mice did not show megalencephaly, leukodystrophy, or seizure characteristic of Alexander disease with R239H mutation. Nevertheless, their mortality after kainate challenge was dramatically increased, whereas transgenic mice lacking aggregates exhibited mortality similar to that of wild type mice. These results indicate that the presence of GFAP aggregates containing mutant GFAP is not sufficient to induce a major phenotype of Alexander disease, even though it causes some abnormalities in the mouse. © 2007 Wiley‐Liss, Inc.
Nodal protrusions, increased Schmidt‐Lanterman incisures, and paranodal disorganization are characteristic features of sulfatide‐deficient peripheral nerves
Authors: Hoshi Tomiko , Suzuki Ayaka , Hayashi Shuichiro , Tohyama Koujiro , Hayashi Akiko , Yamaguchi Yoshihide , Takeuchi Kosei , Baba Hiroko 
Published: February 2007

AbstractGalactocerebroside and sulfatide are two major glycolipids in myelin; however, their independent functions are not fully understood. The absence of these glycolipids causes disruption of paranodal junctions, which separate voltage‐gated Na+ and Shaker‐type K+ channels in the node and juxtaparanode, respectively. In contrast to glial cells in the central nervous system (CNS), myelinating Schwann cells in the peripheral nervous system (PNS) possess characteristic structures, including microvilli and Schmidt‐Lanterman incisures, in addition to paranodal loops. All of these regions are involved in axo–glial interactions. In the present study, we examined cerebroside sulfotransferase‐deficient mice to determine whether sulfatide is essential for axo–glial interactions in these PNS regions. Interestingly, marked axonal protrusions were observed in some of the nodal segments, which often contained abnormally enlarged vesicles, like degenerated mitochondria. Moreover, many transversely cut ends of microvilli surrounded the mutant nodes, suggesting that alignments of the microvilli were disordered. The mutant PNS showed mild elongation of nodal Na+ channel clusters. Even though Caspr and NF155 were completely absent in half of the paranodes, short clusters of these molecules remained in the rest of the paranodal regions. Ultrastructural analysis indicated the presence of transverse bands in some paranodal regions and detachment of the outermost several loops. Furthermore, the numbers of incisures were remarkably increased in the mutant internode. Therefore, these results indicate that sulfatide may play an important role in the PNS, especially in the regions where myelin–axon interactions occur. © 2007 Wiley‐Liss, Inc.
IGF‐1 stimulates de novo fatty acid biosynthesis by Schwann cells during myelination
Authors: Liang Guoying , Cline Gary W. , Macica Carolyn M. 
Published: February 2007

AbstractSchwann cell (SC) differentiation to the myelinating phenotype is characterized by the elaboration of a lipid‐rich membrane and the expression of myelin‐specific proteins. Insulin‐like growth factor‐1 (IGF‐1) has been identified as a growth factor that stimulates the early events of myelination in SCs that signals via the PI3K/Akt pathway. Given the role of IGF‐1 in promoting myelination, we performed studies to determine if the fatty acid biosynthetic pathway was a target of IGF‐1 signaling in the formation of myelin membrane in dorsal root ganglion neuron/Schwann cell (DRG/SC) cocultures. We report that the fatty acid profile of lipid extracts of cocultures treated with IGF‐1 match that reported for native myelin membrane by electrospray mass spectroscopy analysis. We also demonstrate de novo fatty acid biosynthesis in response to IGF‐1 treatment in DRG/SC cocultures metabolically labeled with 13C‐acetate as a carbon source for fatty acid synthesis. Consistent with this finding, Western blot analysis of lysates from both cocultures and purified SCs reveal that IGF‐1 stimulates two key fatty acid synthesizing enzymes. Additionally, we show that stimulation of fatty acid synthesizing enzymes is mediated by the PI3K/Akt signaling pathway. We also show that the fatty acid synthesizing enzymes and associated signaling pathways are elevated during the period of myelin membrane formation in sciatic nerve. Collectively, these findings demonstrate that IGF‐1 plays an important regulatory function during myelin membrane formation. © 2007 Wiley‐Liss, Inc.
Progressivity in the financing of decentralized government health programs: a decomposition
Authors: Wagstaff Adam , Lindelow Magnus 
Published: February 2007

AbstractIn many countries health services and/or health insurance are delivered but also partly financed by subnational entities that vary in their fiscal or financial capacity, e.g. local governments and social health insurance schemes. The central government typically mandates a specific (or at least minimum) level of benefit or expenditure per intended beneficiary, and sets rules about enrollment and coverage. It also typically contributes to the cost of the program, partly because the resources of subnational entities may be insufficient, on average, to meet the expenditure requirements, but partly for equity reasons. These two problems are typically addressed through tax‐transfer schemes. In practice, there is considerable institutional heterogeneity across countries in the mix of vertical and horizontal schemes, and the way each works. In this Note, we show how the progressivity of health outlays by subnational entities can be decomposed into contributions from vertical and horizontal schemes, and how each of these can be further decomposed into contributions from taxes and transfers. We suggest that, in addition to providing a foundation for future empirical work, the decomposition provides some insights into the reasons for different institutional choices, and into the way vertical and horizontal tax‐transfer schemes operate in practice. Copyright © 2007 John Wiley & Sons, Ltd.
A change detection algorithm for terrain surface moisture mapping based on multi‐year passive microwave remote sensing (Examples of SSM/I and TMI Channels)
Authors: Jin Ya‐Qiu , Yan Fenghua 
Published: February 2007

