bluuebunny/crossref_metadata_2025_split huggingface dataset:
A computational stream function method for two‐dimensional incompressible viscous flows
Authors: Kobayashi Marcelo H. , Pereira José Manuel C. 
Published: February 2005

AbstractThis work concerns the development of a numerical method based on the stream function formulation of the Navier–Stokes equations to simulate two‐dimensional—plane or axisymmetric—viscous flows. The main features of the proposed method are: the use of the high order finite‐difference compact method for the discretization of the stream function equation, the implicit pseudo‐transient Newton–Krylov‐multigrid matrix free method for the stationary stream function equation and the fourth order Runge–Kutta method for the integration of non‐stationary flows. Copyright © 2005 John Wiley & Sons, Ltd.
Kinetic studies on the thermal polymerization of N‐chloroacetyl‐11‐aminoundecanoate potassium salt
Authors: Ramis Xavier , Salla Josep María , Puiggalí Jordi 
Published: February 2005

AbstractA potassium salt of N‐chloroacetyl‐11‐aminoundecanoate was thermally polymerized to obtain the corresponding poly(glycolic acid‐alt‐11‐aminoundecanoic acid). A kinetic study was then performed that was based on isothermal and nonisothermal polymerizations performed in a differential scanning calorimeter. The complete kinetic triplet was determined (the activation energy, pre‐exponential factor, and integral function of the degree of conversion). A kinetic analysis was performed with an integral isoconversional procedure (free model), and the kinetic model was determined both with the Coats–Redfern method (the obtained isoconversional value being accepted as the effective activation energy) and through the compensation effect. The polymerization followed a three‐dimensional growth‐of‐nuclei (Avrami) kinetic mechanism. Isothermal polymerization was simulated with nonisothermal data. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1166–1176, 2005
Inhomogeneity control in polymer gels
Authors: Ikkai Fumiyoshi , Shibayama Mitsuhiro 
Published: February 2005

AbstractInhomogeneities, that is, nonrelaxing frozen concentration fluctuations, are inevitably present in polymer gels because they are introduced during the crosslinking of the constituent polymer chains in a solvent. Therefore, inhomogeneities increase as the number of crosslinks increases in a gel. The ionization of polymer gels is one of the methods used to suppress inhomogeneities. However, because crosslinking also means a freezing‐in of the conformation and topology of polymer chains in a solvent according to the chemistry of crosslinking, inhomogeneity control is quite sophisticated. In this article, we discuss the relationship between the inhomogeneities and the molecular/environmental parameters of polymer gels, such as the polymer concentration, the degree of crosslinking, the degree of ionization, and the interaction parameter, by considering the memory effect of gels. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 617–628, 2005
Effects of poly(N‐isopropylacrylamide) on the solution properties of hydrophobically modified acrylamide copolymer
Authors: Duan Ming , Hu Xingqi , Ren Dongmei 
Published: February 2005

AbstractThe hydrophobic interaction between hydrophobically modified acrylamide copolymer (HMPAM) and poly(N‐isopropylacrylamide) (PNIPAM) in aqueous solutions was investigated. The results show that the solution properties of HMPAM are significantly influenced by the addition of PNIPAM. In dilute regime, the intrinsic viscosity of HMPAM in 0.025 wt % PNIPAM/0.1 M NaCl mixed solution is 17.52 dL g−1, about 2 times 8.66 dL g−1, that in 0.1 M NaCl solution, which is due to the attractive interaction between the hydrophobic parts of PNIPAM and HMPAM molecules. In semidilute regime, below the saturation concentration, the addition of PNIPAM can lead to both the apparent viscosity and the modulus of HMPAM solutions increasing, which is attributed to the number of aggregation junctions increasing, responsible for the increase of the contribution of the reversible network to the viscosity increase, the β value. In addition, a thermothickening behavior for the HMPAM/PNIPAM mixed solution is observed with increasing temperature over 15–30 °C, which is consistent with the large increase of the Huggins coefficient of HMPAM in the presence of PNIPAM from 1.95 to 7.59 as temperature increases from 25 to 30 °C. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 709–715, 2005
Progress and challenges in high‐resolution refinement of protein structure models
Authors: Misura Kira M.S. , Baker David 
Published: February 2005

