bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kondo effect in nanostructures
Authors: Pustilnik M. 
Published: March 2006

AbstractKondo effect arises whenever a coupling to the Fermi gas induces transitions within the otherwise degenerate ground state multiplet of an interacting system. Both coupling to the Fermi gas and interactions are naturally present in any nanoscale transport experiment. At the same time, many nanostructures can easily be tuned to the vicinity of a degeneracy point. This is why the Kondo effect in its various forms often influences the low temperature transport in meso‐ and nanoscale systems.In this short review we discuss the basic physics of the Kondo effect and its manifestations in the lowtemperature electronic transport through a single electron transistor. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Computational and spectroscopic studies concerning the solvatochromic behavior of 1,3‐disubstituted azulenes
Authors: Blice‐Baum Anna , Van Dyke Aaron , Sigmon Ian , Salter E. Alan , Wierzbicki Andrzej , Pocker Y. , Spyridis Greg T. 
Published: March 2006

AbstractEstimates of excited‐state dipole moments for various 1,3‐disubstituted azulenes possessing electron‐withdrawing substituents, using the CIS/6‐31+G(d,p) model, reveal that unlike azulene, the excited‐state dipole moments are generally in the same direction as, although smaller in magnitude than, their ground‐state counterparts. This gives rise to hypsochromic shifts in the UV‐visible spectrum of these dipolar indicator molecules as solvent polarity is increased. Furthermore, B3LYP density functional calculations on several 1,3‐diacylazulenes indicate that the s‐cis conformation is preferred over s‐trans. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
New short peptaibols from a marine Trichoderma strain
Authors: Mohamed‐Benkada Mustapha , Montagu Monique , Biard Jean‐François , Mondeguer Florence , Verite Philippe , Dalgalarrondo Michèle , Bissett John , Pouchus Yves François 
Published: March 2006

AbstractThe production of peptaibols by a marine‐related Trichoderma longibrachiatum strain was studied using electrospray ionisation multiple‐stage ion trap mass spectrometry (ESI‐MSn‐IT) and gas chromatography/electron impact mass spectrometry (GC/EI‐MS). Two major groups of peptaibols were identified, those with long sequences (20 amino acids) and others with short sequences (11 amino acids). This paper describes the methodology used to establish the sequences of short peptaibols in a mixture without previous individual separation. Nine peptaibols were identified. Among them, eight are new, namely as trichobrachin A I–IV (Aib9‐Pro10 sequence) and as trichobrachin B I–IV (Val9‐Pro10 sequence). Original Pro6‐Val7 and Val9‐Pro10 sequences have to be noted. Copyright © 2006 John Wiley & Sons, Ltd.
Use of flow injection atmospheric pressure photoionization quadrupole time‐of‐flight mass spectrometry for fast olive oil fingerprinting
Authors: Gómez‐Ariza J. L. , Arias‐Borrego A. , García‐Barrera T. 
Published: March 2006

AbstractThe recently introduced technique of an atmospheric pressure photoionization (APPI) source coupled to quadrupole time‐of‐flight mass spectrometry (QqTOFMS) has been applied to fast olive oil fingerprinting on the basis of the accurate mass measurements obtained with this instrumentation. The key compounds can be characterized as [M+H]+ (produced by proton transfer) or as [M]+. (by charge transfer) ions in the mass spectra. [M+H]+ ions, however, show higher abundance, especially for triacylglycerols. Other ions present in APPI‐MS are the acylium ion [RiCO]+ and [RiCOH2O]+. This latter ion is absent in the electrospray ionization (ESI)‐MS spectra, and this represents valuable complementary information. Several critical parameters in the APPI source were optimized such as LC eluent composition, ion spray voltage and, especially, declustering potential. APPI‐QqTOFMS allows easy discrimination among different edible oils: olive, extra virgin olive, olive‐pomace, hazelnut, sunflower, corn and several mixed oils, with high throughput (approximately 1 min per sample). Cluster analysis was applied to obtain the best experimental conditions for oil discrimination on the basis of declustering potential. Principal components analyses of these APPI‐MS spectra show that the approach can be used for studies of olive oil adulteration with other oils, even in the case of hazelnut oil that exhibits a high chemical similarity with olive oil. Copyright © 2006 John Wiley & Sons, Ltd.
RT‐PSM, a real‐time program for peptide‐spectrum matching with statistical significance
Authors: Wu Fang‐Xiang , Gagné Pierre , Droit Arnaud , Poirier Guy G. 
Published: March 2006

