bluuebunny/crossref_metadata_2025 huggingface dataset:
An engineered folded PLP‐bound monomer of Treponema denticola cystalysin reveals the effect of the dimeric structure on the catalytic properties of the enzyme
Authors: Montioli Riccardo , Cellini Barbara , Bertoldi Mariarita , Paiardini Alessandro , Voltattorni Carla Borri
Published: July 2008

Cystalysin, a dimeric pyridoxal 5′‐phosphate (PLP)‐dependent lyase, is a virulence factor of the human oral pathogen Treponema denticola. Guided by bioinformatic analysis, two interfacial residues (Leu57 and Leu62) and an active site residue (Tyr64*), hydrogen‐bonded with the PLP phosphate group of the neighboring subunit, have been mutated. The wild‐type and the L57A, L62A, Y64*A, L57A/L62A, L57A/Y64*A, L57A/L62A/Y64*A mutants, all having a C‐terminal histidine tag, have been constructed, expressed, and purified. The impact of these mutations on the dimeric state of cystalysin in the apo‐ and holo‐form has been analyzed by size‐exclusion chromatography. The results demonstrate that (i) Leu57 is more critical than Leu62 for apodimer formation, (ii) Tyr64*, more than Leu62, interferes with dimerization of holocystalysin without affecting that of apoenzyme, (iii) while each single mutation is inadequate in significantly altering the extent of monomerization of both apo‐ and holo‐cystalysin, their combination leads to species which remain in a folded monomeric state at a reasonably high concentration in both the apo‐ and holo‐forms. Although L57A/L62A or L57A/Y64*A, even to a different extent, are stimulated to dimer formation in the presence of either unproductive or productive ligands, L57A/L62A/Y64*A remains prevalently monomer at a concentration up to 50 μM. Kinetic analyses show that in this monomeric species the α,β‐eliminase, alanine racemase, and D‐alanine half‐transaminase activities are almost abolished, while the L‐alanine half‐transaminase activity is slightly enhanced when compared with that of wild‐type. The structural basis of the stereospecific transaminase activity displayed by the engineered folded PLP‐bound monomer has been analyzed and discussed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The first high pH structure of Escherichia coli aspartate transcarbamoylase
Authors: Stieglitz Kimberly A. , Xia Jiarong , Kantrowitz Evan R.
Published: July 2008

The activity and cooperativity of Escherichia coli aspartate transcarbamoylase (ATCase) vary as a function of pH, with a maximum of both parameters at approximately pH 8.3. Here we report the first X‐ray structure of unliganded ATCase at pH 8.5, to establish a structural basis for the observed Bohr effect. The overall conformation of the active site at pH 8.5 more closely resembles the active site of the enzyme in the R‐state structure than other T‐state structures. In the structure of the enzyme at pH 8.5 the 80's loop is closer to its position in R‐state structures. A unique electropositive channel, comprised of residues from the 50's region, is observed in this structure, with Arg54 positioned in the center of the channel. The planar angle between the carbamoyl phosphate and aspartate domains of the catalytic chain is more open at pH 8.5 than in ATCase structures determined at lower pH values. The structure of the enzyme at pH 8.5 also exhibits lengthening of a number of interactions in the interface between the catalytic and regulatory chains, whereas a number of interactions between the two catalytic trimers are shortened. These alterations in the interface between the upper and lower trimers may directly shift the allosteric equilibrium and thus the cooperativity of the enzyme. Alterations in the electropositive environment of the active site and alterations in the position of the catalytic chain domains may be responsible for the enhanced activity of the enzyme at pH 8.5. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Prediction of turn types in protein structure by machine‐learning classifiers
Authors: Meissner Michael , Koch Oliver , Klebe Gerhard , Schneider Gisbert
Published: July 2008

We present machine learning approaches for turn prediction from the amino acid sequence. Different turn classes and types were considered based on a novel turn classification scheme. We trained an unsupervised (self‐organizing map) and two kernel‐based classifiers, namely the support vector machine and a probabilistic neural network. Turn versus non‐turn classification was carried out for turn families containing intramolecular hydrogen bonds and three to six residues. Support vector machine classifiers yielded a Matthews correlation coefficient (mcc) of ∼0.6 and a prediction accuracy of 80%. Probabilistic neural networks were developed for β‐turn type prediction. The method was able to distinguish between five types of β‐turns yielding mcc > 0.5 and at least 80% overall accuracy. We conclude that the proposed new turn classification is distinct and well‐defined, and machine learning classifiers are suited for sequence‐based turn prediction. Their potential for sequence‐based prediction of turn structures is discussed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Floral attractants for the female soybean looper, Thysanoplusia orichalcea (Lepidoptera: Noctuidae)
Authors: Stringer Lloyd D , El‐Sayed Ashraf M , Cole Lyn M , Manning Lee‐Anne M , Suckling David M
Published: July 2008

BACKGROUND: The soybean looper, Thysanoplusia orichalcea (F.), is a polyphagous insect pest of vegetable crops. Indonesian in origin, it has spread to Europe, India, Africa, Australia and New Zealand. The identification of an attractant for female T. orichalcea could enable the development of alternative pest management strategies to those provided by insecticides or sex pheromones, which are often only attractive to males.