AbstractAchieving atomic level accuracy in de novo structure prediction presents a formidable challenge even in the context of protein models with correct topologies. High‐resolution refinement is a fundamental test of force field accuracy and sampling methodology, and its limited success in both comparative modeling and de novo prediction contexts highlights the limitations of current approaches. We constructed four tests to identify bottlenecks in our current approach and to guide progress in this challenging area. The first three tests showed that idealized native structures are stable under our refinement simulation conditions and that the refinement protocol can significantly decrease the root mean square deviation (RMSD) of perturbed native structures. In the fourth test we applied the refinement protocol to de novo models and showed that accurate models could be identified based on their energies, and in several cases many of the buried side chains adopted native‐like conformations. We also showed that the differences in backbone and side‐chain conformations between the refined de novo models and the native structures are largely localized to loop regions and regions where the native structure has unusual features such as rare rotamers or atypical hydrogen bonding between β‐strands. The refined de novo models typically have higher energies than refined idealized native structures, indicating that sampling of local backbone conformations and side‐chain packing arrangements in a condensed state is a primary obstacle. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Buoyancy-driven propagation of an isolated fluid-filled crack in rock: implication for fluid transport in metamorphism
Authors: Nakashima Yoshito 
Published: February 2005

Abstract
A new model for upward transport of buoyant fluid released during metamorphism is proposed. The model is fluid transport by buoyancy-driven propagation of isolated fluid-filled cracks. The mechanical behavior of a two-dimensional, isolated, vertical, and fluid-filled crack in impermeable rock is investigated using linear fractire mechanics and fluid dynamics. The results show that steady-state crack propagation which causes long-distance transport of the fluid occurs when the vertical cross-sectional area of the crack exceeds a critical value. Propagation velocity and average thickness of the crack under the steady-state propagation regime are expressed explicitly by the following seven parameters: vertical crack length; rigidity, Poisson's ratio, and fracture toughness of the rock; fluid viscosity; density difference between the rock and the fluid; gravitational acceleration. An isolated H2O-filled crack of vertical length 100 m, for example, propagates upwards in the crust at ∼0.3 m/s with the average thickness ∼0.2 mm when the following likely values are assumed: 0.1 mPa s for the H2O viscosity; 3 MPa m1/2 for the fracture toughness of the crustal rock. The application of the obtained results to the transport of H2O released during metamorphism suggests that the number density of isolated cracks propagating in the crust is very low. Since the propagation velocity is high, our model is suitable particularly for fluid transport through hot quartz-rich rock where fluid-filled cracks have geologically short lifetimes.
Cognitive impairment in patients with chronic hepatitis treated with interferon alpha (IFNα): results from a prospective study
Authors: Lieb Klaus , Engelbrecht Marc A. , Gut Oliver , Fiebich Bernd L. , Bauer Joachim , Janssen Gesa , Schaefer Martin 
Published: February 2005

AbstractBackground.Treatment with low-dose interferon alpha (IFN-α) is often associated with neuropsychiatric side effects. In addition to depression and anxiety, IFN-α associated cognitive impairment significantly affects patient’s mental health and quality of life.Aims of the study.To measure possible effects of low-dose IFN-α on cognitive functioning and its relationship to the development of depression and anxiety.Method.We prospectively followed 38 patients with a chronic hepatitis B or C by neuropsychological tests and psychiatric self-rating scales during 12 weeks of low-dose treatment with IFN-α.Results.Before IFN-α treatment, neuropsychological tests as well as self-ratings in the Beck’s Depression Inventory (BDI), the Hospital Anxiety and Depression Scale (HADS) and the Self-Report Symptom Inventory 90 Items-Revised (SCL-90-R) were within the normal range. Following 12 weeks of treatment with IFN-α resulted in a slight, but significant increase in depression scores. Neuropsychological assessment after 12 weeks of IFN-α treatment showed a significant decrease of the immediate recall in the Auditory-Verbal Learning Test (AVLT) and a significant reduction of words recited in the Controlled Oral Word Association Test (COWA). Cognitive impairment did not significantly correlate with depressive symptoms or anxiety.Conclusion.Our results indicate that even low-dose IFN-α induces cognitive impairment independent from depressive symptoms, which might be related to functional disturbances in the prefrontal cortex and the hippocampus. We suggest close monitoring of cognitive function during IFN-α treatment of chronic hepatitis.
Genetic thrombophilias and uterine artery Doppler velocimetry and preeclampsia
Authors: Driul L. , Damante G. , D'Elia A. , Ianni A. , Springolo F. , Marchesoni D. 
Published: February 2005

AbstractObjectiveThe aim of this study was to evaluate the correlation between genetic thrombophilic mutations, uterine artery Doppler at 24 weeks of gestation and preeclampsia.MethodsIn a case control study we performed the genetic analysis for Leiden mutation of factor V gene (FV), G20210A mutation of the prothrombin gene (PT) and C677T polymorphism of the methylenetetrahydrofolate reductase (MTHFR) gene in 103 women that had already attended routine ultrasonography scanner at 20 weeks at our Department.ResultsThe frequency of heterozygous carriers of the factor V Leiden was 17.4% in the women with preeclampsia and abnormal artery Doppler compared with 3.12% in the patients with normal pregnancies. This difference was statistically significant (P<0.05). The frequency of mutation G20210A of prothrombin gene was 1.5 vs. 4.3% between women with normal pregnancies and with preeclampsia. This difference is not statistically significant. The frequency of homozygous patients for the C677T mutation of MTHFR gene among the patients with preeclampsia was 21.7% and in the control group was 10.3%, but this difference is not statistically significant. No thrombophilic gene variants were found in women with preeclampsia and normal uterine artery Doppler.ConclusionWe demonstrated the important association between factor V Leiden mutation, abnormal uterine Doppler at 24 weeks and preeclampsia in our population.
The emerging molecular structure of the nitrogen cycle: an introduction to the proceedings of the 10th annual N-cycle meeting
Authors: Butler C.S. , Richardson D.J. 
Published: February 2005