AbstractThe analysis of complex biological peptide mixtures by tandem mass spectrometry (MS/MS) produces a huge body of collision‐induced dissociation (CID) MS/MS spectra. Several methods have been developed for identifying peptide‐spectrum matches (PSMs) by assigning MS/MS spectra to peptides in a database. However, most of these methods either do not give the statistical significance of PSMs (e.g., SEQUEST) or employ time‐consuming computational methods to estimate the statistical significance (e.g., PeptideProphet). In this paper, we describe a new algorithm, RT‐PSM, which can be used to identify PSMs and estimate their accuracy statistically in real time. RT‐PSM first computes PSM scores between an MS/MS spectrum and a set of candidate peptides whose masses are within a preset tolerance of the MS/MS precursor ion mass. Then the computed PSM scores of all candidate peptides are employed to fit the expectation value distribution of the scores into a second‐degree polynomial function in PSM score. The statistical significance of the best PSM is estimated by extrapolating the fitting polynomial function to the best PSM score. RT‐PSM was tested on two pairs of MS/MS spectrum datasets and protein databases to investigate its performance. The MS/MS spectra were acquired using an ion trap mass spectrometer equipped with a nano‐electrospray ionization source. The results show that RT‐PSM has good sensitivity and specificity. Using a 55 577‐entry protein database and running on a standard Pentium‐4, 2.8‐GHz CPU personal computer, RT‐PSM can process peptide spectra on a sequential, one‐by‐one basis in 0.047 s on average, compared to more than 7 s per spectrum on average for Sequest and X!Tandem, in their current batch‐mode processing implementations. RT‐PSM is clearly shown to be fast enough for real‐time PSM assignment of MS/MS spectra generated every 3 s or so by a 3D ion trap or by a QqTOF instrument. Copyright © 2006 John Wiley & Sons, Ltd.
Protonation thermochemistry of aminoacetonitrile
Authors: Bouchoux Guy , Guillemin Jean‐Claude , Lemahieu Nadège , McMahon Terrance B. 
Published: March 2006

AbstractThe gas‐phase basicity (GB) of aminoacetonitrile (NH2CH2CN, 1) has been determined from measurement of proton transfer equilibrium constants in an ion cyclotron resonance mass spectrometer (GB(1) = 789.3 ± 1.0 kJ · mol−1). Molecular orbital calculations up to the G2 level demonstrate that protonation occurs preferentially on the nitrogen atom of the NH2 group, and provide a theoretical proton affinity (PA(1)) of 824.0 kJ · mol−1. Exact calculation of the entropy associated with hindered rotations and consideration of Boltzman distribution of conformers allow a theoretical estimate of the molar protonation entropy S°(1H+) − S°(1) = 8.6 J · mol−1 · K−1. Combining this value with experimental GB(1) leads to an ‘experimental’ proton affinity of 819.2 kJ · mol−1, in close agreement with the G2 expectation. Copyright © 2006 John Wiley & Sons, Ltd.
Enhanced mass resolution method development, validation and assay application to support preclinical studies of a new drug candidate
Authors: Pucci Vincenzo , Bonelli Fabio , Monteagudo Edith , Laufer Ralph 
Published: March 2006

AbstractA very highly sensitive and highly selective liquid chromatographic/tandem mass spectrometric (LC/MS/MS) method was developed to evaluate and quantify a new drug candidate in different biological matrices. Following a simple plasma protein precipitation using acetonitrile, the post‐treatment samples were analyzed on a C18 column interfaced with a new generation of triple‐quadrupole mass spectrometer. The recently introduced triple‐quadrupole mass spectrometer, the TSQ Quantum Ultra, with enhanced mass‐resolution capability, demonstrated improved sensitivity (0.05 ng/mL), coupled with suitable accuracy and precision, over a broad linear dynamic range (0.05–1000 ng/mL). A comparison of the assay performance data (dynamic range, calibration curve equation, precision and accuracy) of the enhanced resolution method against a unit resolution method under optimized conditions showed the performance improvement of the enhanced mass resolution method for bioanalytical high‐throughput applications. The enhanced mass resolution method herein described was successfully applied to the evaluation of the pharmacokinetic profile of a new drug candidate in rat, rabbit and dog plasma samples. Copyright © 2006 John Wiley & Sons, Ltd.
Complex formation between a tetramesityl sulfonated resorcarene and alkylammonium ions: a mass spectrometric study of noncovalent interactions
Authors: Ventola Elina , Hyyryläinen Anna , Vainiotalo Pirjo 
Published: March 2006

