bluuebunny/crossref_metadata_2025 huggingface dataset:
What's so special about polymers? A little known organizing principle gives rise to an abundance of polymer phase transitions
Authors: Di Marzio Edmund A.
Published: August 2006

We argue that if an organizing principle exists it must have to do with the linear connectivity of the monomers since this feature is what distinguishes polymers from all other materials. We then compare a linear polymer threading a pore in a membrane (PTM) with an equal number of unconnected monomers which are also allowed to transit through a pore in a membrane. The crucial difference between the two cases is that the connected monomers are distinguishable from one another by virtue of their location along the polymer chain whereas the disconnected monomers are indistinguishable. Because of this, the disconnected monomers obey the ideal gas laws while the connected monomers undergo a first‐order thermodynamic phase transition! Four other phase transitions occurring in isolated linear polymer molecules are known. They are the helix to random coil (HR) transitions in biological polymers, surface adsorption (SA), polymer collapse (C), and a model of polymerization (P). These five kinds of transitions can be coupled to one another resulting in a sizable number of exactly solvable minimal models of phase transitions. There are also five classes of phase transitions in many polymers systems. The coupling of these 10 classes of transitions to each‐other results in a plethora of phases. These in turn provide the basis for the many polymer structures observed in the world about us. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2612–2620, 2006
The phase diagram of a single polymer chain: New insights from a new simulation method
Authors: Rampf F. , Binder K. , Paul W.
Published: August 2006

We present simulation results for the phase behavior of a single chain for a flexible lattice polymer model using the Wang‐Landau sampling idea. Applying this new algorithm to the problem of the homopolymer collapse allows us to investigate not only the high temperature coil–globule transition but also an ensuing crystallization at lower temperature. Performing a finite size scaling analysis on the two transitions, we show that they coincide for our model in the thermodynamic limit corresponding to a direct collapse of the random coil into the crystal without intermediate coil–globule transition. As a consequence, also the many chain phase diagram of this model can be predicted to consist only of gas and crystal phase in the limit of infinite chain length. This behavior is in agreement with findings on the phase behavior of hard‐sphere systems with a relatively short‐ranged attractive square well. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2542–2555, 2006
A Cell Therapy for Chronic Wounds Based Upon a Plasma Polymer Delivery Surface
Authors: Haddow David B. , MacNeil Sheila , Short Robert D.
Published: August 2006

Summary: This contribution chronicles the research history over the past ten years behind a cell therapy product for the treatment of chronic wounds. The product is a plasma coated bandage, which delivers autologous cells (keratinoctyes) to non‐healing wound beds. The account given is chronological, starting with the initial investigations of cell (keratinocyte) attachment to a range of plasma polymer surfaces. It details the subsequent selection of acrylic acid plasma polymer surfaces, on which the growth, proliferation and transfer of keratinoctyes to an in vitro wound model are studied. It concludes with the translation of this technology from the laboratory to the clinic, describing the first “proof of concept” study undertaken with non‐healing diabetic foot ulcers.

Neuropathic foot ulcer on patient 2 persistent for 2 years.

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Neuropathic foot ulcer on patient 2 persistent for 2 years.
Influence of Fluorocarbon Plasma Polymer Films on the Growth of Primary Human Fibroblasts
Authors: Barz Jakob , Haupt Michael , Pusch Kai , Weimer Michaela , Oehr Christian
Published: August 2006

Summary: Pulsed radio‐frequency plasmas containing a mixture of fluorocarbon, argon, and water vapor have been applied to multichamber slides in order to study the biocompatibility in accordance with ISO 10993‐5. According to this standard, the biocompatibility and/or in vitro toxicity of new developed materials is tested with fibroblast cultures. This study deals with the examination of adhesion, proliferation, and cell death of human primary fibroblasts on surfaces gradually coated with fluorocarbon polymer. Besides surface energy, chemical effects as there are chemical functions and the chemical composition of the surface, play an important role in the interaction of human fibroblasts with surfaces. Thus, the data obtained from cell cultivation are correlated to the surface properties as obtained from contact angle measurements and X‐ray photoelectron spectroscopy.

Microscope images reveal the influence of fluorocarbon polymer coatings: The untreated reference surface and the surface treated in a pulsed discharge at 33% duty cycle influence the cell proliferation differently.

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Microscope images reveal the influence of fluorocarbon polymer coatings: The untreated reference surface and the surface treated in a pulsed discharge at 33% duty cycle influence the cell proliferation differently.
Better prediction of the location of α‐turns in proteins with support vector machine
Authors: Wang Yan , Xue Zhidong , Xu Jin
Published: August 2006

We have developed a novel method named AlphaTurn to predict α‐turns in proteins based on the support vector machine (SVM). The prediction was done on a data set of 469 nonhomologous proteins containing 967 α‐turns. A great improvement in prediction performance was achieved by using multiple sequence alignment generated by PSI‐BLAST as input instead of the single amino acid sequence. The introduction of secondary structure information predicted by PSIPRED also improved the prediction performance. Moreover, we handled the very uneven data set by combining the cost factor j with the “state‐shifting” rule. This further promoted the prediction quality of our method. The final SVM model yielded a Matthews correlation coefficient (MCC) of 0.25 by a 10‐fold cross‐validation. To our knowledge, this MCC value is the highest obtained so far for predicting α‐turns. An online Web server based on this method has been developed and can be freely accessed at http://bmc.hust.edu.cn/bioinformatics/ or http://210.42.106.80/. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Crystal structures of the PLP‐ and PMP‐bound forms of BtrR, a dual functional aminotransferase involved in butirosin biosynthesis
Authors: Popovic Bojana , Tang Xiao , Chirgadze Dimitri Y. , Huang Fanglu , Blundell Tom L. , Spencer Jonathan B.
Published: August 2006

