bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spiral phase velocity mapping of left and right coronary artery blood flow: Correction for through‐plane motion using selective fat‐only excitation
Authors: Keegan Jennifer , Gatehouse Peter D. , Yang Guang‐Zhong , Firmin David N. 
Published: November 2004

AbstractPurposeTo develop a method of correcting both right and left coronary artery flow velocities for the through‐plane motion of the vessel, in order to allow details in the temporal flow profiles to be viewed.Materials and MethodsThe methods developed use selective excitation and velocity mapping of the epicardial fat surrounding the artery, either in a separate acquisition (temporal resolution = 22 msec) or interleaved with the water‐excitation acquisition (temporal resolution = 44 msec) used to determine coronary blood flow velocities. The two methods were compared in 10 right and 13 left coronary arteries in healthy volunteers.ResultsFor the right coronary arteries, correction for through‐plane motion significantly reduces the mean systolic flow velocity (75.3 mm/second vs. 90.0 mm/second, P < 0.01), while the mean diastolic flow velocity is unchanged (96.8 mm/second vs. 94.5 mm/second, P = ns). The resulting profiles are biphasic, with approximately equal flow in systole and diastole. For the left arteries, correction for through‐plane motion reduces the mean systolic flow velocity (25.0 mm/second vs. 72.8 mm/second, P < 0.001), resulting in the expected diastolic predominant flow profiles. For the right arteries, there were no significant differences in the mean systolic and mean diastolic velocities after correction with the separate fat‐excitation acquisition, and after correction the poorer temporal resolution combined water excitation/fat excitation acquisition. However, for the left coronary arteries, the combined water excitation/fat excitation acquisition resulted in a slight reduction in the mean diastolic velocity (121.5 mm/second vs. 130.9 mm/second, P < 0.05).ConclusionSelective excitation of the surrounding epicardial fat enables through‐plane correction of both left and right coronary flow velocities, enabling the temporal details of flow velocity to be viewed.With a combined WE/FE acquisition, this can be performed without extending the study duration; however, the reduced temporal resolution and temporal mismatch of the excitations results in a blunting of rapidly changing flow profiles. As such, it may be less suitable for the left coronary artery, which has a greater range of through‐plane motion than the right, and correction using separate WE and FE acquisitions, or the adjacent myocardium, may be preferable. J. Magn. Reson. Imaging 2004;20:953–960. © 2004 Wiley‐Liss, Inc.
Improving the prediction of final infarct size in acute stroke with bolus delay–corrected perfusion MRI measures
Authors: Rose Stephen E. , Janke Andrew L. , Griffin Mark , Strudwick Mark W. , Finnigan Simon , Semple James , Chalk Jonathan B. 
Published: November 2004

AbstractPurposeTo investigate whether bolus delay‐corrected dynamic susceptibility contrast (DSC) perfusion MRI measures allowed a more accurate estimation of eventual infarct volume in 14 acute stroke patients using a predictive tissue classifier algorithm.Materials and MethodsTissue classification was performed using a expectation maximization and k‐means clustering algorithm utilizing diffusion and T2 measures (diffusion‐weighted imaging [DWI], apparent diffusion coefficient [ADC], and T2) combined with uncorrected perfusion measures cerebral blood flow ((CBF) and mean transit time [MTT]), bolus delay–corrected perfusion measures (cCBF and cMTT), and bolus delay–corrected perfusion indices (cCBF and cMTT with bolus delay).ResultsThe mean similarity index (SI), a kappa‐based correlation statistic reflecting the pixel‐by‐pixel classification agreement between predicted and 30‐day T2 lesion volumes, were 0.55 ± 0.19, 0.61 ± 0.15 (P < 0.02) and 0.60 ± 0.17 (P <0.03), respectively. Spearman's correlation coefficients, comparing predicted and final lesion volumes were 0.56 (P < 0.05), 0.70 (P < 0.01), and 0.84 (P < 0.001), respectively. We found a more significant correlation between predicted infarct volumes derived from bolus delay–corrected perfusion measures than from conventional perfusion measures when combined with diffusion measures and compared with final lesion volumes measured on 30‐day T2 MRI scans.ConclusionBolus delay–corrected perfusion measures enable an improved prediction of infarct evolution and evaluation of the hemodynamic status of neuronal tissue in acute stroke. J. Magn. Reson. Imaging 2004;20:941–947. © 2004 Wiley‐Liss, Inc.
Evaluation of a combined penetrometer for simultaneous measurement of penetration resistance and soil water content
Authors: Sun Yurui , Schulze Lammers Peter , Ma Daokun 
Published: November 2004

