bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermomechanical properties and crystallization behavior of layered double hydroxide/poly(ethylene terephthalate) nanocomposites prepared by in‐situ polymerization
Authors: Lee Wan Duk , Im Seung Soon
Published: November 2006

Thermomechanical properties and crystallization behavior of poly(ethylene terephthalate) (PET) nanocomposites containing layered double hydroxide (LDH) were investigated. To enhance the compatibility between PET matrix and LDH, dimethyl 5‐sulfoisophthalate (DMSI) anion intercalated LDH (LDH‐DMSI) was synthesized by coprecipitation method, and its structure was confirmed by Fourier transform infrared (FTIR) spectrometer and X‐ray diffraction (XRD) measurements. Then, PET nanocomposites with LDH‐DMSI content of 0, 0.5, 1.0, and 2.0 wt% were prepared by in‐situ polymerization. The dispersion morphologies were observed by transmission electron microscopy (TEM) and XRD, showing that LDH‐DMSI was exfoliated in PET matrix. Thermal and mechanical properties, such as thermal stability, tensile modulus, and tensile yield strength of nanocomposites, were enhanced by exfoliated LDH‐DMSI nanolayers. However, elongation at break was drastically decreased with LDH loading owing to the increased stiffness and microvoids. The effect of exfoliated nanolayers, which acted as a nucleating agent confirmed by differential scanning calorimeter (DSC), on the microstructural parameters during isothermal crystallization, was analyzed by synchrotron small‐angle X‐ray scattering (SAXS). It is believed that nanocomposites could be crystallized more easily owing to the increased nucleation sites, which lead to the decrease of average amorphous region size and the long period with the increase of LDH‐DMSI content. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 28–40, 2007
Highly Efficient VOC Decomposition Using a Complex System (OH Radical, Ozone‐UV, and TiO2)
Authors: Kogoma Masuhiro , Miki Yuji , Tanaka Kunihito , Takahashi Kazuo
Published: November 2006

Summary: Toluene decomposition is examined using a corona discharge, a UV lamp, and a TiO2 catalyst complex system. The toluene decomposition reaction occurs only with OH and O (1D) radicals. High decomposition ratios are obtained: 98% for the toluene/H2O/O2‐corona/UV system and 70% for the toluene/H2O/air‐corona/UV system. Moreover, if the TiO2 catalyst is combined with the corona‐UV system for 1 000 ppm of toluene, this value increases to 78% (0.31 Wh · m−3 · ppm−1), which is higher than that obtained in a normal corona discharge system.

Relationship of the decomposition ratio with the UV irradiation in air and O2 as a function of toluene concentration.

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Relationship of the decomposition ratio with the UV irradiation in air and O2 as a function of toluene concentration.
The interrupter technique to assess airway responsiveness in children with cystic fibrosis
Authors: Davies Philip L. , Doull Iolo J. , Child Frances
Published: November 2006

The aim of this study was to assess the validity of the interrupter technique (Rint) in measuring airway responsiveness in children with cystic fibrosis. Fifty children (aged 6–16 years) with cystic fibrosis performed six Rint measurements followed by three acceptable forced expiratory maneuvers. Each child then inhaled 5 mg of nebulized salbutamol by facemask. After 20 min the Rint and forced expiratory measurements were repeated. In the population as a whole a moderate but significant correlation between inverse Rint and FEV1 values was observed, both before and after inhaled bronchodilator (r = 0.71 and 0.72, respectively, P < 0.001). However, when changes in Rint and FEV1 readings following inhaled bronchodilator were examined, no relationship was seen. Indeed, the two methods identified completely different subsets of children as being bronchodilator responsive. These results indicate that although a relationship exists between Rint and FEV1 in the whole population, this is not the case in individual children. Rint and FEV1 reflect different aspects of lung function. It is not appropriate to use Rint as a simple alternative for FEV1 in children with cystic fibrosis when assessing airway responsiveness. Pediatr Pulmonol. 2007; 42:23–28. © 2006 Wiley‐Liss, Inc.
Endoscopic Nd:YAG laser therapy of infantile subglottic hemangioma
Authors: Fu Chia‐Hsiang , Lee Li‐Ang , Fang Tuan‐Jen , Wong Kin‐Sun , Li Hsueh‐Yu
Published: November 2006