RESULTS: Traps baited with synthetic lures derived from Canada thistle, Cirsium arvense (L.) Scop., floral volatiles attracted female T. orichalcea. Phenylacetaldehyde, a floral compound attractive to many Lepidoptera and present in C. arvense, was tested alone as an attractant for the soybean looper and caught significantly more female than male T. orichalcea. Trap catch was greatest when phenylacetaldehyde was combined with five prevalent volatiles present in C. arvense headspace collections: 2‐phenylethyl alcohol, methyl salicylate, dimethyl salicylate, benzaldehyde and benzyl alcohol. Twice as many female moths as males were collected.

CONCLUSION: Successful trapping of female T. orichalcea in either a lure‐and‐kill or a mass trapping system may offer an effective way to manage its population size. Copyright © 2008 Society of Chemical Industry
Synthesis of 2‐oxoamides based on sulfonamide analogs of γ‐amino acids and their activity on phospholipase A2
Authors: Antonopoulou Georgia , Magrioti Victoria , Stephens Daren , Constantinou‐Kokotou Violetta , Dennis Edward A. , Kokotos George
Published: July 2008

A variety of lipophilic 2‐oxoamides containing sulfonamide analogs of γ‐amino acids as well as acyl sulfonamides of γ‐aminobutyric acid were synthesized. Their ability to inhibit intracellular GIVA cPLA2 and GVIA iPLA2 as well as secreted GV sPLA2 was evaluated. The sulfonamide group seems a bioisosteric group suitable to replace the carboxyl group in 2‐oxoamide inhibitors of GVIA cPLA2. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Binding of synthetic fragments of β‐endorphin to nonopioid β‐endorphin receptor
Authors: Navolotskaya Elena V. , Kovalitskaya Yulia A. , Zolotarev Yury A. , Sadovnikov Vladimir B.
Published: July 2008

Selective agonist of nonopioid β‐endorphin receptor decapeptide immunorphin (SLTCLVKGFY) was labeled with tritium (the specific activity of 24 Ci/mmol). [3H]Immunorphin was found to bind to nonopioid β‐endorphin receptor of mouse peritoneal macrophages (Kd = 2.0 ± 0.1 nM). The [3H]immunorphin specific binding with macrophages was inhibited by unlabeled β‐endorphin (Ki = 2.9 ± 0.2 nM) and was not inhibited by unlabeled naloxone, α‐endorphin, γ‐endorphin and [Met5]enkephalin (Ki > 10 µM). Thirty fragments of β‐endorphin have been synthesized and their ability to inhibit the [3H]immunorphin specific binding to macrophages was studied. Unlabeled fragment 12–19 (TPLVTLFK, the author's name of the peptide octarphin) was found to be the shortest peptide possessing practically the same inhibitory activity as β‐endorphin (Ki = 3.1 ± 0.3 nM). The peptide octarphin was labeled with tritium (the specific activity of 28 Ci/mmol). [3H]Octarphin was found to bind to macrophages with high affinity (Kd = 2.3 ± 0.2 nM). The specific binding of [3H]octarphin was inhibited by unlabeled immunorphin and β‐endorphin (Ki = 2.4 ± 0.2 and 2.7 ± 0.2 nM, respectively). Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
The structure of S100A11 fragment explains a local structural change induced by phosphorylation
Authors: Kouno Takahide , Mizuguchi Mineyuki , Sakaguchi Masakiyo , Makino Eiichi , Mori Yoshihiro , Shinoda Hiroyuki , Aizawa Tomoyasu , Demura Makoto , Huh Nam‐Ho , Kawano Keiichi
Published: July 2008

S100A11 protein is a member of the S100 family containing two EF‐hand motifs. It undergoes phophorylation on residue T10 after cell stimulation such as an increase in Ca2+ concentration. Phosphorylated S100A11 can be recognized by its target protein, nucleolin. Although S100A11 is initially expressed in the cytoplasm, it is transported to the nucleus by the action of nucleolin. In the nucleus, S100A11 suppresses the growth of keratinocytes through p21CIP1/WAF1 activation and induces cell differentiation. Interestingly, the N‐terminal fragment of S100A11 has the same activity as the full‐length protein; i.e. it is phosphorylated in vivo and binds to nucleolin. In addition, this fragment leads to the arrest of cultured keratinocyte growth. We examined the solution structure of this fragment peptide and explored its structural properties before and after phosphorylation. In a trifluoroethanol solution, the peptide adopts the α‐helical structure just as the corresponding region of the full‐length S100A11. Phosphorylation induces a disruption of the N‐capping conformation of the α‐helix, and has a tendency to perturb its surrounding structure. Therefore, the phosphorylated threonine lies in the N‐terminal edge of the α‐helix. This local structural change can reasonably explain why the phosphorylation of a residue that is initially buried in the interior of protein allows it to be recognized by the binding partner. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Interface electronic structures of zinc oxide and metals: First‐principle study
Authors: Kamiya T. , Tajima K. , Nomura K. , Yanagi Hiroshi , Hosono H.
Published: July 2008

Electronic structures and carrier transport properties were studied based on ab‐initio calculations for Au/ZnO/Au and Mg/ZnO/Mg two‐probe models. Quantum‐mechanically stable structures were obtained by density functional calculations. Electron transmission spectra and current–voltage characteristics were calculated based on a non‐equilibrium Green function method with the relaxed structures. It was found that the electronic structures of the idealized models were a Schottky contact for the Au/ZnO/Au interface and an ohmic contact for the Mg/ZnO/Mg interface. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic structure of oxygen deficient amorphous oxide semiconductor a‐InGaZnO4–x: Optical analyses and first‐principle calculations
Authors: Kamiya Toshio , Nomura Kenji , Hirano Masahiro , Hosono Hideo
Published: July 2008