AbstractA combined penetrometer is an appropriate tool to measure the soil cone resistance and the water‐content profile. As a relatively new technique, a combined capacitance‐penetrometer for the simultaneous measurement of cone index and soil water content was developed at the Department of Agricultural Engineering of Bonn University in 2002. The objective of this study was the evaluation of the effectiveness and applicability of the innovated penetrometer with a focus on three aspects: (1) A capacitance sensor with two electrode configurations was calibrated for silt loam, sandy loam, and sand. The calibration results show that both electrode configurations have sufficient water‐content sensitivity, but soil‐specific calibrations seem necessary. (2) Under laboratory conditions, the dynamic resolution and response of the capacitance‐penetrometer were validated, and its radius of influence was determined. (3) The field measurement results demonstrate that this measurement technique can be used to improve the interpretation quality of soil cone index data.
Using natural 13C abundances to differentiate between three CO2 sources during incubation of a grassland soil amended with slurry and sugar
Authors: Kuzyakov Yakov , Bol Roland 
Published: November 2004

AbstractThis study describes a novel approach to separate three soil carbon (C) sources by one tracer method (here 13C natural abundance). The approach uses the temporal dynamics of the CO2 efflux from a C3 grassland soil amended with added C3 or C4 slurry and/or C3 or C4 sugar to estimate contributions of three separate C sources (native soil, slurry, and sugar) to CO2 efflux. Soil with slurry and/or sugar was incubated under controlled conditions, and concentration and δ13C values of evolved CO2 were measured over a 2‐week period. The main assumption needed for separation of three C sources in CO2 efflux, i.e., identical decomposition of applied C3 and C4 sugars in soil, was investigated and proven. The relative contribution to the CO2 efflux was higher, but shorter with an increased (microbial) availability of the C source, i.e., sugar > slurry > SOM. The shortcomings and limitations as well as possible future applications of the suggested method are discussed.
Contribution of nitrification and denitrification to the emission of N2O in a freeze‐thaw event in an agricultural soil
Authors: Ludwig Bernard , Wolf Inken , Teepe Robert 
Published: November 2004

AbstractThe amounts of N2O released in freeze‐thaw events depend on site and freezing conditions and contribute considerably to the annual N2O emissions. However, quantitative information on the N transformation rates in freeze‐thaw events is scarce. Our objectives were (1) to quantify gross nitrification in a Luvisol during a freeze‐thaw event, (2) to analyze the dynamics of the emissions of N2O and N2, (3) to quantify the contribution of nitrification and denitrification to the emission of N2O, and (4) to determine whether the length of freezing and of thawing affects the C availability for the denitrification. 15NO$ _3^- $ was added to undisturbed soil columns, and the columns were subjected to 7 d of freezing and 5 d of thawing. N2O emissions were determined in 3 h intervals, and the concentrations of 15N2O and 15N2 were determined at different times during thawing. During the 12 d experiment, 5.67 mg NO$ _3^- $‐N (kg soil)–1 was produced, and 2.67 mg NO$ _3^- $‐N (kg soil)–1 was lost. By assuming as a first approximation that production and loss occurred exclusively during thawing, the average nitrate‐production rate, denitrification rate, and immobilization rate were 1.13, 0.05, and 0.48 mg NO$ _3^- $‐N (kg soil)–1 d–1, respectively. Immediately after the beginning of the thawing, denitrification contributed by 83% to the N2O production. The ratios of 15N2 to 15N2O during thawing were narrow and ranged from 1.5 to 0.6. For objective (4), homogenized soil samples were incubated under anaerobic conditions after different periods of freezing and thawing. The different periods did not affect the amounts of N2 and N2O produced in the incubation experiments. Further, addition of labile substrates gave either increases in the amounts of N2O and N2 produced or no changes which suggested that changes in nutrient availability due to freezing and thawing are only small.
The effect of alkaline‐stabilized–sludge application on the microbiological quality of soil and leachate
Authors: Olcay Kocaer Fatma , Alkan Ufuk , Savaş Başkaya Hüseyin 
Published: November 2004