The aminotransferase (BtrR), which is involved in the biosynthesis of butirosin, a 2‐deoxystreptamine (2‐DOS)‐containing aminoglycoside antibiotic produced by Bacillus circulans, catalyses the pyridoxal phosphate (PLP)‐dependent transamination reaction both of 2‐deoxy‐scyllo‐inosose to 2‐deoxy‐scyllo‐inosamine and of amino‐dideoxy‐scyllo‐inosose to 2‐DOS. The high‐resolution crystal structures of the PLP‐ and PMP‐bound forms of BtrR aminotransferase from B. circulans were solved at resolutions of 2.1 Å and 1.7 Å with Rfactor/Rfree values of 17.4/20.6 and 19.9/21.9, respectively. BtrR has a fold characteristic of the aspartate aminotransferase family, and sequence and structure analysis categorises it as a member of SMAT (secondary metabolite aminotransferases) subfamily. It exists as a homodimer with two active sites per dimer. The active site of the BtrR protomer is located in a cleft between an α helical N‐terminus, a central αβα sandwich domain and an αβ C‐terminal domain. The structures of the PLP‐ and PMP‐bound enzymes are very similar; however BtrR‐PMP lacks the covalent bond to Lys192. Furthermore, the two forms differ in the side‐chain conformations of Trp92, Asp163, and Tyr342 that are likely to be important in substrate selectivity and substrate binding. This is the first three‐dimensional structure of an enzyme from the butirosin biosynthesis gene cluster. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network
Authors: Saha Sudipto , Raghava G. P. S.
Published: August 2006

B‐cell epitopes play a vital role in the development of peptide vaccines, in diagnosis of diseases, and also for allergy research. Experimental methods used for characterizing epitopes are time consuming and demand large resources. The availability of epitope prediction method(s) can rapidly aid experimenters in simplifying this problem. The standard feed‐forward (FNN) and recurrent neural network (RNN) have been used in this study for predicting B‐cell epitopes in an antigenic sequence. The networks have been trained and tested on a clean data set, which consists of 700 non‐redundant B‐cell epitopes obtained from Bcipep database and equal number of non‐epitopes obtained randomly from Swiss‐Prot database. The networks have been trained and tested at different input window length and hidden units. Maximum accuracy has been obtained using recurrent neural network (Jordan network) with a single hidden layer of 35 hidden units for window length of 16. The final network yields an overall prediction accuracy of 65.93% when tested by fivefold cross‐validation. The corresponding sensitivity, specificity, and positive prediction values are 67.14, 64.71, and 65.61%, respectively. It has been observed that RNN (JE) was more successful than FNN in the prediction of B‐cell epitopes. The length of the peptide is also important in the prediction of B‐cell epitopes from antigenic sequences. The webserver ABCpred is freely available at www.imtech.res.in/raghava/abcpred/. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Structures of soluble amyloid oligomers from computer simulations
Authors: Melquiond Adrien , Mousseau Normand , Derreumaux Philippe
Published: August 2006

Alzheimer's, Parkinson's, and Creutzfeldt‐Jakob's neurodegenerative diseases are all linked with the assembly of normally soluble proteins into amyloid fibrils. Because of experimental limitations, structural characterization of the soluble oligomers, which form early in the process of fibrillogenesis and are cytotoxic, remains to be determined. In this article, we study the aggregation paths of seven chains of the shortest amyloid‐forming peptide, using an activitated method and a reduced atomic representation. Our simulations show that disordered KFFE monomers ultimately form three distinct topologies of similar energy: amorphous oligomers, incomplete rings with β‐barrel character, and cross‐β‐sheet structures with the meridional but not the equatorial X‐ray fiber reflections. The simulations also shed light on the pathways from misfolded aggregates to fibrillar‐like structures. They also underline the multiplicity of building blocks that can lead to the formation of the critical nucleus from which rapid growth of the fibril occurs. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Rank information: A structure‐independent measure of evolutionary trace quality that improves identification of protein functional sites
Authors: Yao Hui , Mihalek Ivana , Lichtarge Olivier
Published: August 2006

Protein functional sites are key targets for drug design and protein engineering, but their large‐scale experimental characterization remains difficult. The evolutionary trace (ET) is a computational approach to this problem that has been useful in a variety of case studies, but its proteomic scale application is partially hindered because automated retrieval of input sequences from databases often includes some with errors that degrade functional site identification. To recognize and purge these sequences, this study introduces a novel and structure‐free measure of ET quality called rank information (RI). It is shown that RI decreases in response to errors in sequences, alignments, or functional classifications. Conversely, an automated procedure to increase RI by selectively removing sequences improves functional site identification so as to nearly match manually curated traces in kinases and in a test set of 79 diverse proteins. Thus we conclude that RI partially reflects the evolutionary consistency of sequence, structure, and function. In practice, as the size of the proteome continues to grow exponentially, it provides a novel and structure‐free measure of ET quality that increases its accuracy for large‐scale automated annotation of protein functional sites. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Anomalous charge relaxation in channels of pentacene‐based organic field‐effect transistors: a charge transient spectroscopy study
Authors: Thurzo I. , Paez B. , Méndez H. , Scholz R. , Zahn D. R. T.
Published: August 2006