The cover picture of this issue of physica status solidi (c) has been taken from the article [1]. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interface formation in CdTe solar cells: Nucleation of CdTe on CdS(0001) and (10$ \bar 1 $0)
Authors: Siepchen Bastian , Klein Andreas , Jaegermann Wolfram
Published: July 2008

The growth of CdTe on (0001) and (10$ \bar 1 $0) surfaces of CdS was studied using low energy electron diffraction and photoelectron spectroscopy. The results indicate oriented growth of the CdTe films with a faster nucleation of CdTe on CdS(0001), explaining the preferred (111) orientation of CdTe films on polycrystalline substrates. The faster nucleation on the (0001) surface is attributed to the formation of a stable CdS(0001):Te surface termination, which is identified from surface sensitive Te 4d spectra and a 2√3 × 2√3 surface reconstruction. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Using factorial design and multivariate analysis when experimenting in a continuous process
Authors: Vanhatalo Erik , Vännman Kerstin
Published: July 2008

This article discusses the design and analysis of an experiment performed in a continuous process (CP). Three types of iron ore pellets are tested on two levels of a process variable in an experimental blast furnace process, using a full factorial design with replicates. A multivariate approach to the analysis of the experiment in the form of principal component analysis combined with analysis of variance is proposed. The analysis method also considers the split‐plot‐like structure of the experiment. The article exemplifies how a factorial design combined with multivariate analysis can be used to perform product development experiments in a CP. CPs also demand special considerations when planning, performing and analyzing experiments. The article highlights and discusses such issues and considerations, for example, the dynamic characteristic of CPs, a strategy to handle disturbances during experimentation and the need for process control during experimentation. Copyright © 2008 John Wiley & Sons, Ltd.
Evaluating quality measured on a ternary ordinal scale
Authors: Bashkansky Emil , Gadrich Tamar
Published: July 2008

This paper deals with the evaluation of process/product quality measured via a ternary ordinal scale. Recently, a new approach for dealing with ordinal quality variables, based on constructing a quality ladder using rank and dispersion criterion, was proposed. In this method the quality of a given sample is characterized by its relative position on the constructed quality ladder. The present paper proposes a new mechanism for constructing such a quality ladder. This method is called proportion ratio and dispersion (PR&D). The underlying logic, advantage and applications of the proposed method are discussed and demonstrated using software developed by the authors. Copyright © 2008 John Wiley & Sons, Ltd.
Atomic basis sets optimization using the generalized simulated annealing approach: New basis sets for the first row elements
Authors: De Andrade M. D. , Nascimento M. A. C. , Mundim K. C. , Sobrinho A. M. C. , Malbouisson L. A. C.
Published: July 2008

Atomic basis sets equivalent to the standard STO‐3G and STO‐6G ones were optimized for the elements of the first row using the generalized simulated annealing (GSA) approach. The atomic energies obtained with the new basis sets are substantially better than the ones obtained with the standard ones. The new basis sets were tested for several diatomic and triatomic molecules, at different levels of calculation. For the molecules at their geometries of equilibrium, the energies obtained with the GSA optimized basis are in general much better than the respective ones obtained with the standard basis. However, for molecules containing hydrogen atoms, the best results, either at the HF or CI level of calculation, are obtained with a combination of the new and the standard bases, which depend on the nature of the other atoms of the molecule. The analysis of the potential energy surfaces for the LiH, BH, and FH molecules showed that the new basis provide a better description of these molecules in all regions of the respective surfaces, although the equilibrium bond distances. The results are quite encouraging and clearly indicate that basis set of DZ and TZ quality better than the standard ones can probably be generated by the GSA approach. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations
Authors: Pickholz Mónica , Fernandes Fraceto Leonardo , de Paula Eneida
Published: July 2008

In this work, we report a 20‐ns constant pressure molecular dynamics simulation of prilocaine (PLC), an amine–amide local anesthetic, in a hydrated liquid crystal bilayer of 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at ∼12 Å from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, |SCD|, compared to neat bilayers, is found, in good agreement with experimental2H‐NMR studies. The decrease in |SCD| induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Torsional profile of 2,2,2‐trifluoroethanol: A theoretical analysis with basis set extrapolation
Authors: de Amorim Mauro B.
Published: July 2008

The conformational potential for rotation around the CCOH torsional angle of 2,2,2‐trifluoroethanol (TFE) has been investigated at second‐order Möller–Plesset (MP2) perturbation theory with two series of Dunning's correlation consistent basis sets, cc‐pVNZ and aug‐cc‐pVNZ, N = D, T, Q, and 5. Single‐point energy calculations with MP4(SDQ)/(aug‐)cc‐pVTZ and MP4(SDQT)/cc‐pVTZ were also performed. It was found that the geometries of stationary points on this conformational profile are dependent on the basis set size, particularly the torsional angle of the gauche‐isomer and the transition structure between the gauche‐ and anti‐isomers (from 61° and 142°, respectively, at cc‐pVDZ, to 65° and 149° at aug‐cc‐pVQZ), requiring at least a aug‐cc‐pVTZ basis set to be correctly optimized. Additionaly, an even lower barrier height (as low as 0.04 kcal/mol) than that previously calculated by Senent et al. for the conversion of anti‐TFE to its more stable (by about 1.95 kcal/mol) gauche‐conformer has been obtained, which reinforces the prediction that the main, if not the only, component of TFE in gas phase is its gauche‐isomer. The MP2 data were also used in different schemes of basis set extrapolation. Unfortunately, maybe because third‐order correlation energy contributions were not considered, these schemes have failed in providing suitable extrapolated energies. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Fractionation of free and conjugated steroids for the detection of boldenone metabolites in calf urine with ultra‐performance liquid chromatography/tandem mass spectrometry
Authors: Van Poucke Christof , Van Vossel Evy , Van Peteghem Carlos
Published: July 2008