AbstractAs an indication of the surface polarized emission, a polarization index (PI) of microwave radiance from the terrain surface (half‐space of canopy‐soil land) is derived from the radiative transfer model. This PI separates the radiance effects of the canopy‐soil moisture and interference from surface roughness and atmosphere, and is suitable to describe the change of terrain surface moisture, especially for extreme drought or flood conditions. As an example, the statistics of the monthly average < PI > from 6 years' data of the Defense Meteorological Satellite Program (DMSP) SSM/I observations at the lowest frequency 19·35 GHz channel as available are applied for the demonstration of the surface moisture status over a large and heterogeneous territory such as China. The deviation of the PI data at the same month from the average < PI > , i.e. ΔnPI(≡(PI− < PI>)/ < PI>), gives prominence to focusing moisture variation of terrain surface, and its anomaly shows possible drought or flood occurrence in extreme conditions. The ΔnPI mapping is validated by the typical examples of the drought in China's Shanxi area in May 2001 and the flood around China's Yangtze River in August 1998, respectively. Our approach is recommended for lower frequency channels to minimize the influence from vegetation canopy for future applications (such as the channels of the Advanced Microwave Scanning Radiometer [AMSR‐E] launched in May 2002 and microwave imaging radiometer of China's Fengyun satellite series). When the monthly < PI > and the ground truth of average volumetric moisture < mv > of the region are correctly evaluated, it is tractable to retrieve the soil land surface moisture by using the PI data at the same month and the same region without much knowledge of surface roughness, vegetation canopy and other factors. As an example, the retrieval of mv is favourably tested by using the Tropical Rainfall Measuring Mission (TRMM) Tropical Microwave Imager (TMI) data. Copyright © 2007 John Wiley & Sons, Ltd.
Aromatic‐backbone interactions in model α‐helical peptides
Authors: Palermo Nicholas Y. , Csontos József , Owen Michael C. , Murphy Richard F. , Lovas Sándor 
Published: February 2007

AbstractThe effects on helical stability of weak polar interactions between aromatic side‐chains and the peptide backbone were examined. α‐Helical model peptides, hexa‐Ala, with sequential Tyr replacement, were investigated computationally to obtain the geometries and energetics of the interactions. Geometries were obtained with the B3LYP/6‐31G* level of theory. Interaction energies were calculated using BHandHLYP/cc‐pVTZ and an improved method to correct for basis set superposition error when fragmentation caused steric clashes. Both i, i + 1 and i, i − 4 interactions were observed when Tyr was in position i = 5. The position of the aromatic residue in the amino acid sequence was crucial in facilitating aromatic‐backbone interactions. The distance between the center of the aromatic ring of Tyr and the individual interacting backbone atoms ranged from 3.65 to 5.50 Å. The interactions have energies of the same order as hydrogen bonds and, thus, could have a significant impact on the stability of the helix. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Evaluation of coarse grained models for hydrogen bonds in proteins
Authors: De Sancho David , Rey Antonio 
Published: February 2007

AbstractBackbone hydrogen bonds contribute very importantly to the stability of proteins and therefore they must be appropriately represented in protein folding simulations. Simple models are frequently used in theoretical approaches to this process, but their simplifications are often confronted with the need to be true to the physics of the interactions. Here we study the effects of different levels of coarse graining in the modeling of backbone hydrogen bonds. We study three different models taken from the bibliography in a twofold fashion. First, we calculate the hydrogen bonds in 2gb1, an (α + β)‐protein, and see how different backbone representations and potentials can mimic the effects of real hydrogen bonds both in helices and sheets. Second, we use an evolutionary method for protein fragment assembly to locate the global energy minimum for a set of small β‐proteins with these models. This way, we assess the effects of coarse graining in hydrogen bonding models and show what can be expected from them when used in simulation experiments. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Self‐organizing superimposition algorithm for conformational sampling
Authors: Zhu Fangqiang , Agrafiotis Dimitris K. 
Published: February 2007

AbstractA novel self‐organizing algorithm for conformational sampling is introduced, in which precomputed conformations of rigid fragments are used as templates to enforce the desired geometry. Starting from completely random coordinates, the algorithm repeatedly superimposes the templates to adjust the positions of the atoms, thereby gradually refining the conformation of the molecule. Combined with pair‐wise adjustments of the atoms to resolve steric clashes, conformations that satisfy all geometric constraints can be generated from this procedure. The algorithm is demonstrated to achieve good performance and promises potential applications on more challenging modeling problems. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Vibalizer: A free, web‐based tool for rapid, quantitative comparison and analysis of calculated vibrational modes
Authors: Grafton Anthony K. 
Published: February 2007

AbstractThis report describes the development and applications of a software package called Vibalizer, the first and only method that provides free, fast, interactive, and quantitative comparison and analysis of calculated vibrational modes. Using simple forms and menus in a web‐based interface, Vibalizer permits the comparison of vibrational modes from different, but similar molecules and also performs rapid calculation and comparison of isotopically substituted molecules' normal modes. Comparing and matching complex vibrational modes can be completed in seconds with Vibalizer, whereas matching vibrational modes manually can take hours and gives only qualitative comparisons subject to human error and differing individual judgments. In addition to these core features, Vibalizer also provides several other useful features, including the ability to automatically determine first‐approximation mode descriptions, to help users analyze the results of vibrational frequency calculations. Because the software can be dimensioned to handle almost arbitrarily large systems, Vibalizer may be of particular use when analyzing the vibrational modes of complex systems such as proteins and extended materials systems. Additionally, the ease of use of the Vibalizer interface and the straightforward interpretation of results may find favor with educators who incorporate molecular modeling into their classrooms. The Vibalizer interface is available for free use at http://www.compchem.org, and it is also available as a locally‐installable package that will run on a Linux‐based web server. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007