Two types of Si/SiO2/pentacene organic field‐effect transistors (OFET) with bottom Au‐source (S) and – drain (D) electrodes were examined by charge transient spectroscopy (QTS), applying pulsed bias ΔUDSto the channel of an OFET with floating gate electrode. The transient chargeQ(t), flowing through the channel after the removal of the bias pulse, was processed at a constant temperature by a three‐channel correlator yielding the signal ΔQ=Q(t1) – 3/2Q(2t1) + 1/2Q(4t1), the scanned delay t1being related to the trailing edge of the bias pulse. Most of the QTS spectra were characterized by peaks of ΔQ(t1) with FWHM corresponding to discrete time constantsτm≈t1m, while scanningt1from 2 μs to 0.1 s. The common feature of the QTS spectra was alineardependence of the peak height ΔQmon ΔUDSfor both polarities of the latter, thereby resembling what is expected for dielectric relaxation (polarization). Some devices showed anomalous (reversed) sign of the signal with respect to the polarity of ΔUDS, or even features like transitions from the correct sign to the reversed one. In order to customize the anomalies, a model is presented which ignores injection of excess charge carriers and takes into account two contributions to the total transient charge: a/space charge of intrinsic charge carriers piled up at the blocking Au‐electrodes during the pulse, relaxing with the dielectric relaxation timeτD=ϵ0ϵr/σ(σbeing conductivity of the organics); b/orientation of molecular dipoles (τdip) in the relaxing electric field of the space charge. It is the dipolar component that is responsible for the anomalous charge flow direction manifested by the signal reversal. The origin of the permanent dipole moment of the otherwise non‐polar pentacene molecules may be either attached excess or missing atoms (vacancies) of the defect molecules [J. E. Northrup and M. L. Chabinyc, Phys. Rev. B68, 041202 (2003)]. In cases of non‐blocking contacts the dipolar relaxation would lead to QTS peaks of correct sign, to be distinguished from possibly non‐negligible contribution of the dielectric relaxation in the semiconductor. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigation of the electro‐optic activity and the electro‐optic effect of La3Ga5SiO14 crystal
Authors: Liu Zhaojun , Wang Qingpu , Zhang Xingyu , Liu Zejin , Wei Aijian , Wu Fuquan , Chang Jun , Su Fufang , Fan Shuzhen , Tang Hengjing , Jin Guofan
Published: August 2006

The electro‐optic activity (EOA) of La3Ga5SiO14 (langasite, LGS) crystal is studied theoretically and the result shows that the EOA will not change the rotatory power along the optic axis of the LGS. An experiment scheme called “elliptic analyzer” is used to verify this theoretical statement. The electro‐optic effect (EOE) of the LGS crystal is also investigated in the same experiment and the EO coefficient r 11 is obtained to be 2.2 pm/V. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of calcium‐deficiency upon physical properties of La0.6Ca0.4MnO3
Authors: Walha I. , Cheikh‐Rouhou A. , Ehrenberg H. , Fuess H.
Published: August 2006

Structural and magnetic properties of the calcium‐defect La0.6Ca0.4–x□xMnO3 (0 ≤ x ≤ 0.2) perovskite manganites have been investigated. Our powder samples have been prepared by the conventional solid state reaction technique at high temperature. Rietveld analysis show that all our synthesized samples crystallize in the orthorhombic perovskite structure with Pnma space group. The Mn atom is coordinated by six oxygen atoms forming an irregular octahedron. With decreasing Ca content the unit cell volume increases. Magnetic measurements as a function of temperature show that all our samples exhibit a paramagnetic‐ferromagnetic transition with decreasing temperature. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The studies of crystallite size and microstrains in aluminum powder prepared by mechanical milling
Authors: Daly R. , Khitouni M. , Kolsi A. W. , Njah N.
Published: August 2006

The process of nanocrystalline structure formation during mechanical milling was studied in recycled low purity aluminum (98.92%). X‐ray patterns were analyzed to determine the crystallite size and the lattice strain. As a result, nanocrystalline powders have been synthesized with microstructure showing a mixture of highly strained crystallites. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In vitro antiviral activities of Chinese medicinal herbs against duck hepatitis B virus
Authors: Leung K. T. , Chiu Lawrence C. M. , Lam W. S. , Li Yaolan , Sun Samuel S. M. , Ooi Vincent E. C.
Published: August 2006

Fifty‐six different Chinese medicinal herbs from 29 families were evaluated for their antiviral activities against duck hepatitis B virus (DHBV) in vitro. The DHBV DNA level in primary duck hepatocyte cultures was monitored by dot blot hybridization and the cytotoxicity was evaluated by MTT assay. Anti‐DHBV activities were found more strongly in the aqueous extracts of Ardisia chinensis and Pithecellobium clypearia with selective indices of 2.6 and >2.7, respectively, which were comparable to that of 2′,3′‐dideoxycytidine. Further research on the isolation of the active antiviral phytochemicals from these herbs may provide alternative options for the treatment of chronic hepatitis B. Copyright © 2006 John Wiley & Sons, Ltd.
Treating threatened abortion with Chinese herbs: a case report
Authors: Qu Fan , Zhou Jue
Published: August 2006