For over a decade there has been an intensive debate on the possible natural origin of boldenone (androst‐1,4‐diene‐17β‐ol‐3‐one, 17β‐boldenone) in calf urine and several alternative markers to discriminate between endogenously formed boldenone and exogenously administered boldenone have been suggested. The currently approved method for proving illegal administration of β‐boldenone(ester) is the detection of β‐boldenone conjugates. In the presented method the sulphate, glucuronide and free fractions are separated from each other during cleanup on a SAX column to be able to determine the conjugated status of the boldenone metabolites. The sulphate and glucuronide fractions are submitted to hydrolysis and all three fractions are further cleaned up on a combination of C18/NH2 solid‐phase extraction (SPE) columns. Chromatographic separation of the boldenone metabolites was achieved with a Waters Acquity UPLC™ instrument using a Sapphire C18 (1.7 µm; 2 × 50 mm) column within 5 min. Detection of the analytes was achieved by electrospray ionisation tandem mass spectrometry. The decision limits of this method, validated according to Commission Decision 2002/657/EC, were 0.08 ng mL−1 for androsta‐1,4‐diene‐3,17‐dione, 0.13 ng mL−1 for androst‐4‐ene‐3,17‐dione, 0.11 ng mL−1 for 17α‐boldenone, 0.07 ng mL−1 for 17β‐boldenone, 0.24 ng mL−1 for 5β‐androst‐1‐en‐17β‐ol‐3‐one and 0.58 ng mL−1 for 6β‐hydroxy‐17β‐boldenone. Because of the fractionation approach used in this method there is no need for conjugated reference standards which often are not available. The disadvantage of needing three analytical runs to determine the conjugated status of each of the metabolites was overcome by using fast chromatography. Copyright © 2008 John Wiley & Sons, Ltd.
A mobile multimedia satellite system reusing existing satellites
Authors: Midthassel Rolv , Ernst Harald
Published: July 2008

Since 2001, the European Space Agency has investigated a file‐based system for providing satellite radio to the automotive market. This system is significantly different from existing commercial counterparts, such as the American systems XM‐radio and Sirius. In terms of service it not only provides traditional radio services but is also capable of offering multimedia content and data transfer. In terms of infrastructure, it does not require launch of new satellites or deployment of terrestrial repeaters. As such it offers a highly efficient, low‐investment and low‐risk approach to offering satellite radio services to a consumer automotive market. Moreover, it departs from the traditional schedule‐based streaming radio concept to a concept in line with the concurrent developments within the media landscape, providing the user the full control of what entertainment to play and when to play it. This paper presents the system in more detail, outlines its performance and makes comparisons with other existing satellite radio systems. Copyright © 2008 John Wiley & Sons, Ltd.
ETSI technical standards for satellite digital radio
Authors: Krause Jens , Stadali Holger
Published: July 2008

The European Telecommunications Standards Institute (ETSI) is a non‐profit organization that creates technical standards for different areas of telecommunications. The ETSI activity satellite digital radio (SDR) addresses networks where satellite transmission is used for broadcasting directly to mobile receivers and is complemented by terrestrial transmitters. ETSI standards allow implementing parts of such systems in an interoperable way. A standardized radio interface enables a mass market for consumer reception devices and could become a regulatory requirement. ETSI, so far, has created standards for the physical layer of the radio interface. State‐of‐the‐art technology for multiplexing, interleaving, modulation and coding is applied. The system is broken down into parts that are covered by separate standards, which allows combining with other existing or future specifications. The standards cover the direct satellite transmission and the complementary terrestrial transmission, with both their particular impairments and conditions. A sophisticated time interleaving allows one to overcome signal blockage in a way that increases the ‘zapping time’ only slightly. The physical layer standards can be combined with existing standards for audio/video coding and encapsulation, in particular from MPEG and DVB. ETSI is planning to create further standards for the SDR system. First networks that apply the SDR technology are expected in 2008. Copyright © 2008 John Wiley & Sons, Ltd.
Local variability in PTC thermistor grain boundary structures
Authors: Leach C. , Seaton J.
Published: July 2008

Scanning electron microscopy‐based conductive mode (CM) microscopy, using the remote electron beam‐induced current configuration, was carried out on a positive temperature coefficient of resistance thermistor at temperatures below and above the Curie temperature, TC. Below TC, when the thermistor is in a low resistance state, no strong CM contrast was observed. Above TC the thermistor grain boundaries become highly resistive and significant CM contrast formed owing to three mechanisms: all of the areas that were studied showed resistive contrast, but in addition some grain boundaries showed additional contrast due to electron beam‐induced current, the origin of which was consistent with the presence of a back‐to‐back Schottky barrier structure at the grain boundary. Other grain boundaries exhibited additional contrast owing to β‐conductivity, which suggests a slightly different n‐i‐n grain boundary structure at these interfaces. These results suggest that electrically active grain boundaries with different structures coexist within the thermistor. SCANNING 30: 339–346, 2008. © 2008 Wiley Periodicals, Inc.
Maximum likelihood estimation of correction for dilution bias in simple linear regression using replicates from subjects with extreme first measurements
Authors: Berglund Lars , Garmo Hans , Lindbäck Johan , Svärdsudd Kurt , Zethelius Björn
Published: July 2008