Of the many therapeutic modalities that have been developed for infantile subglottic hemangioma (ISH), the most common technique is endoscopic excision with carbon dioxide laser, used alone or combined with other therapeutic techniques. A staged procedure has been proposed as the preferred choice for patients with severe airway obstruction. Nevertheless, ever since the neodymium: yttrium‐aluminum‐garnet (Nd:YAG) laser was developed, this modality has been considered feasible to treat vascular tumor in the airway due to good hemostasis power. We present two cases of ISH with severe airway obstruction that underwent endoscopic surgery using an one‐stage Nd:YAG laser approach. Details of the laser characteristics and surgery techniques are described in this article. Pediatr Pulmonol. 2007; 42:89–92. © 2006 Wiley‐Liss, Inc.
Standardizing lung function laboratories for multicenter trials
Authors: Beardsmore C.S. , Paton J.Y. , Thompson J.R. , Laverty A. , King C. , Oliver C. , Stocks J.
Published: November 2006

Multi‐center studies provide advantages in clinical research but differences between centers can introduce bias. Three specialist pediatric respiratory laboratories standardized their methodology and examined differences between centers. The specific aims were to (i) assess the variability of measurements on adults within and between centers and (ii) to exchange and cross‐analyze data from children to assess the extent of agreement between centers. Each laboratory used identical equipment and software. Inter‐laboratory visits were used to (i) standardize protocols for data collection and analysis and (ii) make spirometric and plethysmographic measurements on participating staff at each location. Staff also had repeat measurements in their home laboratories. Measurements from children in each laboratory were exchanged on disk, cross‐analyzed, and data compared by ANOVA. There were no significant within‐subject, between‐center differences in FVC, FEV1, FEF50, FRCpleth, or VC. There was a slight trend for TLC and RV (P = 0.07) to be higher at one center. The 95% limits of agreement within and between centers were similar for all parameters. There were no differences between centers in cross‐analyzed data from 10 children. By standardizing hardware, software, and protocol, potential inter‐laboratory differences can be minimized. We recommend that this approach be adopted prior to multi‐center studies. Pediatr Pulmonol. 2007; 42:51–59. © 2006 Wiley‐Liss, Inc.
MUPRED: A tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction
Authors: Bondugula Rajkumar , Xu Dong
Published: November 2006

Predicting secondary structures from a protein sequence is an important step for characterizing the structural properties of a protein. Existing methods for protein secondary structure prediction can be broadly classified into template based or sequence profile based methods. We propose a novel framework that bridges the gap between the two fundamentally different approaches. Our framework integrates the information from the fuzzy k‐nearest neighbor algorithm and position‐specific scoring matrices using a neural network. It combines the strengths of the two methods and has a better potential to use the information in both the sequence and structure databases than existing methods. We implemented the framework into a software system MUPRED. MUPRED has achieved three‐state prediction accuracy (Q3) ranging from 79.2 to 80.14%, depending on which benchmark dataset is used. A higher Q3 can be achieved if a query protein has a significant sequence identity (>25%) to a template in PDB. MUPRED also estimates the prediction accuracy at the individual residue level more quantitatively than existing methods. The MUPRED web server and executables are freely available at http://digbio.missouri.edu/mupred. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Automatic procedure for using models of proteins in molecular replacement
Authors: Raimondo Domenico , Giorgetti Alejandro , Giorgetti Alejandro , Bosi Stefania , Tramontano Anna
Published: November 2006

In a crystallography experiment, a crystal is irradiated with X‐rays whose diffracted waves are collected and measured. The reconstruction of the structure of the molecule in the crystal requires knowledge of the phase of the diffracted waves, information that is lost in the passage from the three‐dimensional structure of the molecule to its diffraction pattern. It can be recovered using experimental methods such as heavy‐atom isomorphous replacement and anomalous scattering or by molecular replacement, which relies on the availability of an atomic model of the target structure. This can be the structure of the target protein itself, if a previous structure determination is available, or a computational model or, in some cases, the structure of a homologous protein. It is not straightforward to predict beforehand whether or not a computational model will work in a molecular replacement experiment, although some rules of thumb exist. The consensus is that even minor differences in the quality of the model, which are rather difficult to estimate a priori, can have a significant effect on the outcome of the procedure. We describe here a method for quickly assessing whether a protein structure can be solved by molecular replacement. The procedure consists in submitting the sequence of the target protein to a selected list of freely available structure prediction servers, cluster the resulting models, select the representative structures of each cluster and use them as search models in an automatic phasing procedure. We tested the procedure using the structure factors of newly released proteins of known structure downloaded from the Protein Data Bank as soon as they were made available. Using our automatic procedure we were able to obtain an interpretable electron density map in more than half the cases. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Theoretical model of human apolipoprotein B100 tertiary structure
Authors: Kriško Anita , Etchebest Catherine
Published: November 2006

