bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetics and mechanism of the reactions of aryl chlorodithioformates with pyridines and secondary alicyclic amines
Authors: Castro Enrique A. , Gazitúa Marcela , Santos José G. 
Published: April 2009

AbstractThe reactions of pyridines and secondary alicyclic (SA) amines with phenyl and 4‐nitrophenyl chlorodithioformates (PClDTF and NPClDTF, respectively) are subjected to a kinetic study in aqueous ethanol (44 wt% ethanol) solution, at 25.0 °C, and an ionic strength of 0.2 M (KCl). The reactions are studied spectrophotometrically. Under amine excess, pseudo‐first‐order rate coefficients (kobs) are found. Plots of kobs versus [amine] are linear and pH independent, with slope kN. The Brønsted‐type plots (log kN vs. pKa of aminium ions) are linear for the reactions of PClDTF with SA amines (slope β of 0.3) and pyridines (β  = 0.26) and those of NPClDTF with pyridines (β = 0.30). For the reaction of NPClDTF with SA amines the Brønsted‐type plot is biphasic, with slopes β1 = 0.2 (at high pKa) and β2 = 1.1 (at low pKa). The pKa value at the center of curvature (pK) is 7.7. The magnitude of the slopes indicates that the mechanisms of these reactions are stepwise, with the formation of a zwitterionic tetrahedral intermediate as the rate‐determining step, except for the reaction of NPClDTF with SA amines where there is a change in the rate‐determining step, from formation to breakdown of the tetrahedral intermediate, as the amine basicity decreases. Copyright © 2009 John Wiley & Sons, Ltd.
DNA diffusion in aqueous solution in presence of suspended particles
Authors: Sato Hiroki , Masubuchi Yuichi , Watanabe Hiroshi 
Published: April 2009

AbstractAlthough nanoparticles, which are comparable in size to polymer chains, are widely used as fillers to polymer matrices for developing functional and high performance materials, the dynamics of polymers constrained between solid particles has not been well elucidated. In this study, dynamics of individual polymer under such condition was investigated with fluorescent microscopy using DNA solutions as model systems. For individual T4 and λ DNA molecules in aqueous suspensions of spherical polystyrene particles with diameter of 1 μm, it was found that (i) the radius of gyration of DNA is independent of the particle volume fraction, ϕp, (ii) DNA diffusion is not sensitive to ϕp up to a certain critical ϕp where the average distance between particle surfaces is close to DNA size, and (iii) the DNA diffusion becomes slower at higher ϕp. The diffusion coefficient of DNA was larger, by a factor of 2, in the suspensions at intermediate ϕp than in the corresponding confined geometry (channel/slit between fixed walls), whereas this difference asymptotically vanished with increasing ϕp. This result suggested that the DNA diffusion in the suspensions with intermediate ϕp is accelerated by the particle motion. In fact, the diffusion coefficient measured for DNA in the suspensions was semiquantitatively described by the Rouse constraint‐release model considering the matrix effect on the probe chain diffusion. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1103–1111, 2009
The making of Calabi‐Yau spaces: Beyond toric hypersurfaces
Authors: Kreuzer M. 
Published: April 2009

AbstractWhile Calabi‐Yau hypersurfaces in toric ambient spaces provide a huge number of examples, theoretical considerations as well as applications to string phenomenology often suggest a broader perspective. With even the question of finiteness of diffeomorphism types of CY 3‐folds unsettled, an important idea is Reid's conjecture that the moduli spaces are connected by certain singular transitions. We summarize the results of our recent construction of a large class of new CY spaces with small Picard numbers and of their mirrors via conifold transitions and discuss the benefits of other approaches to interesting locations in the web that have been or should be pursued.
Liposomal gemcitabine (GemLip)—efficient drug against hormone‐refractory Du145 and PC‐3 prostate cancer xenografts
Authors: Jantscheff Peter , Esser Norbert , Graeser Ralph , Ziroli Vittorio , Kluth Jessica , Unger Clemens , Massing Ulrich 
Published: April 2009

