bluuebunny/crossref_metadata_2025 huggingface dataset:
Upper bounds on maximum likelihood for phylogenetic trees
Authors: Hendy Michael D. , Holland Barbara R.
Published: October 2003

We introduce a mechanism for analytically deriving upper bounds on the maximum likelihood for genetic sequence data on sets of phylogenies. A simple ‘partition’ bound is introduced for general models. Tighter bounds are developed for the simplest model of evolution, the two state symmetric model of nucleotide substitution under the molecular clock. This follows earlier theoretical work which has been restricted to this model by analytic complexity. A weakness of current numerical computation is that reported ‘maximum likelihood’ results cannot be guaranteed, both for a specified tree (because of the possibility of multiple maxima) or over the full tree space (as the computation is intractable for large sets of trees). The bounds we develop here can be used to conclusively eliminate large proportions of tree space in the search for the maximum likelihood tree. This is vital in the development of a branch and bound search strategy for identifying the maximum likelihood tree. We report the results from a simulation study of approximately 106 data sets generated on clock-like trees of five leaves. In each trial a likelihood value of one specific instance of a parameterised tree is compared to the bound determined for each of the 105 possible rooted binary trees. The proportion of trees that are eliminated from the search for the maximum likelihood tree ranged from 92% to almost 98%, indicating a computational speed–up factor of between 12 and 44.

Contact: m.hendy@massey.ac.nz

*To whom correspondence should be addressed.
Analyzing resistance phenomena in HIV with bioinformatics
methods
Authors: Lengauer Thomas
Published: October 2003

We report on research that is targeted towards understanding the resistance phenomena that HIV undergoes in the presence of selective pressure presented by combination drug therapies. The ultimate goal of this research is to support the physician with helpful models for HIV resistance and to aid his decision as to how to adapt his therapy to the resistance phenomena observed in a patient. The talk will present the medical background of the problem and the following major results:

1. The Arevir database collecting data on HIV resistance. The data are derived from two sources, namely from genotyped patients (wrt to the dominant HIV strain observed in their blood serum) together with their medical history and from in-vitro measurements of the resistance of many HIV strains against single HIV drugs.

2. Statistical learning methods for predicting the resistance of a given HIV strain against single HIV drugs. This software is available via the geno2pheno server on the internet under http://www.genafor.org

3. New bioinformatics contributions that present a model of HIV resistance against combination drug therapies and makes suggestions for therapy adaption that take estimated future mutational path of the virus into account.

These results were achieved within a cooperation funded by DFG and comprising Niko Beerenwinkel (MPI Saarbücken), Martin Däumer (Univ. Cologne), Daniel Hoffmann (caesar Bonn), Rolf Kaiser (Univ. Cologne), Klaus Korn (Univ. Erlangen), Joachim Selbig (MPI Plant Physiology, Golm) Barbara Schmidt (Univ. Erlangen) and Hauke Walter (Univ. Erlangen).

Contact: lengauer@mpi-sb.mpg.de  http://www.mpi-sb.mpg.de/~lengauer/
Artificial gene networks for objective comparison of analysis
algorithms
Authors: Mendes Pedro , Sha Wei , Ye Keying
Published: October 2003

Motivation: Large-scale gene expression profiling generates data sets that are rich in observed features but poor in numbers of observations. The analysis of such data sets is a challenge that has been object of vigorous research. The algorithms in use for this purpose have been poorly documented and rarely compared objectively, posing a problem of uncertainty about the outcomes of the analyses. One way to objectively test such analysis algorithms is to apply them on computational gene network models for which the mechanisms are completely know.

Results: We present a system that generates random artificial gene networks according to well-defined topological and kinetic properties. These are used to run in silico experiments simulating real laboratory microarray experiments. Noise with controlled properties is added to the simulation results several times emulating measurement replicates, before expression ratios are calculated.

Availability: The data sets and kinetic models described here are available from http://www.vbi.vt.edu/~mendes/AGN/as biochemical dynamic models in SBML and Gepasi formats.

Contact: mendes@vt.edu

*To whom correspondence should be addressed.
Comparative genomics of malaria parasites and its exploitation
in a rodent malaria model
Authors: Waters Andy
Published: October 2003

There is an abundance of malaria parasite genome sequence from both human-infectious and model parasites. It is very clear that the similarity of the biology of different Plasmodium species is reflected in the largely conserved organisation of their genomes. The differences between the parasite genomes are most obviously confined to the sub-telomeric regions where the multigene families that are involved in antigenic variation are located. Comparitive genomics may help improve the annotation of the conserved more centromeric regions of the prototype Plasmodium genome and pinpoint genes under stringent selection or experiencing rapid drift. Detailed comparison of Plasmodium genomes can catalogue genome recombination, gene grouping and perhaps indicate higher order levels of genome structure. The significant conservation of gene content including genes that encode surface proteins involved in cell-cell interactions means that the more extensive repertoire of experimental possibilities afforded by model parasites can be exploited to provide biological insights that remain relevant to drug and vaccine research. This will be illustrated by data drawn from the research activities in which the LUMC group participates.