Low density lipoprotein (LDL) particles are the main cholesterol carriers in human plasma. The organization of the particle, composed of apolar lipids and phospholipid monolayer stabilized by apolipoprotein B100 (apoB), is highly complex and still unknown. ApoB is an extremely large protein (4563 amino acids) and very little is known about its structure. A 3D model of the N‐terminal region has been recently proposed and has provided interesting insights about the physico‐chemical properties of the protein and putative interaction zones with lipids. In the present article, we propose the first tentative 3D modelling for most remaining residues. All predicted features emerging from the models are confronted with agreement to experimental data available. Using different up‐to‐date prediction methods, we decomposed the protein into eight domains and predicted 3D structure for each of them. The analysis of hydrophobic patches, polar regions, coupled with functional predictions based on the 3D models, gives new clues to understanding of the functional role of apoB. We suggest precise regions putatively involved in the lipid interactions, and discuss the position of apoB on the LDL particle. Finally, we propose relative organization of the domains, providing a shape quite compatible with the low resolution electron microscopy map. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Compton profiles and band structure calculations of CdS and CdTe
Authors: Heda N. L. , Mathur S. , Ahuja B. L. , Sharma B. K.
Published: November 2006

In this paper we present the isotropic Compton profiles of zinc‐blende CdS and CdTe measured at an intermediate resolution of 0.39 a.u. using our 20 Ci 137Cs Compton spectrometer. The electronic band structure calculations for both the zinc‐blende structure compounds and also wurtzite CdS have been undertaken using various schemes of ab‐initio linear combination of atomic orbitals calculations implemented in CRYSTAL03 code. The band structure and Mulliken's populations are reported using density functional scheme. In case of wurtzite CdS, our theoretical anisotropies in directional Compton profiles are compared with available experimental data. In case of both the zinc‐blende compounds, the isotropic experimental profiles are found to be in better agreement with the present Hartree–Fock calculations. A study of the equal‐valence‐electron‐density experimental profiles of zinc‐blende CdS and CdTe shows that the CdS is more ionic than CdTe. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of ligand spin–orbit coupling to the g ‐shift in NaCl:V2+ and NaBr:V2+
Authors: Lei Y. , Zu X. T. , Zhao M. G.
Published: November 2006

The paper presents a molecular orbital calculation of the optical spectra and g ‐shift in NaCl:V2+ and NaBr:V2+, in which the contribution due to the electrostatic parameter A0, the Trees correction, the spin–orbit coupling of the central transition metal ion and the ligand are included. The calculated optical spectra and g ‐shift agree well with the available experimental data. The results show that the contribution due to the 3s of the ligand and the conjunct action between the center metal ion and the ligand can not be neglected. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Competing magnetic interactions in (Dy0.375Y0.625)2Cu2O5 solid solution studied by EPR
Authors: Typek J.
Published: November 2006

(Dy0.375Y0.625)2Cu2O5 is an antiferromagnet below TN = 11 K, displaying many signs of low‐dimensional magnetism. Electron paramagnetic resonance (EPR) investigation of different magnetic interactions in (Dy0.375Y0.625)2Cu2O5 solid solution is carried out by analysis of thermal evolution of EPR spectral parameters (integrated intensity, effective resonance field, effective linewidth) evaluated in the paramagnetic phase. A model, proposed earlier to explain metamagnetic transitions in the anntiferromagnetic phase was used to interpret the observed magnetic behaviour. Manifestations of copper chains existing in the (Dy0.375Y0.625)2Cu2O5 structure has been found in the EPR spectrum and the values of appropriate exchange constants connected with a hierarchy of exchange interactions has been calculated. At about 40 K a dimensional crossover from 2D to 3D behaviour has been observed in the temperature dependence of the product of the EPR integrated intensity and temperature. At high temperatures (T > 200 K) the EPR spectrum is suggestive of the presence of defect centres consisting of antferromagnetically coupled copper spins, forming dimers with the S = 0 ground state. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Integral equations and complex resonance energies for analytical potentials
Authors: Kapshai V. , Alferova Tatjana , Elander Nils
Published: November 2006

It is shown that the Volterra integral equation in combination with complex scaling gives a formalism capable to solve Schrödinger‐type problems concerning bound states and resonances. The regular solution of the Schrödinger equation presented at the Volterra integral equation allows us to define the explicit form of the Jost function analytically continued into the lower half complex momentum plane. The resulting formalism is used to develop a numerical method for finding resonances defined as zeros of the Jost function. The numerical method is tested on several analytical potentials; it gives good results for arbitrary orbital momentum l. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Quantum chemical investigation of linear hydrogen bonding in ONCCN···HX (X = F, Cl, Br) dimers
Authors: Varadwaj Pradeep R.
Published: November 2006