AbstractBACKGROUNDGemcitabine (Gemc) is an efficient chemotherapeutic drug in various cancer types (e.g., pancreas) but has only limited effects on hormone‐refractory prostate cancer (HRPCa). Since HRPCa cells are highly sensitive to even low doses of Gemc in vitro, the lack of clinical effects might be due to rapid degradation of Gemc by deaminases combined with impaired accumulation in tumor tissue and PCa cells. Liposomal formulation (GemLip) is expected to protect the entrapped cytotoxic substance from enzymatic degradation and furthermore augment its accumulation within tumor tissues due to an enhanced permeability of the tumor vessels.METHODSAnti‐tumoral and anti‐metastatic activity of GemLip and Gemc were investigated in two luciferase‐expressing, human hormone‐refractory PC‐3 and Du145 HRPCa xenograft models in immunodeficient mice. Tumor growth was monitored by in vivo luminescence imaging (orthotopic) or callipering (subcutaneous). Anti‐metastatic effects of treatment were determined by in vitro luciferase assay of the tissues.RESULTSTumor growth of subcutaneous Du145 xenografts was significantly inhibited only by GemLip (8 mg/kg: P = 0.014 and 6 mg/kg: P = 0.011) but not by conventional Gemc (360 mg/kg). In contrast, growth of orthotopic PC‐3 xenografts was significantly inhibited by both, GemLip (P = 0.041) and Gemc (P = 0.002). The drugs furthermore strongly reduced spleen and liver metastases in this model.CONCLUSIONSAs shown by the very low efficient concentration of GemLip, liposomal entrapment of Gemc greatly enhances its activity. GemLip has, even at very low doses, a significant anti‐tumoral and anti‐metastatic therapeutic effect in HRPCa xenografts in vivo and was beneficial even when the conventional Gemc failed. Prostate 69:1151–1163, 2009. © 2009 Wiley‐Liss, Inc.
The energy profiles of atomic conformational transition intermediates of adenylate kinase
Authors: Feng Yaping , Yang Lei , Kloczkowski Andrzej , Jernigan Robert L. 
Published: April 2009

AbstractThe elastic network interpolation (ENI) (Kim et al., Biophys J 2002;83:1620–1630) is a computationally efficient and physically realistic method to generate conformational transition intermediates between two forms of a given protein. However it can be asked whether these calculated conformations provide good representatives for these intermediates. In this study, we use ENI to generate conformational transition intermediates between the open form and the closed form of adenylate kinase (AK). Based on Cα‐only intermediates, we construct atomic intermediates by grafting all the atoms of known AK structures onto the Cαatoms and then perform CHARMM energy minimization to remove steric conflicts and optimize these intermediate structures. We compare the energy profiles for all intermediates from both the CHARMM force‐field and from knowledge‐based energy functions. We find that the CHARMM energies can successfully capture the two energy minima representing the open AK and closed AK forms, while the energies computed from the knowledge‐based energy functions can detect the local energy minimum representing the closed AK form and show some general features of the transition pathway with a somewhat similar energy profile as the CHARMM energies. The combinatorial extension structural alignment (Shindyalov et al., 1998;11:739–747) and the k‐means clustering algorithm are then used to show that known PDB structures closely resemble computed intermediates along the transition pathway. Proteins 2009. © 2009 Wiley‐Liss, Inc.
A method for determining the flammable limits of gases in a spherical vessel
Authors: Crowl Daniel A. , Jo Young‐do 
Published: April 2009

AbstractThe current method for determining the flammable limits for a gas in a closed spherical vessel is based on a specification of the maximum pressure increase during the combustion, usually from 5 to 10% of the initial ambient pressure. This approach is completely arbitrary and is not fundamentally based. For most hydrocarbons this pressure boundary and hence the flammable limits are easy to determine experimentally since an abrupt pressure drop occurs at the flammable limits as the fuel concentration in air is adjusted. However, for some species, particularly hydrogen mixed with air, the drop in maximum combustion pressure is not very abrupt and the fuel concentration can range several percentage points depending on the arbitrary criterion used for the flammable limits.This article will discuss a new approach for determining the flammable limits for a gas in a spherical vessel. The approach is based on the maximum second derivative of pressure rise. The second derivative is indicative of an acceleration of the combustion process and is, hence, fundamentally based. Furthermore, we have identified a new approach to determine the downward propagating flammable limits based on the combustion time, that is, the time that the gas actually burns in the vessel.Experimental data for methane and hydrogen show that the second derivative flammable limit criterion produces slightly conservative values for combustion in air. Visual inspection of the combustion during the tests showed that no visual combustion was observed at the second derivative criterion. For methane, the second derivative criterion resulted in a flammable range in air from 4.6 to 15.8% methane. For hydrogen these limits are 3.6–75.2%.We believe that this method will provide a much more fundamentally based method to determine both the upper and lower flammable limits of upward flame propagation and also provide a means to determine the downward propagation limits in a spherical combustion vessel. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2009
To what extent are soil amendments useful to control Verticillium wilt?
Authors: Goicoechea Nieves 
Published: April 2009