Over the last 10 years, during the lifetime of the nitrogen cycle meetings, structural biology, coupled with spectroscopy, has had a major impact of our understanding enzymology of the nitrogen cycle. The three-dimensional structures for many of the key enzymes have now been resolved and have provided a wealth of information regarding the architecture of redox active metal sites, as well as revealing novel structural folds. Coupled with structure-based spectroscopic analysis, this has led to new insight into the reaction mechanisms of the diverse chemical transformations that together cycle nitrogen in the biosphere. An overview of the some of the key developments in field over the last decade is presented.
Transcriptional regulation of nitric oxide reduction in Ralstonia eutropha H16
Authors: Büsch A. , Strube K. , Friedrich B. , Cramm R. 
Published: February 2005

Nitric oxide reduction in Ralstonia eutropha H16 is catalysed by the quinol-dependent NO reductase NorB. norB and the adjacent norA form an operon that is controlled by the σ54-dependent transcriptional activator NorR in response to NO. A NorR derivative containing MalE in place of the N-terminal domain binds to a 73 bp region upstream of norA that includes three copies of the putative upstream activator sequence GGT-(N7)-ACC. Mutations altering individual bases of this sequence resulted in an 80–90% decrease in transcriptional activation by wild-type NorR. Similar motifs are present in several proteobacteria upstream of genes encoding proteins of NO metabolism. The N-terminal domain of NorR contains a GAF module and is hypothesized to interact with a signal molecule. A NorR derivative lacking this domain activates the norAB promoter constitutively. Amino acid exchanges within the GAF module identified a cysteine residue that is essential for promoter activation by NorR. Signal sensing by NorR is negatively modulated by the iron-containing protein NorA.
Transcriptional regulation of a hybrid cluster (prismane) protein
Authors: Filenko N.A. , Browning D.F. , Cole J.A. 
Published: February 2005

HCP (hybrid-cluster protein) contains two Fe/S clusters, one of which is a hybrid [4Fe-2S-2O] cluster. Despite intensive study, its physiological function has not been reported. The Escherichia coli hcp gene is located in a two-gene operon with hcr, which encodes an NADH-dependent HCP reductase. E. coli HCP is detected after anaerobic growth with nitrate or nitrite: possible roles for it in hydroxylamine or nitric oxide reduction have been proposed. To study the regulation and role of HCP, an hcp::lacZ fusion was constructed and transformed into fnr, arcA and norR mutant strains of E. coli. Transcription from the hcp promoter was induced during anaerobic growth. Only the fnr mutant was defective in hcp expression. Nitrate- and nitrite-induced transcription from the hcp promoter was activated by the response regulator proteins NarL and NarP. Gel retardation assays were used to show that FNR (fumarate-nitrate regulation) and NarL form a complex with the hcp promoter. Transcription of the hcp-hcr operon initiates at a thymine nucleotide located 31 bp upstream of the translation-initiation codon. HCP has been overexpressed from a recombinant plasmid for physiological studies.
Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria
Authors: Van de Pas-Schoonen K.T. , Schalk-Otte S. , Haaijer S. , Schmid M. , Op den Camp H. , Strous M. , Gijs Kuenen J. , Jetten M.S.M. 
Published: February 2005

In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.
ABC transporters in the balance: is there a role in multidrug resistance?
Authors: Polgar O. , Bates S.E. 
Published: February 2005

Drug resistance can occur at several levels and is the major cause of treatment failure in oncology. The ABC (ATP-binding cassette) transporters, beginning with the discovery of P-gylcoprotein (Pgp) almost 30 years ago, have been intensively studied as potential mediators of drug resistance. Although we understand that drug resistance is almost certainly multifactorial, investigators have attempted to link anticancer drug resistance to overexpression of ABC transporters and the consequent reduction in drug accumulation. A body of evidence implicated Pgp as being important in clinical outcome; however, critical studies aimed at proving the hypothesis using Pgp inhibitors in clinical trials have to date failed. Identification of the MRP (multidrug resistance protein)/ABCC subfamily expanded the possible mechanisms of reduced drug accumulation, and the discovery of ABCG2 added a new chapter in these investigations. Correlative studies examining ABCG2 and the ABCC subfamily members in clinical drug resistance have been less avidly pursued, while basic molecular studies of structure and function have proceeded briskly. Recently, studies have focused on how single nucleotide polymorphism in multidrug transporters might affect the pharmacokinetics and pharmacodynamics of anticancer agents. These studies suggest an important role for ABC transporters in pharmacology, independent of the ultimate determination of their role in multidrug resistance.
Carbon source induced yeast-to-hypha transition in Candida albicans is dependent on the presence of amino acids and on the G-protein-coupled receptor Gpr1
Authors: Maidan M.M. , Thevelein J.M. , Van Dijck P. 
Published: February 2005