Contact: Waters@lumc.nl  http://www.lumc.nl/1040/research/malaria/contact-andy.html
Non-Equilibrium Dynamics in Untying Knots
Authors: Lai Pik-Yin , Sheng Y.-J. , Tsao H.-K.
Published: October 2003

Flexible closed knots with strict topological constraint of no segment crossing are studied in our simulations using the bond-fluctuation model for polymers. A well-equilibrated polymer knot is cut at a randomly chosen segment and allow to relax to it new equilibrium state, which is the indistinguishable from the free linear chain. In the course of the relaxation, the topological information of the original knot is lost and the characteristic relaxation time measures its rate. The average relaxation time is the typical time scale needed to untie the cut knot by random Brownian motion. Some knot is found to have a longer relaxation time than other knots having more crossings. Remarkably, when all the knots are arranged into homologous groups with a common parametrization in terms of their Alexander polynomials, the relaxation times increase monotonically and linearly with C for all the four groups we studied. Our observation indicates that conventional labelling of knots can further be parametrized naturally into groups in a way that has a direct physical meaning in terms of the topological interactions in a knot. The linear stepwise increase of the relaxation time with the essential crossing suggests that the topological energy spectrum has equal spacing of for knots within a group.
Model checking stochastic automata
Authors: Bryans Jeremy , Bowman Howard , Derrick John
Published: October 2003

Modern distributed systems include a class of applications in which non-functional requirements are important. In particular, these applications include multimedia facilities where real time constraints are crucial to their correct functioning. In order to specify such systems it is necessary to describe that events occur at times given by probability distributions; stochastic automata have emerged as a useful technique by which such systems can be specified and verified.However, stochastic descriptions are very general, in particular they allow the use of general probability distribution functions, and therefore their verification can be complex. In the last few years, model checking has emerged as a useful verification tool for large systems. In this article we describe two model checking algorithms for stochastic automata. These algorithms consider how properties written in a simple probabilistic real-time logic can be checked against a given stochastic automaton.
Food Type Effects on the Population Growth Patterns of Littoral Rotifers and Cladocerans
Authors: García C. Enríquez , Nandini S. , Sarma S. S. S.
Published: October 2003

Littoral rotifers and cladocerans feed on bacteria, phytoplankton, and detritus. In comparison to planktonic organisms their species diversity is high, yet little is known about their biology. In this study we present data on the functional response of the cladocerans Macrothrix triserialis and Alona rectangula, and the rotifer Brachionus macracanthus to different levels of the alga Chlorella vulgaris. Based on the incipient limiting level, we chose the food concentration and tested the population growth on four types of diets for three cladoceran species — Macrothrix triserialis, Alona rectangula, and Chydorus sphaericus — and three rotifer species — Brachionus macracanthus, Lecane quadridentata, and Platyias quadricornis. We studied growth rates of each of these species on diets of live Chlorella vulgaris, heat‐killed Chlorella vulgaris, baker's yeast (Saccharomyces cerevisiae), and field collected detritus. The incipient limiting level was around 0.9 · 106 cells mL−1 of Chlorella for the tested zooplankton species. The population growth patterns showed that, in general, the cladocerans took 25…50 d to reach their peak population densities, which ranged from 10…75 ind. mL−11. Among the rotifers L. quadridentata and B. macracanthus had equally high growth rates on live and heat‐killed forms of C. vulgaris while P. quadricornis grew best on detritus. The growth rates ranged from 0.03…0.21 d−1. The similarities and differences between littoral and planktonic organisms in relation to food type and availability have been discussed.
Biodegradation of Nonylphenol Ethoxylate Surfactants in Biofilm Reactors
Authors: Goel Anubha , Müller Margit B. , Sharma Mukesh , Frimmel Fritz H.
Published: October 2003

The primary degradation of a technical nonylphenol ethoxylate surfactant with an average chain length of 10 ethoxylate units (NPEO‐10) was studied in a flow‐through system by means of miniaturized biofilm reactors (mBFR) with bacteria from an activated sludge plant. 5 mg/L of the test compound (total EO concentration) were spiked in synthetic wastewater (SWW) and fed to the reactors continuously for 64 days. Compound removal and the formation of degradation products (DP) were monitored under both oxic and anoxic conditions. Solid‐phase extraction and RP‐HPLC with fluorescence detection were employed for sample preparation and analysis. Better removal of the parent compound was seen with the oxic reactors (50 to 70%) than with the anoxic reactors (30 to 50%). Compared to SWW organic matter, the test compound proved to be of refractory nature. The appearance of degradation products in the effluent was earlier with anoxic reactors despite their lower elimination efficiency. After extraction of biomass only minor amounts of NPEO‐10 and metabolites were found, indicating that small amounts were present in adsorbed or intracellular form. Ultimate biodegradation of NPEO‐10 and of octylphenol ethoxylates (OPEO‐9.5; average chain length of 9.5 EO units) was tested by means of manometric respirometry at a theoretical oxygen demand (ThOD) of 100 mg/L. Whereas NPEO‐10 was biodegraded by only 26%, at best, in 28 days, OPEO‐9.5 degradation amounted to (40 ± 5)%.
Sulfur and Selenium: The Role of Oxidation State in Protein Structure and Function
Authors: Jacob Claus , Giles Gregory I. , Giles Niroshini M. , Sies Helmut
Published: October 2003