AbstractThe genus Verticillium includes several species that attack economically important crops throughout the world. The control of Verticillium spp. becomes especially difficult when they form microsclerotia that can survive in the field soil for several years. It has been common practice to fumigate soil with chemicals such as methyl bromide and/or chloropicrin to control soil‐borne fungal pathogens. Other chemicals that are used against Verticillium spp. are the antifungal antibiotic aureofungin, the fungicides benomyl, captan, carbendazim, thiram, azoxystrobin and trifloxystrobin and the plant defence activator acibenzolar‐S‐methyl. However, the potential risks involved in applying phytochemicals to crop plants for both the environment and human health, together with their limited efficacy for controlling Verticillium‐induced diseases, support the need to find alternatives to replace their use or improve their efficacy. Soil amendment with animal or plant organic debris is a cultural practice that has long been used to control Verticillium spp. However, today the organic farming industry is becoming a significant player in the global agricultural production scene. In this review, some of the main results concerning the efficacy of several soil amendments as plant protectors against Verticillium spp. are covered, and the limitations and future perspectives of such products are discussed in terms of the control of plant diseases. Copyright © 2009 Society of Chemical Industry
Trichogin GA IV: an antibacterial and protease‐resistant peptide
Authors: De Zotti Marta , Biondi Barbara , Formaggio Fernando , Toniolo Claudio , Stella Lorenzo , Park Yoonkyung , Hahm Kyung‐Soo 
Published: April 2009

AbstractThe antibacterial and hemolytic activities of the amphiphilic helical, membrane‐active, lipopeptaibol trichogin GA IV and its [Leu11‐OMe] analogue were compared to those of the partially helical or non‐helical 8‐meric or 4‐meric, C‐terminal short sequences, respectively. The study on trichogin GA IV was extended to several methicillin‐resistant Staphylococcus aureus strains. Using a large set of enzymes, we also evaluated the resistance to proteolysis of all of the four peptides. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Demonstration of confocal sum frequency microscopy [Phys. Status Solidi C 6, No. 1, 304–306 (2009)]
Authors: Locharoenrat Kitsakorn , Sano Haruyuki , Mizutani Goro 
Published: April 2009

AbstractThe magnification of the objective lens used in the above paper and the related values were erroneously reported and should be corrected. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positive mode electrospray tandem mass spectrometry of poly(methacrylic acid) oligomers
Authors: Giordanengo Rémi , Viel Stéphane , Allard‐Breton Béatrice , Thévand André , Charles Laurence 
Published: April 2009

AbstractThe dissociation of small poly(methacrylic acid) (PMAA) cations produced by electrospray was characterized by tandem mass spectrometry. Similarly to PMAA ions produced in the negative ion mode, the two electrosprayed cationic forms, namely [PMAA+Na]+ and [PMAA‐H+2Na]+, were shown to fragment via a major pathway consisting of successive dehydration steps. Elimination of a water molecule would occur between two consecutive acid groups in a charged‐remote mechanism and was shown to proceed as many times as pairs of acidic pendant groups were available. As a result, comparing the number of dehydration steps observed in the MS/MS spectrum of two consecutive oligomers from the polymeric distribution reveals the degree of polymerization of the molecule. Secondary less informative reactions were shown to consist of losses of CO and/or CO2, depending on the nature of the precursor ion. These fragmentation rules could be used to characterize PMAA‐based copolymers, as successfully demonstrated for a polymeric impurity in the tested PMAA sample. Copyright © 2009 John Wiley & Sons, Ltd.
Empirical evaluation of ductility factors for the special steel moment‐resisting frames in view of soil condition
Authors: Kang Cheol Kyu , Choi Byong Jeong 
Published: April 2009