AbstractThe influences of fly ash and fly‐ash–quicklime‐treated‐sludge mixtures (with fly‐ash doses of 40%, 80%, and 120% on dry‐weight basis) on the microbial numbers in soil and leachate were investigated by using 60 cm soil columns. Heterotrophic bacteria and total coliform numbers were determined in soil and leachate samples following an artificial rainfall event.The results indicated that land application of untreated sludge and fly‐ash–sludge mixtures appear to introduce large numbers of bacteria to leachates and soil. Although the numbers in leachates and soils were found to decrease with increasing ash ratios, they were still all significantly above the control levels. Application of alkaline‐stabilized and pasteurized sludge did not increase bacterial numbers significantly in soil and leachate. Distribution of heterotrophic bacteria through soil profile clearly showed no increase in soils amended with alkaline‐stabilized and pasteurized sludges. Additionally, no significant inhibitory effect of lignite fly ash on soil microbial population was observed.
Alkyl C and hydrophobicity in B and C horizons of an acid forest soil
Authors: Rumpel Cornelia , Seraphin Ariane , Goebel Marc‐Oliver , Wiesenberg Guido , Gonzales‐Vila Francisco , Bachmann Jörg , Schwark Lorenz , Michaelis Walter , Mariotti André , Kögel‐Knabner Ingrid 
Published: November 2004

AbstractAliphatic C most probably derived from ester‐bound moieties was found to be present in sandy subsoil horizons. The hydrophobic nature of such compounds may increase their stabilization potential. Therefore, the aim of this study was to investigate the potential of aliphatic compounds in mineral soil horizons along a Dystric Cambisol profile under beech forest to increase hydrophobicity. The conceptual approach included the analyses of soil samples before and after solvent extraction and base hydrolysis for elemental and isotopic composition. Additionally, the advancing contact angle was measured to quantify hydrophobicity. Curie‐point pyrolysis GC/MS was carried out to characterize the nature of alkyl C present in subsoil samples. A close correlation between the 14C activity and the stable‐C‐isotope ratio (δ13C) indicates isotopic fractionation upon C stabilization in subsoils. Free lipids contributed less than 10% to the organic C found in subsoil horizons. Base hydrolysis revealed very high amounts of hydroxyalkanoic acids in the B horizons of the acid forest soil. Hydrophobicity of SOM was not found to be correlated to esterified‐ or free‐lipid content. The contact angle was in a similar range for all bulk soil horizons, suggesting greater hydrophobicity of organic matter in subsoil horizons considering their very low concentrations of organic C compared to the A horizon. The quantity and nature of pyrolysis products change with increasing depth in the soil profile. Aliphatic products cannot be detected in B and C horizons by Curie‐point pyrolysis GC/MS.
Adversarial models for priority‐based networks
Authors: Àlvarez C. , Blesa M. , Díaz J. , Serna M. , Fernández A. 
Published: November 2004

AbstractIn this article, we propose several variations of the adversarial queueing model and address stability issues of networks and protocols in those proposed models. The first such variation is thepriority model, which is directed at static network topologies and takes into account the case in which packets can have different priorities. Those priorities are assigned by an adversary at injection time. A second variation, thevariable priority model, is an extension of the priority model in which the adversary may dynamically change the priority of packets at each time step. Two more variations, namely thefailure modeland thereliable model, are proposed to cope with dynamic networks. In the failure and reliable models the adversary controls, under different constraints, the failures that the links of the topology might suffer. Concerning stability of networks in the proposed adversarial models, we show that the set ofuniversally stablenetworks in the adversarial model remains the same in the priority, variable priority, failure, and reliable models. From the point of view of protocols (or queueing policies), we show that several protocols that are universally stable in the adversarial queueing model remain so in the priority, failure, and reliable models. However, we show that thelongest‐in‐system(LIS) protocol, which is universally stable in the adversarial queueing model, is not universally stable in any of the other models we propose. Moreover, we show that no queueing policy is universally stable in the variable priority model. Finally, we analyze the problem of deciding stability of a given network under a fixed protocol. We provide a characterization of the networks that are stable underfirst‐in‐first‐out(FIFO) and LIS in the failure model (and therefore in the reliable and priority models). This characterization allows us to show that the stability problem under FIFO and LIS in the failure model can be solved in polynomial time. © 2004 Wiley Periodicals, Inc. NETWORKS, Vol. 45(1), 23–35 2005
Synthesis of new amphiphilic and lypophilic polymer networks containing 2‐methyl‐ and 2‐nonyl‐2‐oxazoline by the macroinitiator method
Authors: Rueda Juan Carlos , Komber Hartmut , Voit Brigitte 
Published: November 2004