Sulfur and selenium occur in proteins as constituents of the amino acids cysteine, methionine, selenocysteine, and selenomethionine. Recent research underscores that these amino acids are truly exceptional. Their redox activity under physiological conditions allows an amazing variety of posttranslational protein modifications, metal free redox pathways, and unusual chalcogen redox states that increasingly attract the attention of biological chemists. Unlike any other amino acid, the “redox chameleon” cysteine can participate in several distinct redox pathways, including exchange and radical reactions, as well as atom‐, electron‐, and hydride‐transfer reactions. It occurs in various oxidation states in the human body, each of which exhibits distinctive chemical properties (e.g. redox activity, metal binding) and biological activity. The position of selenium in the periodic table between the metals and the nonmetals makes selenoproteins ideal catalysts for many biological redox transformations. It is therefore apparent that the chalcogen amino acids cysteine, methionine, selenocysteine, and selenomethionine exhibit a unique biological chemistry that is the source of exciting research opportunities.
Adherence and satisfaction of rheumatoid arthritis patients with a long‐term intensive dynamic exercise program (RAPIT program)
Authors: Munneke Marten , de Jong Zuzana , Zwinderman Aeilko H. , Jansen Annemarie , Ronday H. Karel , Peter Wilfred F. H. , Boonman Dies C. G. , van den Ende Cornelia H. M. , Vlieland Theodora P. M. Vliet , Hazes Johanna M. W.
Published: October 2003

Objective

To evaluate adherence and satisfaction of patients with rheumatoid arthritis (RA) in a long‐term intensive dynamic exercise program.

Methods

A total of 146 RA patients started an intensive (strength and endurance training for 75 minutes, twice a week, for 2 years) exercise program (Rheumatoid Arthritis Patients In Training) aimed at improving physical fitness. Program attendance and satisfaction were examined. Additional assessments at baseline were done to find possible predictors of attendance.

Results

Median (interquartile range) age and disease duration of the patients were 54 (45–61) and 5 (3–10) years, respectively. After 2 years, 118 (81%) patients still participated in an exercise class. The median attendance rate of all patients was 74%. Low attendance was weakly associated with high disease activity, low functional ability, and low quality of life at baseline but not with the severity of joint damage at baseline. At the end, 78% of all participants would (strongly) recommend the program to other RA patients.

Conclusion

Adherence and satisfaction of RA patients with an intensive dynamic exercise program over a prolonged time can be high. Disease severity parameters do not strongly predict the compliance of participants in an intensive exercise program.
Learning on the Job: Moving From Faculty to Administration
Authors: McCarthy Chris
Published: October 2003

With administrative roles come many changes for faculty leaders, including the perceptions of others, the perception of self, and the skills necessary to remain credible.
Leadership Development Programs
Authors: Kim Karen A.
Published: October 2003

This chapter describes a sample of nondegree and degree programs currently offered to administrators, staff, and faculty in community college leadership.
The Effect of Hydrogen Bonding on Allylic Alkylation and Isomerization Reactions in Ionic Liquids
Authors: Ross James , Xiao Jianliang
Published: October 2003

Neutral allylic alkylation reactions, in which a base is generated in situ and which hence require no external bases, can significantly be retarded when carried out in the ionic liquid 1‐butyl‐3‐methylimidazolium tetrafluoroborate ([bmim][BF4]). Evidence suggests that the base or base precursor enters into hydrogen bonding with the imidazolium cation and is thus made less readily available for deprotonation of pre‐nucleophiles. However, the reaction proceeds well in the presence of stronger bases that are capable of deprotonation. Whilst the phenomenon of hydrogen bonding in ionic liquids can be detrimental to reactions such as allylic alkylation, it can be exploited to suppress unwanted allylic isomerization.
Equation of state and electrical conductivity of strongly correlated aluminum and copper plasmas
Authors: Clérouin J. , Renaudin P. , Recoules V. , Noiret P. , Desjarlais M.
Published: October 2003

Theoretical isochore equation of state and electrical conductivity of hot expanded plasmas of aluminum (ρ = 0.3 g/cm3) and copper (ρ = 0.5 g/cm3) are presented for temperatures 5 000 < T < 30 000 K. Our calculations are carried out in the framework of density functional theory and the local density approximation. Ionic configurations and equation of state are determined by quantum molecular dynamics simulations, from which the conductivity was computed using the Kubo‐Greenwood formula [1, 2]. Theoretical calculations are compared with experimental results obtained in an isochoric plasma closed‐vessel designed to confine electrical plasma discharges up to 1.5 GPa [3]. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ground state and structural transitions in mesoscopic electron hole bilayers
Authors: Ludwig P. , Filinov A.V. , Bonitz M. , Lozovik Yu.E.
Published: October 2003

Few‐particle clusters of spatially separated electrons and holes in vertically coupled two‐dimensional quantum dots are analyzed. As a function of interdot distance d, the inlayer interaction between electrons (and holes) changes from Coulomb repulsion at large d to dipole repulsion of e‐h pairs at small d. The change of the structural properties (cluster shell configuration and symmetry) and energy with variation of d is investigated. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Temperature‐dependent pseudopotential between two pointlike electrical charges
Authors: Gombert M.‐M.
Published: October 2003