In the report a patient who suffered from threatened abortion was successfully cured with Chinese herbs. After treatment, vaginal bleeding stopped and the aching sensation in the loins and prolapsing sensation in the abdomen disappeared. The gestational ring changed from a crescent moon shape to a normal shape. Copyright © 2006 John Wiley & Sons, Ltd.
Reduction of fat storage in mice fed a high‐fat diet long term by treatment with saponins prepared fromKochia scopariafruit
Authors: Han Li‐Kun , Nose Rumiko , Li Wei , Gong Xiao‐Jie , Zheng Yi‐Nan , Yoshikawa Masayuki , Koike Kazuo , Nikaido Tamotsu , Okuda Hiromichi , Kimura Yoshiyuki
Published: August 2006

The fresh fruit (Japanese name, Tonburi) ofKochia scopariahas been used as a food garnish in Japanese‐style dishes from ancient times, and may prevent metabolic syndromes such as hyperlipidemia, hypertension, obesity and atherosclerosis. This study was performed to clarify whether an ethanol extract ofK. scopariafruit prevented obesity induced in mice by a high‐fat diet for 9 weeks. The ethanol extract ofK. scopariafruit prevented the increases in body weight and parametrial adipose tissue weight induced by the high‐fat diet. Furthermore, consumption of a high‐fat diet containing 1% or 3%K. scopariaextract significantly increased the fecal content and the fecal triacylglycerol level at day 3 compared with those in the high‐fat diet group. The ethanol extract (250 mg/kg) and total saponins (100 mg/kg) ofK. scopariainhibited the elevation of the plasma triacylglyccerol level 2 or 3 h after the oral administration of the lipid emulsion. Total saponins, momordin Ic, 2′‐O‐β‐d‐glucopyranosyl momordin Ic and 2′‐O‐β‐d‐glucopyranosyl momordin IIc isolated fromK. scopariafruit inhibited the pancreatic lipase activity (in vitro). These findings suggest that the anti‐obesity actions ofK. scopariaextract in mice fed a high‐fat diet may be partly mediated through delaying the intestinal absorption of dietary fat by inhibiting pancreatic lipase activity. Copyright © 2006 John Wiley & Sons, Ltd.
Preparation, Characterization and Evaluation of Anionic Starch Derivatives as Flocculants and for Metal Removal
Authors: Aly Amal A.
Published: August 2006

Anionic starch derivatives bearing carboxyl groups were prepared by reacting maize starch and hydrolyzed maize starch with a previously synthesized citric acid adduct (2‐hydroxy‐3‐chloropropylcitric acid) using the dry process. Different factors affecting the preparation, i.e. catalyst concentration, citric acid adduct concentration, duration and temperature have been studied. The modified starch was characterized by IR spectroscopy, X‐ray diffraction analysis and scanning electronic microscopy. The anionic starch derivatives were evaluated as flocculants. Different factors affecting the flocculation efficiency of the prepared flocculants were studied. These factors include effect of dose, acid content, pH of the flocculation medium and molar mass. The anionic starch samples were chelated with different metal cations such as Cu2+, Co2+, Mg2+, and Hg2+, in the form of acetates, chlorides and sulfates.
Fundamental and Derived Properties of Yam (Dioscorea Spp.) Starch Powders and Implications in Tablet and Capsule Formulation
Authors: Riley Cliff K. , Adebayo Sarafadeen A. , Wheatley Andrew O. , Asemota Helen N.
Published: August 2006

A comparative investigation of the fundamental and derived properties of starches from some species of yam (Dioscorea spp.) was conducted with a view to establishing their suitability as excipients in tablet and capsule formulations. Variations were observed in the mean granular diameter of the starches obtained from the different Dioscorea species. Granular diameter ranged from 5.4 µm (Chinese yam) to 34.5 µm (Round leaf yellow yam). Chinese yam and Bitter yam had the highest specific surface area (625.91 m2/kg and 258.76 m2/kg, respectively) while Round leaf yellow yam and Negro yam had the lowest (117.4 m2/kg and 154.34 m2/kg, respectively). Chinese yam had the lowest granular volume (6.00 µm3), surface area (5.67 µm2) and granule surface‐mean diameter (6.74 µm), while Round leaf yellow yam had the largest mean granular diameter, highest granular volume (35.2 µm3), surface area (34.8 µm2) and granule surface mean diameter (35.88 µm). Particle size distribution plots of Chinese yam, Round leaf yellow yam and Negro yam displayed a Gaussian size distribution pattern while Bitter yam displayed a negatively skewed distribution. The variations observed in the granular size and shape may influence the observed derived properties of the starches.
Starch Structure and Digestibility of Rice High in Resistant Starch
Authors: Shu Xiaoli , Jiao Guiai , Fitzgerald Melissa A. , Yang Chaozhu , Shu Qingyao , Wu Dianxing
Published: August 2006

Starch digestibility and starch structure of a high‐resistant starch (RS) rice (RS111) was compared to that of a wild rice type (R7954). RS111 exhibited high RS content and incomplete starch hydrolysis in both cooked rice and retrograded rice flour. High RS rice RS111 had a higher λmax of absorbance and blue value of iodine‐binding starch complex and contained a higher percentage of intermediate chains of amylopectin than R/954. X‐ray diffraction pattern of RS isolated from cooked high RS rice displayed a mixture of B‐ and V‐type that was more resistant to starch hydrolysis by alpha‐amylase. Resistant starch in RS111 is composed mainly of linear amylose and some low‐molecular‐weight amylopectin.
A LabVIEW‐controlled portable x‐ray fluorescence spectrometer for the analysis of art objects
Authors: Desnica Vladan , Schreiner Manfred
Published: August 2006