AbstractNoncovalent complex formation between a tetramesityl sulfonated tetramethyl resorcarene and primary, secondary, and tertiary alkylammonium ions was investigated by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry. Competition measurements, collision‐induced dissociation, and gas‐phase hydrogen/deuterium (H/D)‐exchange reactions were employed to elucidate the interactions involved in complexation, the stability of the complexes, and the position of the guest with relation to the resorcarene. The complex formation ability of tetramesityl sulfonated resorcarene and the stability of the compexes were compared with the corresponding properties of tetratosylium tetraethyl resorcarene, which has been studied previously. Complex formation and the properties of the complexes were most strongly determined by the steric properties of the guests and their ability to form hydrogen bonds. Comparison of the two host molecules revealed the impact of steric hindrance in tetramesityl sulfonated tetramethyl resorcarene. Copyright © 2006 John Wiley & Sons, Ltd.
Analysis of androgenic steroid Girard P hydrazones using multistage tandem mass spectrometry
Authors: Kirk Jayne M. , Tarbin Jonathan , Keely Brendan J. 
Published: March 2006

AbstractSeven androgenic steroids have been converted into steroid hydrazones using Girard P hydrazine and analysed by electrospray ionisation multistage tandem mass spectrometry. The cationic derivatives 17α‐testosterone hydrazone, 17β‐nortestosterone hydrazone, 17β‐bolasterone hydrazone, 17α‐boldenone hydrazone, 17β‐fluoxymesterone hydrazone, 17α‐trenbolone hydrazone and 4‐chloroandrosten‐3,17‐dione hydrazone show good response in positive ion mode with enhancements for the method of up to 33 times relative to the native species. Detailed characterisation of fragmentation pathways reveals structurally specific ions formed by fragmentation of the hydrazine moiety. Comparison of structural similarities among the androgenic steroids allows recognition of common ions/fragmentation processes as well as analyte‐specific transitions. The suitability of the derivatisation approach in the screening of heifer urine for the presence of administered hormones has been demonstrated using partially purified urine spiked with a mixture of androgenic steroids. Copyright © 2006 John Wiley & Sons, Ltd.
Bayesian analysis of latent variable models with non‐ignorable missing outcomes from exponential family
Authors: Song Xin‐Yuan , Lee Sik‐Yum 
Published: March 2006

AbstractTo provide a comprehensive framework for analysing complex non‐normal medical and biological data, we propose a Bayesian approach for a non‐linear latent variable model with covariates, and non‐ignorable missing data, under the exponential family of distributions. The non‐ignorable missing mechanism is defined via a logistic regression model. Based on conjugate prior distributions, full conditional distributions for the implementation of Markov chain Monte Carlo methods in simulating observations from the joint posterior distribution are derived. These observations are used in computing the Bayesian estimates, as well as in implementing a path sampling procedure to evaluate the Bayes factor for model comparison. The proposed methods are illustrated using real data from a study on the non‐adherence of hypertension patients. Copyright © 2006 John Wiley & Sons, Ltd.
Analysis of cluster randomized cross‐over trial data: a comparison of methods
Authors: Turner Rebecca M. , White Ian R. , Croudace Tim 
Published: March 2006