The pair distribution functions for particles electrically charged, at a temperature T, expressed in terms of density matrices and the corresponding pseudopotentials are studied. For an electron pair, the symmetry of the wave functions is taken into account. Exact expansions with respect to the separation distance and to a quantum parameter (∼ T−½) are carried out. The known results are recovered. For high temperature, accurate approximations are derived. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the effect of runaway electrons in dense plasma
Authors: Ramazanov T.S. , Turekhanova K.M.
Published: October 2003

The effect of runaway electrons has been studied in this work. There were derived the conditions runaway electrons, the influence of electric field on the electron velocity distribution is considered for nonideal classical plasma models. The dependence of friction force on electrons on their velocities,electron‐ion collision frequency as a function of the coupling parameter and the strength of critical electric field on particle density and temperature are determined. The results are compared with the asymptotic theory. It has been shown that for the definite density and temperature ranges the difference between critical electric field values is essential for various plasma models. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Combined activity‐virial expansions
Authors: Rogers F.J. , DeWitt H.E.
Published: October 2003

We describe a mixed expansion method that combines the best features of the virial and activity expansions. The mixed expansion has the important feature that it can be applied to mixtures of plasma and neutrals that involve both attractive and repulsive interactions. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Intense heavy ion beams as a tool to induce high‐energy‐density states in matter
Authors: Tahir N.A. , Deutsch C. , Fortov V.E. , Gryaznov V.C. , Hoffmann D.H.H. , Juranek H. , Lomonosov I.V. , Piriz A.R. , Redmer R. , Shutov A. , Spiller P. , Temporal M. , Udrea S. , Varentsov D.
Published: October 2003

Because of the volume character of energy deposition of energetic ions in matter, an intense heavy ion beam is a very suitable laboratory tool to create large samples of high‐energy‐density matter. This paper shows with the help of two‐dimensional numerical simulations how such an intense heavy ion beam can be employed to achieve this goal. The beam parameters considered in this study are those of the beams that are delivered by the existing heavy ion synchrotron, SIS18 and that which will be available at the future facility SIS100, respectively at the Gesellschaft für Schwerionenforschung (GSI), Darmstadt. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Pycnonuclear reactions and the nature of supranuclear matter
Authors: Yakovlev D. G. , Levenfish K. P.
Published: October 2003

We discuss pycnonuclear burning in a strongly nonideal plasma of atomic nuclei at densities up to 1013 g cm−3. As an application, we consider pycnonuclear burning of matter accreted on a neutron star in a binary system. The energy released in this burning, while the matter sinks into the stellar crust under the weight of newly accreted material, is sufficient to warm the star. Its surface thermal radiation becomes dependent of poorly known equation of state of supranuclear matter in the stellar core, which gives a method to explore this equation of state. The results of such studies are outlined. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Evaluation by numerical analysis of magnetic shielding characteristics of bulk high‐Tc superconductor containing weak links
Authors: Fukuoka Katsuhiro , Hashimoto Mitsuo , Tomita Masaru , Murakami Masato
Published: October 2003

High‐Tc superconductors (HTS), which have the characteristics of critical current density over 3 × 104 A/cm2 at liquid nitrogen temperature (77 K) and 1 T, can be produced. Thus, they are promising for many practical applications such as a magnetic bearing, magnetic levitation, flywheel, and magnetic shielding. Since the HTS characteristics are not homogeneous in some specimens due to grain boundaries and cracks, the distribution of magnetic characteristics should be assessed. Thus, we have measured the distribution of the magnetic flux density on the surface of the HTS using a Hall element, and have evaluated its magnetic characteristics. The measurement of magnetic characteristics using a Hall element is difficult regarding the distribution of the magnetic flux density on the actual surface and inside of the HTS sample. In this research, we conducted a quantitative evaluation of the magnetic shielding characteristics of the HTS including weak links under a static magnetic field with the three‐dimensional finite element method analysis. © 2003 Wiley Periodicals, Inc. Electr Eng Jpn, 146(1): 9–17, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.10209
Spectroelectrochemical Measurements at Colloidal Au Multilayer Optically Transparent Electrodes
Authors: Richardson John N. , Osisek Andrea J. , Dyer Aubrey L.
Published: October 2003

Application of thin colloidal Au multilayers on glass substrates as optically transparent electrodes is reported herein. Evaluation of the electrode by scanning electron microscopy and as an optically transparent thin layer electrode (OTTLE) illustrate its use for spectroelectrochemical applications. A spectroelectrochemical Nernst plot acquired for the oxidation of o‐tolidine yielded a value of E°=0.605 V (vs. Ag/AgCl) and n=1.88. Both of these values are in excellent agreement with previously published values obtained using a traditional Au minigrid OTTLE. The colloidal Au multilayer electrode is expected to offer many advantages over the minigrid OTTLE in specific applications. These advantages include direct control over microscopic surface topography, large electrochemical surface area, applicability to many different electrode geometries, and increased microscopic surface roughness for SERS and SPR applications.
A New Evaluation Method for 2‐D Fluorescence Spectra Based on Theoretical Modeling
Authors: Geissler D. , Solle D. , Stärk E. , Scheper T. , Märkl H. , Hitzmann B.
Published: October 2003