A field‐portable x‐ray fluorescence (XRF) analyzer was developed and assembled at the Academy of Fine Arts in Vienna in order to permit in situ examinations in the field of archeometry. The system is based on energy‐dispersive XRF using an Oxford XTF5011 50‐W x‐ray tube, a Röntec XFlash 1000 silicon drift detector and two lasers as locating devices. A software package based on National Instruments LabVIEW was developed for simultaneous digital control of all system components, for readout of the acquired data and for convenient presentation and preliminary analysis of the spectra. Subsequently, the measured or stored data could be analyzed using a conventional software package such as WinAxil from Canberra Eurisys. In this paper, the system's analytical capabilities are compared with the results obtained using a laboratory XRF system and a comparative evaluation of the two instruments is made. In combination with the overall miniaturization of all devices, it was possible to assemble an easily portable computer‐controlled measurement system which can be used for in situ examinations and studies of, e.g., art objects in museums and galleries, ceiling frescos in churches and cathedrals and archeological findings at the excavation sites. Copyright © 2006 John Wiley & Sons, Ltd.
History of the atomic physics group of the University of Lisbon
Authors: Carvalho M. L. , Parente F. , Salgueiro Lídia
Published: August 2006

A summary is given of the history of and developments in the atomic physics group of the University of Lisbon. Copyright © 2006 John Wiley & Sons, Ltd.
Angelic nondeterminism in the unifying theories of programming
Authors: Cavalcanti Ana , Woodcock Jim , Dunne Steve
Published: August 2006

Hoare and He’s unifying theories of programming (UTP) is a model of alphabetised relations expressed as predicates; it supports development in several programming paradigms. The aim of Hoare and He’s work is the unification of languages and techniques, so that we can benefit from results in different contexts. In this paper, we investigate the integration of angelic nondeterminism in the UTP; we propose the unification of a model of binary multirelations, which is isomorphic to the monotonic predicate transformers model and can express angelic and demonic nondeterminism.
An approximation algorithm for state minimization in 2-MDFAs
Authors: Subramani K. , Tauras C.
Published: August 2006

In this paper, we analyze the problem of state minimization in a class of Finite State Automata called Two Start State Deterministic Finite State Automata (2-MDFAs). A 2-MDFA is similar to a deterministic finite state automaton (DFA), in that on a given input, each state has precisely one destination state; however, it differs from a DFA in that there are two start states.
A string is accepted by a 2-MDFA if and only if there exists a transitional path from either start state to a finish state, on that string
. Observe that 2-MDFAs provide a limited amount of non-determinism and hence investigating their properties from the perspective of state minimization is a worthwhile pursuit. In case of unbounded non-determinism, i.e., Non-deterministic finite state automata (NFAs), it is well-known that the state minimization problem is PSPACE-complete [Jiang and Ravikumar in Proceedings of the 18th International Colloquium on Automata, Languages and Programming, ICALP’91, Madrid, Spain, July 8–12, 1991] and further that such automata can be exponentially more succinct than DFAs [Meyer and Fischer in Proceedings of the 12th SWAT(Annual Symposium on switching and automata theory), pp 188-191, 1971]. Even in the case of 2-MDFAs, the minimization problem remains non-trivial; indeed, Malcher in Theor Comput Sci 327(3):375–390, 2004 shows that the corresponding decision problem is NP-complete. We focus on deriving approximability bounds for the state minimization problem in 2-MDFAs. Our main contribution in the current paper, is the design of an
n
-approximation algorithm for state minimization in 2-MDFAs, where
n
denotes the minimum number of states required to represent the input language as a 2-MDFA. We also present a proof that this bound is tight for our algorithm.
Spatial pattern analysis in forest dynamics: deviation from power law and direction of regeneration waves
Authors: Schlicht Robert , Iwasa Yoh
Published: August 2006

Grid‐based models have been used to understand spatial heterogeneity of the vegetation height in forests and to analyze spatio‐temporal dynamics of the forest regeneration process. In this report, we present two methods of identifying lattice models when spatio‐temporal data are given. The first method detects directionality of regeneration waves based on the timing of local disturbance events. The second evaluates the forest pattern by recording the fraction of high and low vegetation areas at multiple spatial scales. We illustrate these methods by applying them to patterns generated using three simple stochastic lattice models: (1) two‐state model, distinguishing sites with high and low vegetation, (2) three‐state model, in which sites can be in an additional disturbed state, and (3) Shimagare model, which considers a continuous range of states. The combination of the two methods provides efficient means of distinguishing the models. The first method has a more direct ecological meaning, while the second is useful when forest data are limited in time.
Factors determining plant–neighbour interactions on different spatial scales in young species‐rich grassland communities
Authors: Milbau Ann , Reheul Dirk , De Cauwer Benny , Nijs Ivan
Published: August 2006

In naturally colonised species‐rich grassland communities, we examined the properties of a plant's aboveground neighbourhood that affect its performance (aboveground biomass). To this end a range of neighbourhood parameters were measured: number, biomass and species richness of the neighbours, number and biomass of the conspecific neighbours, and light availability at the base of the target plant. We also determined at which neighbourhood size the strongest target plant–neighbour interactions occurred, and whether conspecific neighbours affected competitively stronger or weaker target species differently. Target plant performance varied with target identity, and was significantly affected by light availability and the number of neighbouring plants (neighbourhood density). Depending on the target species, there was also an effect of total neighbour biomass on plant performance. The target plants were most strongly affected by their neighbours within a 3‐cm distance, which could account for 78% of the variance in target biomass. Number or biomass of the conspecific neighbours did not contribute to the explanation of target performance in any of the target species. Whereas in an 8‐cm neighbourhood the amount of light penetration was the strongest predictor of target performance, the number of neighbours was more important in a 3‐cm neighbourhood. These experimental results might be useful to extend existing neighbourhood competition models for one or two species to multi‐species competition models.
Assessment of left ventricular asynchrony using volume—time curves of 16 segments by real‐time 3 dimensional echocardiography: Comparison with tissue Doppler imaging
Authors: Park Seong‐Mi , Kim Ki‐Chang , Jeon Min‐Jae , Lee Chang‐Kun , Kim Dae‐Hyeok , Park Keum‐Soo , Lee Woo‐Hyung , Kwan Jun
Published: August 2006

Background:

Recent technical developments with high‐resolution real‐time 3 dimensional echocardiography (RT3DE) facilitate the acquisition of high quality images and the analysis of segmental volume—time curves (VTCs).