AbstractIn a cluster randomized cross‐over trial, all participating clusters receive both intervention and control treatments consecutively, in separate time periods. Patients recruited by each cluster within the same time period receive the same intervention, and randomization determines order of treatment within a cluster. Such a design has been used on a number of occasions. For analysis of the trial data, the approach of analysing cluster‐level summary measures is appealing on the grounds of simplicity, while hierarchical modelling allows for the correlation of patients within periods within clusters and offers flexibility in the model assumptions. We consider several cluster‐level approaches and hierarchical models and make comparison in terms of empirical precision, coverage, and practical considerations. The motivation for a cluster randomized trial to employ cross‐over of trial arms is particularly strong when the number of clusters available is small, so we examine performance of the methods under small, medium and large (6, 18, 30) numbers of clusters. One hierarchical model and two cluster‐level methods were found to perform consistently well across the designs considered. These three methods are efficient, provide appropriate standard errors and coverage, and continue to perform well when incorporating adjustment for an individual‐level covariate. We conclude that choice between hierarchical models and cluster‐level methods should be influenced by the extent of complexity in the planned analysis. Copyright © 2006 John Wiley & Sons, Ltd.
Comparing two crossing hazard rates by Cox proportional hazards modelling
Authors: Liu Kejian , Qiu Peihua , Sheng Jun 
Published: March 2006

AbstractMotivated by a clinical trial of zinc nasal spray for the treatment of the common cold, we consider the problem of comparing two crossing hazard rates. A comprehensive review of the existing methods for dealing with the crossing hazard rates problem is provided. A new method, based on modelling the crossing hazard rates, is proposed and implemented under the Cox proportional hazards framework. The main advantage of the proposed method is the utilization of the Box–Cox transformation which covers a wide range of hazard crossing patterns. Simulation studies are conducted for comparing the performance of the existing methods and the proposed one, which show that the proposed method outperforms some of its peers in certain cases. Applications to a kidney dialysis patients data and the zinc nasal spray clinical trial data are discussed. Copyright © 2006 John Wiley & Sons, Ltd.
Polyethylenimine, a cost‐effective transfection reagent
Authors: Ehrhardt Christina , Schmolke Mirco , Matzke Andreas , Knoblauch Alexander , Will Carola , Wixler Viktor , Ludwig Stephan 
Published: March 2006

AbstractIn search for a cheap and effective transfection reagent we used the positively charged polyplex‐forming compound polyethylenimine (PEI). This compound is commercially available from different companies either as a non‐modified chemical reagent or with additives as a more cost intensive transfection reagent. Here we used the non‐modified PEI reagent to optimize transfection protocols for different cell‐lines. With these optimized conditions we were able to transiently transfect a number of cell‐lines up to 40–90%.
Interactions of synaptojanin
Authors: Rosivatz Erika 
Published: March 2006

AbstractSynaptojanin is a phosphoinositide phosphatase that plays a crucial role in synaptic vesicle recycling. The focus of this review is on the major direct interacting partners of synaptojanin with respect to recognition motifs in synaptojanin isoforms and splice variants. Those proteins that bind synaptojanin are mainly involved in endocytosis and function at the interface between actin and the endocytic machinery. Some interaction partners underline synaptojanin's emerging role in signaling and pathophysiological processes.
Competition and cooperation: Signal transduction by CD28 and CTLA‐4
Authors: Hoff Holger , Burmester Gerd‐R. , Brunner‐Weinzierl Monika C. 
Published: March 2006

AbstractThe closely related members of the Ig‐family of co‐stimulators CD28 and CTLA‐4 (CD152) show distinct functions regarding T cell activation but have also many features in common during T cell differentiation. Although CD28 and CTLA‐4 share some of their intracellular binding partners, CD28 is the main activating co‐stimulator of T cells while the role of CTLA‐4 is to mainly down regulate T cell responses. Despite the well known function of CTLA‐4 as a negative regulator of T cell function, new data suggest that CTLA‐4 is also able to transmit positive signals for increased survival and might be involved in the generation of the memory compartment. The knowledge of how both molecules transmit their respective signals and how these signals are integrated during a T cell response is of importance for the understanding of T cell mediated immune responses and future therapeutic interventions in immune pathologies.
Continuous convergence of relations – a principle in discretization procedures –
Authors: Ansorge R. 
Published: March 2006

AbstractThere are situations in Numerical Analysis concerning the convergence and properties of discretization procedures which seem to be of different type (e.g. convergence to genuine or to weak solutions, convergence to entropy solutions, creation of dicrete solutions which have to imitate properties of the seeked solutions known in advance etc.) but can uniformly be descibed by a property introduced here, called continuous convergence of relations. Historical examples demonstrate this standardization.
Heterogeneity ratio: a measure of beta‐diversity and its use in community classification
Authors: Kobayashi Shiro 
Published: March 2006