This article presents a new evaluation procedure of 2‐D fluorescence spectra obtained during a yeast cultivation without performing a calibration measurement. The 2‐D fluorescence spectra are used to predict the process variables biomass, glucose and ethanol. The new calibration procedure uses a theoretical model of these process variables, i.e., differential equations, to replace any calibration measurement. The theoretical model parameters are identified simultaneously during the calculation of the chemometric models. The root mean square error of prediction of the chemometric models with respect to off‐line measurements are 1.5 g/L, 0.40 g/L and 0.56 g/L for glucose, biomass and ethanol, respectively.
Modeling of the Biosynthesis of Cephalosporin C by Acremonium chrysogenum
Authors: Rhee J.I. , Seidel G. , Schügerl K.
Published: October 2003

In this work, a mathematical model of the biosynthesis of cephalosporin C by Acremonium chrysogenum is presented. It is based on the intracellular and extracellular concentrations of cephalosporin C and its precursors and the activities of the intracellular enzymes of the biosynthesis which were determined experimentally in the laboratory, as well as on data reported in the literature.
Analysis of twin data ascertained through probands: The double‐entry approach
Authors: Hindsberger Charlotte , Bryld Lars Erik
Published: October 2003

Twin pairs are sometimes included in studies because at least one of them is a proband, and conventionally the analysis of the data is based on the conditional distribution of the cotwin given the proband. In the case of more than one proband in each pair, an often used “ad hoc” method of analysis is to allow each twin to act as proband as well as cotwin. An example of this is the probandwise concordance, which is used as an estimate of the casewise concordance under incomplete ascertainment. In this paper, we show that the method of double entry under a regularity condition provides consistent estimates of parameters, but that conventional standard errors as well as a correction suggested by Stevenson et al. ([1993] J. Child Psychol. Psychiatry 34:1137–1152) will be wrong. Instead, we recommend the use of an easily calculated sandwich estimator. We illustrate the method with twin data from a study of the genetic component in hand eczema. Genet Epidemiol 25:225–235, 2003. © 2003 Wiley‐Liss, Inc.
Transplantation and microsurgical anastomosis of free omental grafts: Experimental animal model of a new operative technique in dogs
Authors: Pap‐Szekeres Jozsef , Cserni Gabor , Furka Istvan , Svebis Mihaly , Cserni Tamas , Brath Endre , Nemeth Norbert , Miko Iren
Published: October 2003

Our objective was the elaboration of a new animal model for the free transplantation of an omental flap and the examination of its viability in dogs. The cooled omental flap from the abdomen was freely transplanted to the lateral cervical region, and its blood supply was established with microsurgical anastomoses. The technique was developed in 5 dogs, and short‐term survival examinations were later carried out in 3 cases by means of this method. Postoperative viability was assessed by angiography, methylene blue testing, and histology. Of the 3 transplanted grafts, 2 still survived 1 week after the operation. For technical reasons, 1 flap thrombotized. For determination of the viability of the transplanted graft, histology proved best. Vital reactions, including granulation tissue and angiogenesis, were present on the histological slides. The short‐term survival of an omental flap can be ensured with microsurgical transplantation in dogs.

A cseplesz lebeny szabad átültetésére, valamint az átültetett lebenyek életképességének vizsgálata céljából új állatkísérletes modellt dolgoztunk ki. Módszerünket 5 állaton dolgoztuk ki, majd további 3, műtött állatnál rövidtavu túlélési vizsgálatokat végeztünk. Hasüregből nyert, megfelelően előkészített és hűtött cseplesz lebenyt szabadon ültettünk át a laterális nyaki régióra. Az átültetett lebeny érellátását mik‐rosebészeti módszerrel létrehozott anasztomózisokkal biztosítottuk. Az átültetett lebenyek életképességét angiográfia, metilénkék‐festés és szövettani módszerekkel vizsgáltuk. A 3 átültetett lebeny közül 2 életképesnek bizonyult 1 héttel a műtét után, technikai ok miatt 1 lebeny trombotizált. Az életképesség igazolására a szövettani vizsgálat bizonyult a legjobbnak, melynek segítségével granulációs szövet és angiogenezis is ábrázolható volt. Cseplesz lebeny rövidtávú túlélése biztosítható mikrosebészeti módszerrel történő átültetéssel kutyán. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:414–418 2003
Contact optimization in polymer light‐emitting diodes
Authors: Brown T. M. , Cacialli F.
Published: October 2003