Aims:

To assess left ventricular (LV) asynchrony using the VTCs of 16 segments by RT3DE, and to evaluate accuracy compared to tissue Doppler imaging (TDI).

Methods:

Twenty‐three heart failure (HF) patients (LVEF: 25±6%, age: 60±13 years) and 16 normal controls underwent TDI and RT3DE. The standard deviation (SD3) of the end systolic time reaching minimal systolic volume for the 16 segments on VTCs was obtained by RT3DE. The standard deviation (SD2) of the electromechanical coupling time for the 8 segments was measured using TDI.

Results:

SD3 was markedly higher in HF patients than in controls (7.7±2.5 vs 1.5±1.0%, P<0.01) and increased as LVEF decreased (r=−0.85, P<0.01). SD2 was also significantly higher in HF patients (27.0±8.6 vs 12.6±5.0 ms, P<0.01) and had a good negative correlation with LVEF (r=−0.72, P<0.01). SD3 was well correlated to SD2 (r=0.66, P<0.01).

Conclusions:

We suggest that analysis of VTCs in 16 segments using RT3DE may be a useful alternative to TDI for the evaluation of LV asynchrony.
Left bundle branch block as a risk factor for progression to heart failure
Authors: Zannad Faiez , Huvelle Etienne , Dickstein Kenneth , van Veldhuisen Dirk J. , Stellbrink Christoph , Køber Lars , Cazeau Serge , Ritter Philippe , Maggioni Aldo Pietro , Ferrari Roberto , Lechat Philippe
Published: August 2006

The prevalence of conduction disturbances, particularly left bundle branch block (LBBB), is strongly correlated with age and with the presence of cardiovascular disease. LBBB has been reported to affect approximately 25% of the heart failure (HF) population and it is likely that the deleterious role of such conduction disorders in the progression to HF has been underestimated.

The purpose of this article is to review the data from the literature indicating that LBBB may have a causative role, mediated through the resulting intra‐ventricular asynchrony, in the deterioration of cardiac function and the development of cardiac remodelling and HF. It also aims to address the potential for future clinical therapies for this conduction disorder.
Pheochromocytoma induced cardiogenic shock with rapid recovery of ventricular function
Authors: Wu Grace Y. , Doshi Amit A. , Haas Garrie J.
Published: August 2006

Pheochromocytoma is a rare cause of secondary hypertension. It may present atypically as cardiogenic shock with significant morbidity and mortality. We present a patient in cardiogenic shock dependant on an intra‐aortic balloon pump and vasopressor support who completely recovered cardiac function within 96 h of hospitalization.
Heterotopic noxious conditioning stimulation (HNCS) reduced the intensity of spontaneous pain, but not of allodynia in painful peripheral neuropathy
Authors: Tuveson Birgitta , Leffler Ann‐Sofie , Hansson Per
Published: August 2006

In 15 patients with painful peripheral neuropathy and dynamic mechanical allodynia, the influence of spontaneous ongoing neuropathic pain on pain sensitivity in a remote pain‐free area was examined, as was the influence of ischemia‐induced heterotopic noxious conditioning stimulation (HNCS) on the intensity of ongoing pain and brush‐evoked allodynia. In addition, the modulating effect of HNCS on pain sensitivity in a pain‐free area was investigated. Pain thresholds to pressure and heat as well as the sensitivity to suprathreshold pressure‐ and heat pain were assessed in the pain‐free area. Dynamic mechanical allodynia was induced by a recently developed semi‐quantitative brushing technique and the patients continuously rated the intensity of the allodynia using a computerized visual analogue scale (VAS). The total brush‐evoked pain intensity was calculated as the area under the VAS curve. At baseline, no significant difference in pain sensitivity was found between patients and their healthy controls in the pain‐free area, indicating a lack of activation of pain modulatory systems from the spontaneous pain. Compared to baseline, the patients rated the ongoing neuropathic pain intensity significantly lower during the HNCS‐procedure (p<0.05). In contrast, there was no influence from HNCS on the total brush‐evoked pain intensity. In the pain‐free area higher pressure pain thresholds were demonstrated during conditioning stimulation in patients and controls alike (p<0.01). In controls only, a significantly higher heat pain threshold was found during the HNCS‐procedure (p<0.01). The main finding of the present study was that HNCS altered differentially spontaneous and brush‐provoked pain in patients with painful peripheral neuropathy.
NMR studies of the fifth transmembrane segment of Na+,K+‐ATPase reveals a non‐helical ion‐binding region
Authors: Underhaug Jarl , Jakobsen Louise Odgaard , Esmann Mikael , Malmendal Anders , Nielsen Niels Chr.
Published: August 2006