The least‐squares estimator of the slope in a simple linear regression model is biased towards zero when the predictor is measured with random error. A corrected slope may be estimated by adding data from a reliability study, which comprises a subset of subjects from the main study. The precision of this corrected slope depends on the design of the reliability study and estimator choice.

Previous work has assumed that the reliability study constitutes a random sample from the main study. A more efficient design is to use subjects with extreme values on their first measurement. Previously, we published a variance formula for the corrected slope, when the correction factor is the slope in the regression of the second measurement on the first. In this paper we show that both designs improve by maximum likelihood estimation (MLE). The precision gain is explained by the inclusion of data from all subjects for estimation of the predictor's variance and by the use of the second measurement for estimation of the covariance between response and predictor. The gain of MLE enhances with stronger true relationship between response and predictor and with lower precision in the predictor measurements. We present a real data example on the relationship between fasting insulin, a surrogate marker, and true insulin sensitivity measured by a gold‐standard euglycaemic insulin clamp, and simulations, where the behavior of profile‐likelihood‐based confidence intervals is examined. MLE was shown to be a robust estimator for non‐normal distributions and efficient for small sample situations. Copyright © 2008 John Wiley & Sons, Ltd.
Flexible regression models for estimating postmortem interval (PMI) in forensic medicine
Authors: Muñoz Barús José Ignacio , Febrero‐Bande Manuel , Cadarso‐Suárez Carmen
Published: July 2008

Correct determination of time of death is an important goal in forensic medicine. Numerous methods have been described for estimating postmortem interval (PMI), but most are imprecise, poorly reproducible and/or have not been validated with real data. In recent years, however, some progress in PMI estimation has been made, notably through the use of new biochemical methods for quantifying relevant indicator compounds in the vitreous humour. The best, but unverified, results have been obtained with [K+] and hypoxanthine [Hx], using simple linear regression (LR) models. The main aim of this paper is to offer more flexible alternatives to LR, such as generalized additive models (GAMs) and support vector machines (SVMs) in order to obtain improved PMI estimates. The present study, based on detailed analysis of [K+] and [Hx] in more than 200 vitreous humour samples from subjects with known PMI, compared classical LR methodology with GAM and SVM methodologies. Both proved better than LR for estimation of PMI. SVM showed somewhat greater precision than GAM, but GAM offers a readily interpretable graphical output, facilitating understanding of findings by legal professionals; there are thus arguments for using both types of models. R code for these methods is available from the authors, permitting accurate prediction of PMI from vitreous humour [K+], [Hx] and [U], with confidence intervals and graphical output provided. Copyright © 2008 John Wiley & Sons, Ltd.
Fitting stratified proportional odds models by amalgamating conditional likelihoods
Authors: Mukherjee Bhramar , Ahn Jaeil , Liu Ivy , Rathouz Paul J. , Sánchez Brisa N.
Published: July 2008

Classical methods for fitting a varying intercept logistic regression model to stratified data are based on the conditional likelihood principle to eliminate the stratum‐specific nuisance parameters. When the outcome variable has multiple ordered categories, a natural choice for the outcome model is a stratified proportional odds or cumulative logit model. However, classical conditioning techniques do not apply to the generalK‐category cumulative logit model (K>2) with varying stratum‐specific intercepts as there is no reduction due to sufficiency; the nuisance parameters remain in the conditional likelihood. We propose a methodology to fit stratified proportional odds model by amalgamating conditional likelihoods obtained from all possible binary collapsings of the ordinal scale. The method allows for categorical and continuous covariates in a general regression framework. We provide a robust sandwich estimate of the variance of the proposed estimator. For binary exposures, we show equivalence of our approach to the estimators already proposed in the literature. The proposed recipe can be implemented very easily in standard software. We illustrate the methods via three real data examples related to biomedical research. Simulation results comparing the proposed method with a random effects model on the stratification parameters are also furnished. Copyright © 2008 John Wiley & Sons, Ltd.
A survey of the likelihood approach to bioequivalence trials
Authors: Choi Leena , Caffo Brian , Rohde Charles
Published: July 2008

Bioequivalence (BE) trials are abbreviated clinical trials whereby a generic drug or new formulation is evaluated to determine if it is ‘equivalent’ to a corresponding previously approved brand‐name drug or formulation. In this paper, we survey the process of testing BE and advocate the likelihood paradigm for representing the resulting data as evidence. We emphasize the unique conflicts between hypothesis testing and confidence intervals in this area—which we believe are indicative of the existence of the systemic defects in the frequentist approach—that the likelihood paradigm avoids. We suggest the direct use of profile likelihoods for evaluating BE. We discuss how the likelihood approach is useful to present the evidence for both average and population BE within a unified framework. We also examine the main properties of profile likelihoods and estimated likelihoods under simulation. This simulation study shows that profile likelihoods offer a viable alternative to the (unknown) true likelihood for a range of parameters commensurate with BE research. Copyright © 2008 John Wiley & Sons, Ltd.
Quantifying the usefulness of PD biomarkers in Phase 2 screening trials of oncology drugs
Authors: Holmgren Eric
Published: July 2008