To fully exploit the properties of light‐emitting polymers (LEPs) in electroluminescent applications, it is of paramount importance to develop efficient electrical contacts. An ideal electrode is highly conductive, stable, provides a low barrier to carrier injection, and does not degrade the LEP upon contact. It is difficult to find a single homogeneous material that satisfies all of these requirements. Hence, contact optimization has often required the development of multilayer structures. In particular, indium tin oxide covered by a film of poly(ethylene‐dioxythiophene):poly(styrene sulfonic acid) {ITO/PEDOT:PSS} has become a favorite combination for the transparent anode, and heterostructures of LiF and CsF with metals (Al and Ca) have proven to be efficient electron‐injecting contacts. Here we review our progress in the understanding of the operation of light‐emitting diodes incorporating such contacts, in particular by gauging the materials' energy‐level lineup via electroabsorption measurements. Among the series of LEDs investigated, using a high‐energy‐gap blue polyfuorene polymer, CsF/Ca/Al and LiF/Ca/Al electrodes lead to the best improvements in electron injection. The most promising performance for applications, where a high luminance (∼1600 cd/m2 at 5 V) is also accompanied by a high maximum efficiency (∼3 lm/W), was obtained with LiF/Ca/Al cathodes and ITO/PEDOT:PSS anodes. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2649–2664, 2003
Spin and lattice configurationsin p‐conjugated organic ferromagnetic polymerwith open boundary condition
Authors: Zhao L. , Yao K. L. , Wang W. Z. , Tian X.
Published: October 2003

By employing the extended Su–Schrieffer–Heeger Hamiltonian including on‐site and inter‐site Coulomb repulsions, we investigate the spin and lattice configurations in π‐conjugated organic ferromagnetic polymer under the open boundary condition. The results display that for a certain on‐site Coulomb repulsion, the domain solitons in varying appearances will successively appear along the main chain with increasing of electron–phonon interaction while the spin ones come into view at the side radicals, and, moreover, the inter‐site Coulomb repulsion will exert a great influence on both kinds of solitons.
Molecular field theory analysis of Gd2Co2Al and Gd2Co2Ga compounds
Authors: Kervan S.
Published: October 2003

The molecular field theory based on two‐sublattice model was employed to analyse the temperature dependence of the magnetization of Gd2Co2Al and Gd2Co2Ga compounds. The molecular field coefficients nCoCo, nGdCo and nGdGd were obtained by a numerical fitting process. The theoretically calculated Curie temperatures were found to agree well with the experimental results. The exchange fields HCo(T) and HGd(T) were presented.
Mechanical, elastic and anharmonic properties of zinc blende MgS compound
Authors: Jha Prafulla K. , Talati Mina
Published: October 2003

The mechanical, elastic and anharmonic properties of zinc blende MgS compound have been investigated using a three‐body force potential arising from the charge transfer effects due to the deformation of the electronic shell of overlapping ions. The agreement between the results for elastic constants and bulk modulus and the available data is generally satisfactory. Values for the zone center LO phonon frequency, Debye temperature and specific heat at constant volume have also been obtained. In the case of anharmonic properties, such as third‐order elastic constants, physically significant and systematic values have been obtained similar to other compounds of the zinc blende structure.
Thermal analysis, Raman scattering and infrared spectroscopy versus temperature of hydrogen bonds in sodium p‐nitrophenolate dihydrate (NPNa), [Na(C6H4ONO2)] · 2H2O
Authors: Salah M. Ben , Becker P. , Carabatos‐Nédelec C.
Published: October 2003

This work deals with the hydrogen bonds in p‐nitrophenolate sodium dihydrate (NPNa). Differential scanning calorimetry (DSC) and thermogravimetric analysis (TG) were performed in the temperature range 293–673 K (20–400 °C) in order to control the dehydration process and decomposition of the crystal. The energy necessary to break each type of hydrogen bond has been determined. The O…O vibration of the two hydrogen bonds, denoted O…O1 and O…O2, have been studied by Raman spectroscopy versus temperature. The O–H stretching modes of hydrogen bonds have been also identified in infrared and micro‐Raman spectra. Raman spectra functions of temperature allowed to evidence an order‐disorder transition at ca 138 K related to the molecular configuration in the lattice.
Fostering Collaboration Among Students in Problem‐Based Learning
Authors: Speck Bruce W.
Published: October 2003

To foster positive interaction among students in collaborative groups, professors can establish behavioral norms by the way they form groups and train students to work effectively in goups.
Setting domain boundaries for convergence of biological and psychological perspectives on cognitive coordination in schizophrenia
Authors: Ginsberg J. P.
Published: October 2003

The claim that the disorganized subtype of schizophrenia results from glutamate hypofunction is enhanced by consideration of current subtypology of schizophrenia, symptom definition, interdependence of neurotransmitters, and the nature of the data needed to support the hypothesis. Careful specification clarifies the clinical reality of disorganization as a feature of schizophrenia and increases the utility of the subtype.
Do metamers matter?
Authors: Hahn Martin
Published: October 2003

Metamerism is a rather common feature of objects. The authors see it as problematic because they are concerned with a special case: metamerism in standard conditions. Such metamerism does not, however, pose a problem for color realists. There is an apparent problem in cases of metameric light sources, but to see such metamers as problematic is to fail to answer Berkeley's challenge.
Guarding against over-inclusive notions of “context”: Psycholinguistic and electrophysiological studies of specific context functions in schizophrenia
Authors: Titone Debra , Debruille J. Bruno
Published: October 2003