Yeast-to-hypha transition in Candida albicans can be induced by a wide variety of factors, including specific nutrients. We have started to investigate the mechanism by which some of these nutrients may be sensed. The G-protein-coupled receptor Gpr1 is required for yeast-to-hypha transition on various solid hypha-inducing media. Recently we have shown induction of Gpr1 internalization by specific amino acids, e.g. methionine. This suggests a possible role for methionine as a ligand of CaGpr1. Here we show that there is a big variation in methionine-induced hypha formation depending on the type of carbon source present in the medium. In addition high glucose concentrations repress hypha formation whereas a concentration of 0.1%, which mimics the glucose concentration present in the bloodstream, results in maximal hypha formation. Hence, it remains unclear whether Gpr1 senses sugars, as in Saccharomyces cerevisiae, or specific amino acids like methionine.
Social Capital and the Growth of the Nonprofit Sector*
Authors: Saxton Gregory D. , Benson Michelle A. 
Published: February 2005

Objectives. This article examines the extent to which nonprofit organizational foundings are determined by various forms of social capital. Our hypothesis is that, controlling for other relevant social, political, and economic factors, communities with higher levels of social capital should experience more extensive growth in their nonprofit sectors.Methods. Using data derived from the Social Capital Community Benchmark Survey and the IRS “charitable organization” Business Master Files, we test our hypothesis using a negative binomial event count regression on nonprofit organization foundings in 284 U.S. counties in the year 2001.Results. We find that two core dimensions of social capital—political engagement and “bridging” social ties—have a significant impact on county‐level nonprofit foundings. Surprisingly, a key element of social capital in the literature, the level of interpersonal trust, does not lead to an increase in foundings of new not‐for‐profit organizations.Conclusions. This study provides further evidence of the strength of political engagement and bridging ties for the vitality of the community. It also shows that the different dimensions of social capital do not manifest a uniform effect on nonprofit sector growth. These results further demonstrate that the growth of a community's not‐for‐profit sector is dependent on a mix of ecological and environmental factors, especially preexisting organizational density, median household income, unemployment, and levels of governmental spending. Overall, social capital can usefully be seen as another key “environmental” factor in explanations of organizational foundings.
A Meta‐Analysis of Campaign Contributions' Impact on Roll Call Voting*
Authors: Roscoe Douglas D. , Jenkins Shannon 
Published: February 2005

Objectives. Conventional wisdom about the link between campaign contributions and roll call votes is that contributions rarely matter because groups tend to give to like‐minded legislators. This meta‐analysis examines the conventional wisdom by analyzing published research on this topic.Methods. More than 30 studies are pooled to produce more than 350 individual tests of the contributions‐roll call link. Extending meta‐regression (Stanley and Jarrell, 1989), a logit meta‐analysis is conducted to summarize the literature and assess the importance of various modeling choices.Results. We find that some, but not all, model specifications have an impact on whether significant results are present. Models that control for friendly giving by including a measure of legislators' ideology and that include more than one contributions variable are less likely to produce significant results.Conclusions. After considering the impact of model choice on study results, we conclude that one‐third of roll call votes exhibit the impact of campaign contributions.
When Southern Symbolism Meets the Pork Barrel: Opportunity for Executive Leadership*
Authors: Bullock Charles S. , Hood M. V. 
Published: February 2005

Objectives. Many empirical studies have sought to explain executive‐legislative relations at the federal level; however, much less research on this topic is available at the state level. This article examines legislative‐gubernatorial relations in Georgia using the highly visible, emotion‐laden, and politically costly issue of changing the state flag.Methods. Using probit models, estimated probabilities for various sets of hypothetical legislators are constructed to explain the vote in each house of the Georgia General Assembly.Results. In the absence of executive pressure, constituency characteristics, specifically district racial composition, dominated legislative decision making on the governor's initiative. In the Senate, where there was adequate time for lobbying before the vote, the carrot of additional school construction funding weighed heavily in legislators' vote calculus.Conclusions. This study demonstrates that governors can, and do, use district‐specific benefits as a tool to help ensure the success of their legislative agendas.