This paper develops a framework for evaluating the usefulness of a PD biomarker as a primary endpoint in a Phase 2 screening trial of an oncology drug. We judge the contribution of the PD biomarker by assessing its impact on the efficiency of the drug development process. ‘Efficiency’ is defined as the probability that an active drug is found to be effective in Phase 3 divided by the sum of the expected number of events in Phase 3 and the pre‐Phase 2 drug development costs appropriately normalized. We show that 20 Phase 2 trials of different experimental treatments can provide a reasonable answer as to whether a PD biomarker makes a positive or negative contribution to the drug development process. Copyright © 2008 John Wiley & Sons, Ltd.
Rheinbrücke Wesel – Konstruktion und statische Berechnung
Authors: Anistoroaiei Christian , Eilzer Wolfgang , Jung Rolf , Romberg Martin , Sagner Erik , Walser Peter
Published: July 2008

Die neue Rheinbrücke Wesel ist Teil des Gesamtkonzeptes der Verkehrsumgehung der beiden Städte Wesel und Büderich. Mit einer Gesamtlänge von rd. 773 m und einer Hauptöffnung von 335 m ist sie die zur Zeit größte im Bau befindliche Schrägseilbrücke in Deutschland. Der Aufsatz befasst sich mit der Konstruktion und statischen Berechnung des Brückenzuges.
Die MaChang‐Brücke in Südkorea – Schrägkabelbrücke mit Verbundüberbau für Straßenverkehr
Authors: Hopf Siegfried , Patsch Armin , Walser Peter
Published: July 2008

Die 1700 m lange MaChang‐Brücke ist Teil der Schnellstraßenverbindung zwischen den Städten Masan und Changwon im Süden von Korea und führt in etwa 68 m Höhe über die Bucht von Masan. Diese Hochbrücke besteht aus 550 bzw. 410 m langen Vorlandbrücken und einer 740 m langen Hauptbrücke. Die Hauptbrücke, eine 400 m weit gespannte Schrägseilbrücke mit zwei Pylonen, stellt das dominierende Bauwerk dieser Verbindung dar. Sie überspannt den 350 m breiten Schifffahrtskanal, welcher für Durchfahrten von Schiffen mit bis zu 80000 dwt ausgelegt ist.
Effect of Hydroxypropylation on the Properties of White Yam (Dioscorea rotundata) Starch
Authors: Lawal Olayide S. , Ogundiran Olusegun O. , Adesogan Ezekiel K. , Ogunsanwo Babatunde M. , Sosanwo Olumide A.
Published: July 2008

Starch isolated from white yam (Dioscorea rotundata) was subjected to hydroxypropylation under different conditions. Corresponding increases were observed between the molar substitution (MS) and the volume of propylene oxide added to the reaction mixture. After hydroxypropylation, a slight reduction in the intensity of the peak at 2θ = 19.6° was observed and the doublet peak at 23.8°, which was present in native starch, was no longer seen. Hydroxypropylation enhanced the free swelling capacity (FSC) and solubility. Setback and retrogradation of native starch declined after hydroxypropylation. Turbidity of native starch paste and syneresis were higher with storage time. The results also indicate that enzymatic digestibility improved as the MS increased, while the reverse was observed for starch paste turbidity, syneresis, setback and retrogradation. This study presents relevant information that could strategically position D. rotundata starch and its hydroxypropylated derivatives for industrial applications.
Electrically Conductive Carbon Black (CB)/Glycerol Plasticized‐Starch (GPS) Composites Prepared by Microwave Radiation
Authors: Ma Xiaofei , Chang Peter R. , Yu Jiugao , Lu Peilin
Published: July 2008

No abstracts.
Structure and Viscoelastic Properties of Starches Separated from Different Legumes
Authors: Singh Narpinder , Nakaura Yoshiko , Inouchi Naoyoshi , Nishinari Katsuyoshi
Published: July 2008

A comparison between the morphological, structural, thermal and viscoelastic properties of starches separated from pigeon pea, chickpea, field pea, kidney bean and blackgram was made. The shape of the starch granules in the different legumes varied from oval to elliptical or spherical. X‐ray diffraction of the legume starches indicated a typical C‐pattern (mixture of A‐ and B‐type). Granules of blackgram and pigeon pea starch had a higher degree of crystallinity than those of field pea and kidney bean starches. Apparent amylose content of field pea, kidney bean, chickpea, blackgram and pigeon pea starch was 37.9%, 36.0%, 34.4‐35.5%, 32.9‐35.6% and 31.8%, respectively. Distribution of isoamylase‐branched materials among the starches revealed that the proportions of long and short side chains of amylopectin ranged between 13.6‐18.5% and 41.7‐46.5%, respectively. Field pea and kidney bean starch had the highest apparent amylose content and the lowest amount of long side chains of amylopectin, respectively. Blackgram and pigeon pea starch possessed higher proportions of both long and short side chains of amylopectin than field pea and chickpea starches. The onset, peak and conclusion temperatures of gelatinization (To Tp and Tc, respectively) were determined by differential scanning calorimetry. To and Tc ranged from 59.3 to 77.3°C, 66.8 to 79.6°C, 55.4 to 67.6°C and 68.3 to 69.3°C, respectively, for chickpea, blackgram, field pea and kidney bean starch. The enthalpy of gelatinization (ΔHgel) of field pea, kidney bean, chickpea, blackgram and pigeon pea starches was 3.6, 3.0, 2.6‐4.2, 1.6‐1.7 and 2.6 J/g, respectively. Pastes of blackgram and pigeon pea starches showed lower storage and loss shear moduli G′ than field pea, kidney bean and chickpea starches. The changes in moduli during 10 h at 10°C revealed retrogradation in the order of: field pea> kidney bean> chickpea> blackgram> pigeon pea starch. In blackgram and pigeon pea starches, the lower proportion of amylose plus intermediate fraction and higher proportion of short and long side chains of amylopectin are considered responsible for the higher crystallinity, gelatinization temperature and enthalpy of gelatinization.
First‐trimester uterine artery Doppler indices in term and preterm pre‐eclampsia
Authors: Melchiorre K. , Wormald B. , Leslie K. , Bhide A. , Thilaganathan B.
Published: July 2008