Phillips & Silverstein offer an exciting synthesis of ongoing efforts to link the clinical and cognitive manifestations of schizophrenia with cellular accounts of its pathophysiology. We applaud their efforts but wonder whether the highly inclusive notion of “context” adequately captures some important details regarding schizophrenia and NMDA/glutamate function that are suggested by work on language processing and cognitive electrophysiology.
Stratospheric drain over Indonesia and dehydration within the tropical tropopause layer diagnosed by air parcel trajectories
Authors: Hatsushika Hiroaki , Yamazaki Koji
Published: October 2003

The structures of temperature and velocity fields in the tropical tropopause layer (TTL) in boreal winter are investigated using an atmospheric general circulation model (AGCM). The model reveals strong upward motions in the lower part of the TTL over the maritime continent and the western tropical Pacific, corresponding to the “stratospheric fountain” region, and downward motions in the upper part of the TTL over Indonesia, representing the stratospheric drain. In the TTL, strong easterlies prevail, and the cold ascent region tilts eastward. A down‐slope flow over the upward‐bulging isentropic surface produces the downward p velocity over Indonesia. In addition, reduction of longwave heating over deep convection suppresses the upward motion. The model simulates the observed stratospheric drain signature well, without convective overshootings. A trajectory analysis using the AGCM‐simulated three‐dimensional wind and temperature is performed to clarify the entry process of air parcels from the tropical troposphere to the stratosphere and to investigate the dehydration process during passage through the TTL. Tropospheric air parcels are advected upward to the bottom of the TTL mainly from the stratospheric fountain region. A pair of anticyclonic circulations in the tropical western Pacific entrains air parcels, which then pass through the equatorial cold region several times during the slow ascent in the TTL. This slow spirally ascending motion brings about low humidity in the stratosphere, despite the local downward motion over Indonesia. In addition, transient disturbances, particularly low‐frequency disturbances, produce intermittent upward motions over the fountain region, resulting in effective dehydration of the air. The spiral ascent and transient mechanisms are key factors in the dehydration process in the TTL. The interannual variation in the water vapor mixing ratio into the tropical lower stratosphere with the El Niño/Southern Oscillation cycle is also estimated, and it is found that in La Niña years, air is more dehydrated.
Evaluation of in‐channel gravel storage with morphology‐based gravel budgets developed from planimetric data
Authors: Gaeuman David A. , Schmidt John C. , Wilcock Peter R.
Published: October 2003

Gravel budgets developed from changes in river morphology have emerged as an important tool for exploring stream dynamics and sediment transport. In many cases, old aerial photographs are the only data available by which to evaluate past morphologic changes. Existing methods for building morphology‐based gravel budgets from air photos are subject to several sources of uncertainty, including difficulty in identifying deposition within the active channel. In‐channel deposition sites consist of submerged bars or general increases in bed elevation, both of which are virtually impossible to detect on air photos. However, bed deposition can be inferred when measured gravel storage losses are greater than the quantity of gravel exiting the study area at its downstream boundary. An integrated method combining measurements of gravel storage changes with a gravel routing procedure based on estimated gravel transport path lengths was developed to identify sites of bed aggradation. Inclusion of storage change results in the routing procedure reduces the uncertainty associated with the selection of appropriate transport path lengths. The method was applied to development of gravel budgets for a 50‐year period in the lower Duchesne River, Utah. Areas in which the predicted bed aggradation was greatest displayed higher rates of channel activity and greater channel instability during subsequent time periods.
Damped fluctuations in Chinese loess grain size
Authors: Xiong S. F. , Ding Z. L. , Jiang W. Y. , Yang S. L. , Liu T. S.
Published: October 2003

The sediment record of the loess‐paleosol sequence in the Chinese Loess Plateau reveals a strong relationship between grain size fluctuations and glacial‐interglacial cycles documented by marine oxygen isotope variations. However, on tectonic time scales, differences between the loess‐paleosol grain size record and the marine oxygen isotope record can be identified. Analytical results from the Baishui, Jingchuan and Lingtai sections show that the grain size of eolian loess, superimposed on a coarsening trend, has two abrupt shifts at about 2.55 and 1.25 Ma, which are followed by significantly damped fluctuations in grain size. This is different from the global oxygen isotope record which demonstrates higher amplitude variations since the late Pliocene‐early Pleistocene and lacks analogs of the abrupt shifts. We propose that the progressive uplift of the Tibetan plateau may have forced the regional environmental system across two thresholds at the late Pliocene‐early Pleistocene and the middle Pleistocene, respectively, inducing two pulses of climatic and environmental changes over north‐western China which are superimposed on the global cooling trend and orbital climate changes.
Long‐term climate variations in China and global warming signals
Authors: Hu Zeng‐Zhen , Yang Song , Wu Renguang
Published: October 2003