AbstractNew amphiphilic and lypophilic polymer networks were obtained by the copolymerization of 2‐methyl‐2‐oxazoline (MeOXA), and/or 2‐nonyl‐2‐oxazoline (NoOXA) and 2,2′‐tetramethylenebis(2‐oxazoline) (BisOXA), respectively, initiating the copolymerization by random copolymers of chloromethylstyrene and methyl methacrylate or of chloromethylstyrene and styrene (macroinitiator method). Potassium iodide was used as an activator agent and the reaction was carried out in benzonitrile at 110 °C. In general, the polymer gels were obtained with a yield of 62 to 88%. The networks were characterized by high‐resolution magic angle spinning (HRMAS) NMR spectroscopy and by its absorption of polar and nonpolar solvents. In the case of amphiphilic polymer networks, the absorption of solvents depends on the molar ratio of 2‐methyl‐ to 2‐nonyl‐2‐oxazoline inside the polymer network favoring the absorption of polar solvents with a higher content of 2‐methyl‐2‐oxazoline. These gels showed a maximal swelling degree of 13 mL of water, 20 mL of methanol, and 13 mL of chloroform, respectively, per g of polymer. The lypophilic polymer networks containing only 2‐nonyl‐2‐oxazoline showed a maximal swelling degree of 8 mL of toluene, 14 mL of chloroform, and 2 mL of methanol, respectively, per g of the lypophilic network. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 122–128, 2005
Differential scanning calorimetry study on thermal behaviors of freeze‐dried poly(L‐lactide) from dilute solutions
Authors: Sasaki Takashi , Yamauchi Nobutaka , Irie Satoshi , Sakurai Kensuke 
Published: November 2004

AbstractGlass transition, cold crystallization, and melting of freeze‐dried poly(L‐lactide) (PLLA) prepared from dilute 1,4‐dioxane solutions were investigated by differential scanning calorimetry (DSC). Conventional DSC measurements of heating scans revealed that freeze‐dried PLLA prepared from a 0.07 wt % solution undergoes a two‐step cold crystallization (or reorganization) with a lower exotherm appearing at about 78 °C and with a higher broad exotherm between 110–155 °C. The peak temperature of the former exotherm is about 50 K lower than that observed for a reference bulk sample. Step‐scan mode DSC, which provides information essentially equivalent to that obtained from the temperature‐modulated DSC, revealed that the glass‐transition temperature is about 6 K lower than that of the reference bulk. These findings suggest enhanced chain mobility for freeze‐dried PLLA. Freeze‐dried PLLA that crystallized at 80 °C for 40 min was revealed to contain a rather large amount of rigid amorphous material (42%). © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 115–124, 2005
Rational discovery of a novel interface for a coactivator in the peroxisome proliferator‐activated receptor γ: Theoretical implications of impairment in type 2 diabetes mellitus
Authors: Shiraki Takuma , Kodama Takashi S. , Jingami Hisato , Kamiya Narutoshi 
Published: November 2004

AbstractThe peroxisome proliferator‐activated receptor γ (PPARγ) is important to adipocyte differentiation and glucose homeostasis, and mutations in the gene have been observed in type 2 diabetes mellitus. The mutated residues, V290 and P467, bind to neither ligands nor a coactivator peptide in the reported crystal structures of the PPARγ ligand binding domain. To understand the mechanism of type 2 diabetes mellitus caused by germline mutations in the PPARγ ligand‐binding domain, theoretical models of the PPARγ–ligand–coactivator complex were built at an atomic resolution. In the models, the secondary coactivator peptide was docked next to the conventional coactivator peptide, which both contain the LXXLL motif. The secondary interface in PPARγ for the secondary coactivator peptide has not been demonstrated by experiments. Binding energy calculations of the complex, considering the solvent effect, revealed that the secondary coactivator peptide, derived from nuclear receptor box 1 of steroid receptor coactivator 1, can be favorably bound to the secondary interface. The secondary coactivator peptide forms hydrogen bonds and a hydrophobic core with PPARγ and the primary coactivator peptide. Next, we applied mutations to PPARγ in silico and found that the V290M mutation, observed in type 2 diabetes mellitus, adversely affected the binding of the secondary peptide. Thus, our model provides structural insight into the impairment of PPARγ function in type 2 diabetes mellitus. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine‐scanning mutagenesis of residues at the protein–DNA interface
Authors: Radlinska Monika , Kondrzycka‐Dada Aneta , Piekarowicz Andrzej , Bujnicki Janusz M. 
Published: November 2004