Objectives

To assess the relationship between first‐trimester uterine artery Doppler measurements and the development of term and preterm pre‐eclampsia.

Methods

This prospective study of uterine artery Doppler findings at 11–14 weeks in 3058 singleton pregnancies included 57 and 33 cases of term and preterm pre‐eclampsia, respectively.

Results

The first‐trimester uterine artery resistance index (RI) was significantly higher in women who subsequently developed preterm pre‐eclampsia (mean RI, 0.79) than in those with a normal outcome (mean RI, 0.70; P = 0.0001) or those who developed pre‐eclampsia at term (mean RI, 0.72; P = 0.002). There were no significant differences in first‐trimester mean uterine artery RI (P = 0.136) or prevalence of bilateral notches (P = 0.459) between women who had a normal pregnancy outcome and those who developed pre‐eclampsia at term. The receiver–operating characteristics curves for the prediction of term and preterm pre‐eclampsia by uterine artery Doppler imaging demonstrated a significant association with development of preterm pre‐eclampsia (P = 0.0001; area under the curve (AUC), 0.76; 95% CI, 0.66–0.86) but not term pre‐eclampsia (P = 0.25; AUC, 0.54; 95% CI, 0.46–0.63).

Conclusions

The uterine artery Doppler data in this study suggest that preterm pre‐eclampsia is strongly associated with defective invasion of the spiral arteries, in contrast to the findings in term pre‐eclampsia which may be a consequence of placental deterioration at term. Our study findings support, but do not prove, a rigid separation between the etiology of early‐ and late‐onset pre‐eclampsia. Although there is a strong relationship between first‐trimester uterine artery Doppler indices and the subsequent development of preterm pre‐eclampsia, our data do not support its routine introduction into clinical practice. Copyright © 2008 ISUOG. Published by John Wiley & Sons, Ltd.
Triage for surgical management of ovarian tumors in asymptomatic women: assessment of an ultrasound‐based scoring system
Authors: Alcázar J. L. , Royo P. , Jurado M. , Mínguez J. Á. , García‐Manero M. , Laparte C. , Galván R. , López‐García G.
Published: July 2008

Objectives

To prospectively evaluate an ultrasound‐based scoring system as a method for triaging asymptomatic women presenting with an adnexal mass for surgical treatment.

Methods

Two hundred and four adnexal masses in 189 asymptomatic women undergoing elective surgical treatment at our institution were included in this prospective study. Patients were evaluated by transvaginal power Doppler ultrasound imaging before surgery. Patients were classified as low risk or high risk for malignancy according to an ultrasound‐based scoring system. Women with a low risk for malignancy were scheduled for laparoscopy and patients with a high risk for malignancy were scheduled for laparotomy. However, patients classified as low risk by the ultrasound scoring system, but with a tumor size ≥ 10 cm or clinical suspicion of pelvic adhesions, were instead considered to be at intermediate risk and were scheduled for laparotomy. Some patients classified as high risk were scheduled for an operative laparoscopy by an expert in gynecological oncology.

Results

One hundred and thirty‐four (65.7%) masses were considered to be low risk and were treated by a laparoscopically guided procedure. All these tumors were benign. Forty‐seven (23%) masses were classified as high risk, of which 39 tumors were malignant and eight benign. Twenty‐three (11.3%) tumors were considered to be intermediate risk and were scheduled for primary laparotomy. In this group, 21 (91.3%) tumors proved to be benign and two (8.7%) were malignant.

Conclusions

Ultrasound‐based triage of asymptomatic women diagnosed with a persistent adnexal mass is effective for selecting the surgical approach. Copyright © 2008 ISUOG. Published by John Wiley & Sons, Ltd.
An analytical model for reverse data channel scheduling techniques in cdma2000 1xEV‐DO
Authors: Basyouni Ayda , Agarwal Anjali , Elhakeem Ahmed
Published: July 2008