AbstractIt is well known that the response modification factor (R) takes into account the ductility, over‐strength, redundancy and damping of structural systems. The ductility factor has played an important role in seismic design, as it is a key component of R. In this study, the ductility factors (Rμ,MDOF) of special steel moment‐resisting frames are calculated by multiplying the ductility factor of single degree of freedom (SDOF) systems (Rμ,SDOF) with the multi‐degree of freedom (MDOF) modification factors (RM). The ductility factors (Rμ,SDOF) of SDOF systems are computed from non‐linear dynamic analysis undergoing different levels of displacement ductility demands and periods when subjected to a large number of recorded earthquake ground motions. To compute the Rμ,SDOF, a group of 1,860 ground motions recorded from 47 earthquakes were considered. RM factors are proposed to account for the MDOF systems, based on previous studies. A total of 108 prototype steel frames were designed to investigate the ductility factors, considering design parameters such as the number of stories (4, 8 and 16), framing systems (perimeter frames and distributed frames), failure mechanisms (strong column‐weak beam and weak column‐strong beam), soil profiles (SA, SC and SE in Uniform Building Code 1997) and seismic zone factors (Z = 0·075, 0·2, and 0·4 in UBC 1997). The effects of these design parameters on the Rμ,MDOF of special steel‐moment‐resisting frames were investigated. Copyright © 2009 John Wiley & Sons, Ltd.
Ultrasound‐derived fetal size nomogram for a sub‐Saharan African population: a longitudinal study
Authors: Landis S. H. , Ananth C. V. , Lokomba V. , Hartmann K. E. , Thorp J. M. , Horton A. , Atibu J. , Ryder R. W. , Tshefu A. , Meshnick S. R. 
Published: April 2009

AbstractObjectivesTo create a fetal size nomogram for use in sub‐Saharan Africa and compare the derived centiles with reference intervals from developed countries.MethodsFetal biometric measurements were obtained at entry to antenatal care (11–22 weeks' gestation) and thereafter at 4‐week intervals from pregnant women enrolled in a longitudinal ultrasound study in Kinshasa, Democratic Republic of Congo. The study population comprised 144 singleton gestations with ultrasound‐derived gestational age within 14 days of the menstrual estimate. A total of 755 monthly ultrasound scans were included with a mean ± SD of 5 ± 1 (range, 2–8) scans per woman. Estimated fetal weight (EFW) was calculated at each ultrasound examination using the Hadlock algorithm. A general mixed‐effects linear regression model that incorporated random effects for both the intercept and slope was fitted to log‐transformed EFW to account for both mean growth and within‐fetus variability in growth. Reference centiles (5th, 10th, 50th, 90th and 95th centiles) were derived from this model.ResultsNomograms derived from developed populations consistently overestimated the 50th centile EFW value for Congolese fetuses by roughly 5–12%. Differences observed in the 10th and 90th centiles were inconsistent between nomograms, but generally followed a pattern of overestimation that decreased with advancing gestational age.ConclusionsIn low‐resource settings, endemic malaria and maternal nutritional factors, including low prepregnancy weight and pregnancy weight gain, probably lead to lower fetal weight and utilization of nomograms derived from developed populations is not appropriate. This customized nomogram could provide more applicable reference intervals for diagnosis of intrauterine growth restriction in sub‐Saharan African populations. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
The impact of crown–rump length measurement error on combined Down syndrome screening: a simulation study
Authors: Salomon L. J. , Bernard M. , Amarsy R. , Bernard J. P. , Ville Y. 
Published: April 2009

AbstractObjectiveTo evaluate the impact of a 5‐mm error in the measurement of crown–rump length (CRL) in a woman undergoing ultrasound and biochemistry sequential combined screening for Down syndrome.MethodsBased on existing risk calculation algorithms, we simulated the case of a 35‐year‐old‐woman undergoing combined screening based on nuchal translucency (NT) measurement and early second‐trimester maternal serum markers (human chorionic gonadotropin (hCG) and alpha‐fetoprotein (AFP) expressed as multiples of the median (MoM)). Two measurement errors were considered (+ or − 5 mm), for four different CRLs (50, 60, 70 and 80 mm), with five different NT measurements (1, 1.5, 2, 2.5 and 3 mm) in a patient undergoing biochemistry testing at 14 + 4, 15, 16, 17 or 18 weeks' gestation. Four different values for each maternal serum marker were tested (1, 1.5, 2 and 2.5 MoM for hCG, and 0.5, 0.8, 1 and 1.5 MoM for AFP), leading to a total of 3200 simulations of the impact of measurement error. In all cases the ratio between the risk as assessed with or without the measurement error was calculated (measurement error‐related risk ratio (MERR)).ResultsOver 3200 simulated cases, MERR ranged from 0.53 to 2.14. In 586 simulations (18.3%), it was < 0.66 or > 1.33. Based on a risk cut‐off of 1/300, women would have been misclassified in 112 simulations (3.5%). This would go up to 33 (27.5%) out of the 120 simulations in women with ‘borderline’ risk, with 1.5 MoM for hCG and 0.5 MoM for AFP, and NT measurement of 1 or 2mm.ConclusionDown syndrome screening may be highly sensitive to measurement errors in CRL. Quality control of CRL measurement should be performed together with quality control of NT measurement in order to provide the highest standard of care. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
A retransmission‐based scheme for video streaming over wireless channels
Authors: Hassan Mohamed , Landolsi Taha 
Published: April 2009