The structure of a synthetic peptide corresponding to the fifth membrane‐spanning segment (M5) in Na+,K+‐ATPase in sodium dodecyl sulfate (SDS) micelles was determined using liquid‐state nuclear magnetic resonance (NMR) spectroscopy. The spectra reveal that this peptide is substantially less α‐helical than the corresponding M5 peptide of Ca2+‐ATPase. A well‐defined α‐helix is shown in the C‐terminal half of the peptide. Apart from a short helical stretch at the N‐terminus, the N‐terminal half contains a non‐helical region with two proline residues and sequence similarity to a non‐structured transmembrane element of the Ca2+‐ATPase. Furthermore, this region spans the residues implicated in Na+ and K+ transport, where they are likely to offer the flexibility needed to coordinate Na+ as well as K+ during active transport.
Treatment of HNSCC cell lines with the EGFR‐specific inhibitor cetuximab (Erbitux®) results in paradox phosphorylation of tyrosine 1173 in the receptor
Authors: Mandic Robert , Rodgarkia-Dara Chantal J. , Zhu Li , Folz Benedikt J. , Bette Michael , Weihe Eberhard , Neubauer Andreas , Werner Jochen A.
Published: August 2006

Overexpression of the epidermal growth factor receptor (EGFR, ErbB1, HER1) is frequent in head and neck squamous cell carcinomas (HNSCCs) and correlates with disease progression. Inhibition of EGFR with the kinase inhibitor AG1478 abolished receptor phosphorylation and reduced cell proliferation. However, treatment of HNSCC cells with cetuximab (Erbitux®), a monoclonal antibody designed to block the EGFR ligand binding site, led to paradox EGFR activation due to hyperphosphorylation of tyrosine 1173, however, with a concomitant reduction in Erk1/2 phosphorylation levels. No pronounced influence on cell proliferation levels could be observed after treatment with this antibody. Since cetuximab appears able to activate EGFR in HNSCC cell lines, it is necessary to rethink the exact mechanisms by which cetuximab that recently was approved for the treatment of advanced head and neck cancer, inhibits tumor growth.
Calponin binds G‐actin and F‐actin with similar affinity
Authors: Ferjani Imen , Fattoum Abdellatif , Maciver Sutherland K. , Manai Mohamed , Benyamin Yves , Roustan Claude
Published: August 2006

Calponins are actin‐binding proteins that are implicated in the regulation of actomyosin. Calponin binds filamentous actin (F‐actin) through two distinct sites ABS1 and ABS2, with an affinity in the low micromolar range. We report that smooth muscle calponin binds monomeric actin with a similar affinity (K
d of 0.15 μM). We show that the arrangement of binding is similar to that of F‐actin by a number of criteria, most notably that the distance between Cys273 on calponin and Cys374 of actin is 29 Å when measured by fluorescent resonance energy transfer, the same distance as previously reported for F‐actin.
TRIM11 binds to and destabilizes a key component of the activator‐mediated cofactor complex (ARC105) through the ubiquitin–proteasome system
Authors: Ishikawa Hideaki , Tachikawa Hiroyuki , Miura Yutaka , Takahashi Nobuhiro
Published: August 2006

TRIM11 is a member of the tripartite‐motif‐containing protein family and is known to destabilize humanin, an inhibitor of Alzheimer‐like neuronal insults. In this study, we demonstrate that TRIM11 interacts with activator‐recruited cofactor 105‐kDa component (ARC105) that mediates chromatin‐directed transcription activation and is a key regulatory factor for transforming growth factor β (TGFβ) signaling. Co‐expression of TRIM11 increased ARC105 degradation but a proteasome inhibitor suppressed this. Co‐expression of TRIM11 and ARC105 also increased ubiquitination of ARC105. In addition, TRIM11 suppressed ARC105‐mediated transcriptional activation induced with TGFβ in a reporter assay. These results suggest that TRIM11, with the ubiquitin–proteasome pathway, regulates ARC105 function in TGFβ signaling.
Phosphoproteomics toolbox: Computational biology, protein chemistry and mass spectrometry
Authors: Hjerrild Majbrit , Gammeltoft Steen
Published: August 2006

Protein phosphorylation is important for regulation of most biological functions and up to 50% of all proteins are thought to be modified by protein kinases. Increased knowledge about potential phosphorylation of a protein may increase our understanding of the molecular processes in which it takes part. Despite the importance of protein phosphorylation, identification of phosphoproteins and localization of phosphorylation sites is still a major challenge in proteomics. However, high‐throughput methods for identification of phosphoproteins are being developed, in particular within the fields of bioinformatics and mass spectrometry. In this review, we present a toolbox of current technology applied in phosphoproteomics including computational prediction, chemical approaches and mass spectrometry‐based analysis, and propose an integrated strategy for experimental phosphoproteomics.
New insights on the use of desipramine as an inhibitor for acid ceramidase
Authors: Elojeimy Saeed , Holman David H. , Liu Xiang , El-Zawahry Ahmed , Villani Maristella , Cheng Joseph C. , Mahdy Ayman , Zeidan Youssef , Bielwaska Alicja , Hannun Yusuf A. , Norris James S.
Published: August 2006