AbstractFifteen previously proposed similarity indices are examined for the effects of sample size and/or group size (the number of samples included in a cluster). The three indices of Cλ, NESS, and C′λ are free from effects, but the former two are unsuitable for arithmetic averaging unless all of the sample sizes are equal. Thus clustering using C′λ is found to be superior to the combination of any other similarity index and the group‐average strategy. Unfortunately none of these measures have the desirable property of measuring the difference in component species among samples independent of the alpha‐diversity. A new index of similarity (HR) is developed based on the assumption that community from which samples are taken is described by a logseries distribution. This new index measures the beta‐diversity among samples without the influence of sample size and group size, and has the advantage that the significance of fusing samples can statistically be tested. An example clustering with HR is shown and compared with those obtained by other clustering strategies.
Nitrification and nitrogen accumulation in the early stages of primary succession on Mt. Fuji
Authors: Tateno Masaki , Hirose Tadaki 
Published: March 2006

AbstractThe relationship between nitrification potential and nitrogen accumulation was studied in an early successional sere on Mt. Fuji. Soil organic nitrogen accumulated with the invasion of Polygonum cuspidatum and successively with Miscanthus oligostachyus and other species. Laboratory incubation experiments showed a higher nitrification potential at the M. oligostachyus state. The numbers of nitrifying bacteria increased with the progress of succession. No significant difference in nitrate reductase activity was found between pioneer and succeeding species. The soil solution at the M. oligostachyus stage contained a lower level of nitrate than rainwater, while that of the bare ground and the P. cuspidatum stage contained a higher nitrate level than rainwater. It was concluded that the high nitrate levels in the soil solution of the bare ground and the P. cuspidatum stage were due to lower nitrate‐absorbing activity, leading to loss of nitrogen with precipitation, while the lower nitrate levels at the M. oligostachyus stage when higher nitrification activity occurred were due to higher nitrate‐absorbing activity, preventing net loss of nitrogen from the ecosystem.
Seasonal changes in abundance and spatial distribution of the soil arthropods in a Japanese cedar (Cryptomeria japonica D.Don) plantation, with special reference to collembola and acarina
Authors: Hijii Naoki 
Published: March 2006

AbstractSeasonal changes in abundance and distribution pattern of soil micro‐arthropods were studied in connection with a few environmental factors in a Japanese cedar (Cryptomeria japonicaD. Don) plantation. The soil arthropods were sampled from three different depths at intervals of two months for two years. Of the collected animals (total 51000–155000 m−2), Collembola (20000–76000 m−2), oribatid mites (19000–55000 m−2) and carnivorous mites (6200–21000 m−2) were the numerically dominant animal groups. Low seasonal variations in abundance indicated their seasonal stability in population levels. The trends in seasonal fluctuation were similar among these groups and between the two years, showing bimodal pattern with little peaks in early summer and winter. The pattern of seasonal fluctuation in abundance of carnivorous mites (Pd) was significantly synchronized with that in the total abundance of Collembola and oribatid mites (Pτ). Thus, the number‐ratios (Pd/Pτ) were fairly constant, ranging from 0.10 to 0.25. Seasonal changes in vertical distribution of the three animal groups showed a similar pattern for both years. The downward migrations were shown to be more affected by low temperatures in winter accompanied by snow coverage rather than by the desiccation of the surface soil in summer. All the three groups demonstrated as a whole slightly aggregated patterns of horizontal distribution throughout the two years. Temporal increases in the patchiness indices were observed from summer to autumn when the moisture content of the surface soil was low.
Egg size of skippers (Lepidoptera: Hesperiidae) in relation to their host specificity and to leaf toughness of host plants
Authors: Nakasuji Fusao 
Published: March 2006

AbstractThe adaptive significance of egg size of skippers (Lepidoptera; Hesperiidae) in Japan was evaluated in relation to the leaf toughness of their major host grasses. The hesperids that fed on tougher grasses laid larger eggs. Hesperids that laid larger eggs were larger in body size, but lower in fecundity. They also had a wider host range. Thus, despite the lower fecundity, hesperids may benefit from large eggs by having a wider host range of larvae. Grass feeders had wider range of host plants than broadleaf feeders.