In this work, the authors analyze the observed long‐term variations of seasonal climate in China and then investigate the possible influence of increases in greenhouse gas concentrations on these variations by comparing the observations with the simulations of the second phase of the Coupled Model Intercomparison Project (CMIP2). The long‐term variations of precipitation and temperature in China are highly seasonally dependent. The main characteristic of summer precipitation in China is a drying trend in the north and a wetting trend in the central part. The precipitation in winter shows an increasing trend in southern and eastern‐central China. Interesting features have also been found in the transitional seasons. In spring, precipitation variations are almost opposite to those in summer. In autumn the precipitation decreases in almost the whole country except for the middle and lower reaches of the Yangtze River Valley. In addition, the seasonality of precipitation has become slightly weaker in recent decades in southern and eastern China. Pronounced warming is observed in the entire country in winter, spring, and autumn, particularly in the northern part of China. In summer a cooling trend in central China is particularly interesting, and cooling (warming) trends generally coexist with wetting (drying) trends. The correlativity between precipitation and temperature variations is weak in spring, autumn, and winter. It has also been found that the long‐term climate variations in winter and summer in China may be connected to the warming trend in the sea surface temperature of the Indian Ocean. A comparison between the observed seasonal climate variations and the CMIP2 simulations of 16 models indicates that the observed long‐term variations of winter, spring, and autumn temperature in China may be associated with increases in greenhouse gas concentrations. However, such a connection is not found for the summer temperature. The tremendous uncertainties among the models in precipitation simulations make it difficult to link the precipitation variations to global warming.
Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer
Authors: Yang Haw , Luo Guobin , Karnchanaphanurach Pallop , Louie Tai-Man , Rech Ivan , Cova Sergio , Xun Luying , Xie X. Sunney
Published: October 2003

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.
Critical Phenomena Near Bifurcations in Nonequilibrium Systems
Authors: Ahlers Guenter , Oh Jaechul
Published: October 2003

The usual deterministic description of spatially-extended nonlinear dissipative systems far from equilibrium yields a sharp bifurcation point at a crtical value R=Rc of the control parameter where the system makes a transition from the spatially uniform ground state to a state with spatial variation. However, when the effect of thermal noise is considered, then even below the bifurcation there are fluctuations of the macroscopic variables away from the uniform state and the relevant fields, although they have zero mean, have a positive mean square. Here we review measurements of the properties of these fluctuations. In the case of Rayleigh–Bénard convection (RBC) in common fluids, fluctuation amplitudes are small and the exponent of the powerlaw which describes their mean square has its classical (mean-field) value γMF=1/2 in experimentally accessible parameter ranges. However, for RBC of a fluid near its liquid-gas critical point fluctuation amplitudes are much larger and nonlinear interactions between them yield a first-order transition as predicted by Swift and Hohenberg. Electroconvection in nematic liquid crystals (NLC) does not belong to the same universality class as RBC, and fluctuation interactions leave the bifurcation supercritical; but the critical behavior is renormalized.
Control of Spatiotemporal Turbulence in Oscillatory and Excitable Media
Authors: Hu Bambi , Zhang Hong
Published: October 2003

A new method of the control of spatiotemporal turbulence in two-dimensional oscillatory and excitable media is proposed. By applying a suitable periodic stimulation at a single point, we have successfully controlled spatiotemporal turbulence by developing spiral waves or target waves. This method of control is very general, robust and efficient.
Tunneling Between Floquet States in Atom Optics Experiments
Authors: Luter Robert , Reichl L. E.
Published: October 2003

Dynamical tunneling has been observed in atom optics experiments by two groups, one in Texas and the other at NIST. The oscillations observed in these experiments are due to a few Floquet states that were excited by the initial conditions in the experiment. In this paper we focus on the Texas experiment and discuss the properties of the dominant Floquet states for a range of experimental parameters.
Three-Wave Parametric Simultons in Nonlinear Lattices
Authors: Huang Guoxiang , Hu Bambi , Szeftel Jacob
Published: October 2003

A new type of nonlinear excitations, i.e. three simultaneous lattice solitons (simultons), in a nonlinear diatomic lattice is predicted. We show that three-wave resonance condition can be fulfilled in the diatomic lattice. Using a quasi-discrete multi-scale method we derive nonlinear amplitude equations for the three-wave resonance with the dispersion of the system taken into account. We provide several types of exact lattice simultons solutions and show that the lattice simultons can be non propagating and their oscillating frequencies may be within the gap of phonon spectrum bands.
Monte Carlo Study on the Statistical Properties of Ising Polymer Chain
Authors: Luo Meng-Bo
Published: October 2003

The configurational and magnetic properties of magnetic polymers are investigated based on an Ising polymer chain model with nearest-neighbor spin-spin interaction on the simple cubic lattice. Dynamic Monte Carlo simulation shows that the model has spontaneous magnetization at low temperature, i.e. the mean-square magnetization  approaches to 1 below the critical temperature Tc. Near Tc, a transition of chain spatial configuration from extended coil to compacted globule is found. A nonlinear magnetization - field curve is observed, in agreement with experimental findings for magnetic polymers.
Mean Flow Effects in the Faraday Instability
Authors: Martín Elena , Martel Carlos , Vega José M.
Published: October 2003

We study the weakly nonlinear evolution of Faraday waves in a 2D container that is vertically vibrated. In the small viscosity limit, the evolution of the surface waves is coupled to a non-oscillatory mean flow that develops in the bulk of the container. The corresponding long time (Navier-Stokes+amplitude) equations are derived and analyzed numerically. The results indicate that the (usually ignored) mean flow plays an essential role in the stability of the surface waves and in the bifurcated wave patterns.