Treatment of different cancer cell lines with desipramine induced a time‐ and dose‐dependent downregulation of acid ceramidase. Desipramine's effect on acid ceramidase appeared specific for amphiphilic agents (desipramine, chlorpromazine, and chloroquine) but not other lysomotropic agents such as ammonium chloride and bafilomycin A1, and was not transcriptionally regulated. The cathepsin B/L inhibitor, CA074ME, but not the cathepsin D inhibitor, pepstatin A, blocked desipramine's effect on acid ceramidase. Desipramine led to a more pronounced downregulation of sphingosine compared to ceramide suggesting acid ceramidase inhibition is important to desipramine's mechanism of action. This study reveals a new mechanism of action for desipramine.
A variant System I for cytochrome c biogenesis in archaea and some bacteria has a novel CcmE and no CcmH
Authors: Allen James W.A. , Harvat Edgar M. , Stevens Julie M. , Ferguson Stuart J.
Published: August 2006

C‐type cytochromes are characterized by post‐translational covalent attachment of heme to thiols that occur in a Cys‐Xxx‐Xxx‐Cys‐His motif. Three distinct biogenesis systems are known for this heme attachment. Archaea are now shown to contain a significantly modified form of cytochrome c maturation System I (the Ccm system). The most notable adaptation relative to the well‐studied apparatus from proteobacteria and plants is a novel form of the heme chaperone CcmE, lacking the highly conserved histidine that covalently binds heme and is essential for function in Escherichia coli. In most archaeal CcmEs this histidine, normally found in a His‐Xxx‐Xxx‐Xxx‐Tyr motif, is replaced by a cysteine residue that occurs in a Cys‐Xxx‐Xxx‐Xxx‐Tyr motif. The CcmEs from two halobacteria contain yet another form of CcmE, having HxxxHxxxH approximately corresponding in alignment to the H/CxxxY motif. The CxxxY‐type of CcmE is, surprisingly, also found in some bacterial genomes (including Desulfovibrio species). All of the modified CcmEs cluster together in a phylogenetic tree, as do other Ccm proteins from the same organisms. Significantly, CcmH is absent from all of the complete archaeal genomes we have studied, and also from most of the bacterial genomes that have CxxxY‐type CcmE.
Phosphorylation of the liver X receptors
Authors: Chen Mingyi , Bradley Michelle N. , Beaven Simon W. , Tontonoz Peter
Published: August 2006

The liver X receptors (LXRs) function as nutritional sensors for cholesterol and have important roles in lipid metabolism, glucose homeostasis, and inflammation. We provide the first evidence that LXRs are phosphorylated proteins. Mutational analysis and metabolic labeling indicate LXRα is phosphorylated on serine 198 in the hinge region. This is a consensus target for the MAPK family. A phosphorylation‐deficient mutant, LXRα S198A, remains nuclear and responds to ligands like the wild‐type protein. The biological significance of LXR phosphorylation remains to be elucidated but could provide a novel mechanism for the regulation of LXR signaling pathways and cellular metabolism.
A comparison of polysomnography and the SleepStrip in the diagnosis of OSA
Authors: Pang Kenny P. , Dillard Thomas A. , Blanchard Amy R. , Gourin Christine G. , Podolsky Robert , Terris David J.
Published: August 2006

Objective

To investigate the role of a portable screening device (SleepStrip) in the diagnosis of obstructive sleep apnea (OSA).

Methods and Materials

Prospective, nonrandomized double‐blinded single cohort study at an academic health center. Patients with suspected OSA scheduled for an attended overnight Level I polysomnogram (PSG) and who consented to participate in the study wore the SleepStrip device at home the night after the PSG. The apnea‐hypopnea index (AHI) determined by PSG was compared with the results of the SleepStrip recording.

Results

Thirty‐seven patients with a mean age of 52.1 ± 12.2 years and mean body mass index of 35.7 ± 5.2 participated in the study. The overall agreement between the AHI and the SleepStrip results using Cohen's Kappa value was 0.139 (P = 0.19). The sensitivity and specificity of the SleepStrip for diagnosing severe OSA when the AHI was >40 were 33.3% and 95% (P = 0.05). When the AHI was >25, the SleepStrip sensitivity and specificity were 43.8% and 81.3% (P = 0.26). The sensitivity and specificity of the SleepStrip for diagnosing OSA in patients with an AHI >15 were 54.6% and 70%, respectively (P = 0.26).

Conclusion

The SleepStrip has a low correlation with the AHI as measured by PSG. Further studies are needed before this device can be recommended as a screening tool for the diagnosis of OSA.

EBM rating: B‐2b
Management of recurrent sinus disease in children with cystic fibrosis: A combined approach
Authors: Anat Shatz
Published: August 2006

Objective

To determine whether a combined approach consisting of functional endoscopic sinus surgery (FESS), Caldwell‐Luc operation, and medial maxillectomy is beneficial for children with cystic fibrosis (CF) with refractory sinonasal disease previously treated with endoscopic procedures alone.

Study Design

Retrospective review and comparison of outcomes of CA and FESS alone for each CF patient. Outcomes measured: sinonasal symptoms, endoscopic findings, number of hospitalizations, antibiotic courses, and forced expiratory volume in 1 second (FEV1).

Setting

Referral hospital.

Results

Fifteen children underwent CA between 1996 and 2000 (7 males, 8 females; 13.8 years mean age; 42 months average follow‐up period). Significant decrease in number of hospitalizations and intravenous antibiotic courses, with increased mean FEV1 (from 70.2% preoperation to 89.3% postoperation, P <0.0001) were found. Marked clinical improvement persisted for several years.

Conclusion

Applying the CA after multiple failed endoscopic procedures in CF patients reduced morbidity and resulted in successful management of sinonasal disease. CA is suggested after multiple failed endoscopic procedures. Further studies of CA as a first‐line procedure for difficult sinus cases in children with CF is recommended.

EBM rating: C‐4