AbstractEfficient resource allocation is a key factor to improve the efficiency of video transmission over wireless channels. To increase the number of correctly received video frames at the decoder, it is desirable to reduce the video source rate while increasing error protection when the wireless channel is anticipated to be bad or when the receiver buffer is approaching starvation. In this study, we introduce a retransmission‐based adaptive source‐channel rate control scheme for video transmission over wireless packet networks. In this scheme, the level of adaptiveness is optimized to reduce the bandwidth requirement while guaranteeing delay and loss bounds. The proposed scheme has the advantage of providing closed‐form expressions of the near‐optimum parameters of the proposed model, which are then fed back to the transmitter to scale both the source and channel rates adaptively. Simulation and numerical investigations are carried out to verify the adequacy of the analysis and study the impact of the adaptive process on the continuity of the video playback process. Copyright © 2009 John Wiley & Sons, Ltd.
Nanoparticle vaccines against respiratory viruses
Authors: Adair Brian M. 
Published: April 2009

AbstractInfluenza virus, respiratory syncytial virus (RSV), and parainfluenza type 3 virus (PI‐3V) are the major viral agents which are consistently involved in causing lower respiratory tract disease in humans and animals. The virus infection begins in the upper respiratory tract, where immune responses are initiated, and then progresses to the lower respiratory tract where destruction of cells and tissues leads to bronchitis, bronchiolitis, and pneumonia, which is occasionally fatal. Nanoparticle vaccines, incorporating antigenic components from influenza, RSV, or PI‐3V have been shown to be capable of stimulating mucosal and systemic immune responses, which can prevent the spread of infection to the lower respiratory tract. The encapsulation of viral proteins within nanoparticles may also facilitate production of respiratory vaccines which are efficacious in infants, where presence of maternally derived antibodies can reduce vaccine efficacy. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease
Expression of GFP using Pichia pastoris vectors with zeocin or G‐418 sulphate as the primary selectable marker
Authors: Papakonstantinou Theo , Harris Simon , Hearn Milton T. W. 
Published: April 2009

AbstractPichia pastoris is a popular host organism for expressing heterologous proteins, and various expression vectors for this yeast are currently available. Recently, vectors containing novel dominant antibiotic resistance markers have become a strong and developing field of research for this methylotropic yeast strain. We have developed new P. pastoris expression vectors, the pPICKanMX6 and pPICKanMX6α series. These vectors were constructed by replacing the zeocin resistance gene of the pPICZA, B, C and pPICZαA, B and C vectors with the Tn903 kanR marker from pFA6a KanMX6, which confers G‐418 sulphate resistance in P. pastoris. The limits of antibiotic resistance in two transformant yeast strains were investigated, and the selection marker was shown to be stably retained. To demonstrate their usefulness, a gene encoding hexa‐histidine‐tagged green fluorescent protein (GFPH6) was cloned into one of the new vectors and GFP expression examined in P. pastoris cells. The protein expression levels using the pPICKanMX6B vector were comparable with that using the original plasmid, based on zeocin resistance as seen by yeast cell fluorescence. Moreover, GFPH6 was able to be isolated by immobilized metal ion affinity chromatography (IMAC) from lysates of both yeast strains. A model reporter construct has been used to demonstrate successful recombinant protein expression and its subsequent purification using these new vectors. Corresponding vectors can now also be engineered with foreign gene expression under the control of various different promoters, to increase the flexibility of P. pastoris as a cellular factory for heterologous protein production. Copyright © 2009 John Wiley & Sons, Ltd.