Efficient utilization of bandwidth and high data rates have a great impact on the performance of wireless networks. The cdma2000 1xEV‐DO standard provides high‐speed wireless data services to mobile subscribers based on CDMA technology. In this paper, we study the bandwidth utilization for the 1xEV‐DO packet mode standard. In particular, we develop an analytical model for lowest‐rate‐first, highest‐rate‐first priority scheduling techniques, and two round‐robin fair scheduling techniques over the reverse data channel in cdma2000 1xEV‐DO. For these four scheduling techniques, the distribution of the mobile stations (MSs) among the possible data rates is modeled as a Markov process. An analytical expression for the steady state system throughput is derived from the steady state distribution of the above Markov process. The developed model is validated through simulations. Copyright © 2008 John Wiley & Sons, Ltd.
PAS: probability and sub‐optimal distance‐based lifetime prolonging strategy for underwater acoustic sensor networks
Authors: Dou Jinfeng , Zhang Guangxu , Guo Zhongwen , Cao Jiabao
Published: July 2008

Lifetime prolonging is one of the most significant issues in the research on underwater acoustic sensor networks (UASNs). Unbalanced energy consumption influences greatly the network lifetime. First this study discusses a probability‐based energy balance (PEB) scheme. The sensor nodes report the data to the sink by single‐hop direct transmission (DT) or by multi‐hop transmission (MT) under the probabilities. A centralized probabilities finding algorithm (PFA) can find a set of transmission probabilities to better balance the energy consumption. Then, a sub‐optimal distance (SOD)‐based data transmission scheme is proposed which is a distributed scheme and operates on each sensor node. It optimizes the slice width and selects the relays near the optimum transmission range. Simulations show that the two schemes can save more energy and prolong the network lifetime efficiently. Copyright © 2008 John Wiley & Sons, Ltd.
Target tracking based on a distributed particle filter in underwater sensor networks
Authors: Huang Yan , Liang Wei , Yu Hai‐bin , Xiao Yang
Published: July 2008

In this paper, based on a distributed particle filter, two tracking algorithms are proposed for tracking mobile targets in cluster‐based underwater sensor networks (USNs). Both tracking algorithms run local particle filter sequentially at each cluster along target trajectories, but they adopt different methods of selecting measurements from sensor nodes to balance the information contribution against the cost. Performance metrics are proposed and discussed in terms of tracking performance, communication cost, energy cost, and tracking response time. Simulations are conducted to quantitatively compare the proposed algorithms as well as another tracking algorithm based on extended Kalman filter (EKF). Our results indicate that one tracking algorithm achieves higher tracking accuracy while the other achieves dramatic reduction of communication cost, energy cost, and tracking response time. Furthermore, performance of two tracking algorithms has been studied in terms of detection threshold and sensor density. Copyright © 2008 John Wiley & Sons, Ltd.
Efficient clusterhead rotationviadomatic partition in self‐organizing sensor networks
Authors: Misra Rajiv , Mandal Chittaranjan
Published: July 2008

Nodes in wireless sensor networks (WSN) are deployed in an unattended environment with non re‐chargeable batteries. Thus, energy efficiency becomes a major design goals in WSNs. Clustering becomes an effective technique for optimization energy in various applications like data gathering. Although aggregation aware clustering addresses lifetime and scalability goals, but suffers from excessive energy overhead at clusterhead nodes. Load balancing in existing clustering schemes often use rotation of clusterhead roles among all nodes in order to prevent any single node from complete energy exhaustion. We considered important aspects of energy and time overhead in rotation of the clusterhead roles in various node clustering algorithms with goals to further prolong the network lifetime by minimizing the energy overheads in rotation setup. The problem of clusterhead rotation is abstracted as the graph‐theoretic problem of domatic partitioning, which is also NP‐complete. The dense deployment and unattended nature rules out the possibility of manual or external control in existing domatic partition (DP) techniques to be used for WSNs. To our knowledge, no self‐organizing technique exists for domatic partitioning. We developed a distributed self‐organizing one‐domatic partitioning scheme with approximation factor of at least 1/16 for unit‐disk‐graphs (UDGs). In this work, we demonstrate that the benefits of self‐organization is achieved without sacrificing the quality of domatic partitioning. We demonstrated through simulations that our self‐organizing DP without sacrificing on the size of DP achieves self‐organization capability which is able to reduce time and energy overheads of clusterhead rotation resulting to an improved network lifetime compared to the existing clustering protocols for sensor networks. Copyright © 2008 John Wiley & Sons, Ltd.
Marine yeasts—a review
Authors: Kutty Sreedevi N. , Philip Rosamma
Published: July 2008

Yeasts are ubiquitous in their distribution and populations mainly depend on the type and concentration of organic materials. The distribution of species, as well as their numbers and metabolic characteristics were found to be governed by existing environmental conditions. Marine yeasts were first discovered from the Atlantic Ocean and following this discovery, yeasts were isolated from different sources, viz. seawater, marine deposits, seaweeds, fish, marine mammals and sea birds. Near‐shore environments are usually inhabited by tens to thousands of cells per litre of water, whereas low organic surface to deep‐sea oceanic regions contain 10 or fewer cells/litre. Aerobic forms are found more in clean waters and fermentative forms in polluted waters. Yeasts are more abundant in silty muds than in sandy sediments. The isolation frequency of yeasts fell as the depth of the sampling site is increased. Major genera isolated in this study were Candida, Cryptococcus, Debaryomyces and Rhodotorula. For biomass estimation ergosterol method was used. Classification and identification of yeasts were performed using different criteria, i.e. morphology, sexual reproduction and physiological/biochemical characteristics. Fatty acid profiling or molecular sequencing of the IGS and ITS regions and 28S gene rDNA ensured accurate identification. Copyright © 2008 John Wiley & Sons, Ltd.