AbstractDNA:m5C MTases comprise a catalytic domain with conserved residues of the active site and a strongly diverged TRD with variable residues involved in DNA recognition and binding. To date, crystal structures of 2 DNA:m5C MTases complexed with the substrate DNA have been obtained; however, for none of these enzymes has the importance of the whole set of DNA‐binding residues been comprehensively studied. We built a comparative model of M.NgoPII, a close homologue and isomethylomer of M.HaeIII, and systematically analyzed the effect of alanine substitutions for the complete set of amino acid residues from its TRD predicted to be important for DNA binding and target recognition. Our data demonstrate that only 1 Arg residue is indispensable for the MTase activity in vivo and in vitro, and that mutations of only a few other residues cause significant reduction of the activity in vitro, with little effect on the activity in vivo. The identification of dispensable protein–DNA contacts in the wild‐type MTase will serve as a platform for exhaustive combinatorial mutagenesis aimed at the design of new contacts, and thus construction of enzyme variants that retain the activity but exhibit potentially new substrate preferences. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Analysis of pH‐dependent elements in proteins: Geometry and properties of pairs of hydrogen‐bonded carboxylic acid side‐chains
Authors: Wohlfahrt Gerd 
Published: November 2004

AbstractA rather frequent but so far little discussed observation is that pairs of carboxylic acid side‐chains in proteins can share a proton in a hydrogen bond. In the present article, quantum chemical calculations of simple model systems for carboxyl–carboxylate interactions are compared with structural observations from proteins. A detailed structural analysis of the proteins deposited in the PDB revealed that, in a subset of proteins sharing less than 90% sequence identity, 19% (314) contain at least one pair of carboxylic acids with their side‐chain oxygen atoms within hydrogen‐bonding distance. As the distance between those interacting oxygen atoms is frequently very short (∼2.55 Å), many of these carboxylic acids are suggested to share a proton in a strong hydrogen bond. When situated in an appropriate structural environment (low dielectric constant), some might even form a low barrier hydrogen bond. The quantum chemical studies show that the most frequent geometric features of carboxyl–carboxylate pairs found in proteins, and no or symmetric ligation, are also the most stable arrangements at low dielectric constants, and they also suggest at medium and low pH a higher stability than for isosteric amide–carboxylate pairs. The presence of these pairs in 119 different enzymes found in the BRENDA database is set in relation to their properties and functions. This analysis shows that pH optima of enzymes with carboxyl–carboxylate pairs are shifted to lower than average values, whereas temperature optima seem to be increased. The described structural principles can be used as guidelines for rational protein design (e.g., in order to improve pH or temperature stability). Proteins 2005. © 2004 Wiley‐Liss, Inc.
First‐principles calculations on the origins of the gap bowing in BeSxSe1–x, BeSxTe1–x and BeSexTe1–x alloys
Authors: El Haj Hassan F. 
Published: November 2004

AbstractFirst‐principles calculations have been used to investigate the electronic structure and disorder effects in beryllium chalcogenides alloys (BeSxSe1–x, BeSxTe1–x and BeSexTe1–x) using the full potential‐linearized augmented‐plane wave method (FP‐LAPW) within density‐functional theory. We used the local‐density approximation within the generalized gradient correction as well as the Engel–Vosko GGA formalism to calculate the electronic structure at equilibrium volume. The ground‐state properties are determined for the bulk materials (BeS, BeSe, and BeTe) as well as for the average concentration (x = 0.5) of the alloys. Using the approach of Zunger and coworkers, the microscopic origins of compositional disorder have been detailed and explained. The disorder parameter (gap bowing) is found to be mainly caused by the chemical charge‐transfer effect, while the volume deformation and the structural relaxation contribute to the gap bowing parameter at smaller magnitude. This should be expected since there is a weak lattice mismatch between the binary compounds and a considerable electronegativity difference between Be and X (X = S, Se, Te) atoms. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)