Linear hydrogen bonding formed between the nitrogen end of cyanogen‐N‐oxide (ONCCN) and hydrogen halides HX (X = F, Cl, Br) has been observed in their ground Σ states. The order of agreement of energetic stabilities between the correlated functionals used in this calculation is: B3LYP < PBE0 <PBE< PW91 in conjunction with the 6–311++G(3df,3pd) basis set. Analysis of various parameters describing the existence of H‐bonds in these dimers follows the conventional trend: ONCCN···HF > ONCCN···HCl > ONCCN···HBr in the series, except H‐bond lengths and static dipole polarizabilities which are in reverse order. The atomic charges obtained from the Mulliken and natural population analysis is used to assess the charge transfer effects that accompany the dimer formation. It is found from the investigation that the dimers having highest binding energy are accompanied by the highest transfer of charge. The14N nuclear quadrupole coupling constants of the monomer ON1CCN2are found to be decreased upon complection and in the series it increases from F through Br. We observed enhancements in the values of the dimer dipole moment and intrinsic dipole polarizabilities compared with the sum of the monomer values by intermolecular electrical interaction. Investigation reveals vibrational spectral shifts of HX and CN stretching modes similar to the conventional red‐shifted H‐bonded dimers; for the former case, the infrared band intensity increases significantly. Finally, the new vibrational modes originated from the intermolecular interaction are outlined. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical study of the gas‐phase SN2 reactions of X− with CH3OY (X, Y = Cl, Br, I)
Authors: Gai Jing‐Gang , Ren Yi
Published: November 2006

The gas‐phase nucleophilic substitution reactions at saturated oxygen X− + CH3OY (X, Y = Cl, Br, I) have been investigated at the level of CCSD(T)/6‐311+G(2df,p)//B3LYP/6‐311+G(2df,p). The calculated results indicate that X− preferably attacks oxygen atom of CH3OY via a SN2 pathway. The central barriers and overall barriers are respectively in good agreement with both the predictions of Marcus equation and its modification, respectively. Central barrier heights (ΔH and ΔH) correlate well with the charges (Q) of the leaving groups (Y), Wiberg bond orders (BO) and the elongation of the bonds (OY and OX) in the transition structures. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical studies of structures and stabilities of endohedral fullerenes X0/n+ @C32 (X = H, Li, Na, K, Be, Mg, Ca, B, Al, C, Si, N, P, n = 1–3)
Authors: Sun Lili , Chang Yingfei , Hong Bo , Wang Rongshun
Published: November 2006

Based on the D3 C32 fullerene, the equilibrium geometries, electronic structures, and binding energies of the endohedral fullerenes X0/n+@C32 (X = H, Li, Na, K, Be, Mg, Ca, B, Al, C, Si, N, P, n = 1–3) have been calculated using the DFT/B3LYP/6‐31G(d) method. The results show that the C32 cages are slightly enlarged due to encapsulation, and the sizes of non‐neutral molecules are smaller than the corresponding neutral ones. Cages containing Li, Na, and Ca and most of the cations, except Na+ and K+, are energetically favorable. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Some continuous geometry transitions and the consequences for a transition‐metal atom
Authors: Springborg Michael , Hegetschweiler Kaspar
Published: November 2006

By considering a transition‐metal ion in the field of some symmetrically placed ions, we illustrate the consequences of a continuous change of the structure of the ligands on the energies of the 3d electrons of the transition‐metal atom. Both a rigorous mathematical derivation and an analysis based on group theory are presented. For six ions surrounding the transition‐metal atom, a continuous D∞h → D3d → Oh→ D3d→ D6d transition is observed, whereas for four ions, a continuous D∞ h→ D2d→ Td→ D2d→ D4d transition results. Although the two systems possess many similarities, interesting differences are found as well. Finally, we demonstrate that when including orbital interactions between the ligands and the transition‐metal atom, quantitative differences occur. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Electron attachment to the DNA bases adenine and guanine and dehydrogenation of their anionic derivatives: Density functional study
Authors: Xie Hujun , Cao Zexing
Published: November 2006

Density functional theory (DFT) calculations have been used to explore electron attachment to the purines adenine and guanine and their hydrogen atom loss. Calculations show that the dehydrogenation at the N9 site in the adenine and guanine transient anions is the lowest‐cost channel of hydrogen loss, and the N9H bond scission has Gibbs free energies of dissociation ΔG° of 8.8 kcal mol−1 for the anionic adenine and 13.9 kcal mol−1 for the anionic guanine. The relatively high feasibility of low‐energy electron (LEE)‐induced N9H bond cleavage in the purine nucleobases arises from high electron affinities of their H‐deleted counterparts. Unlike adenine, other NH bond dissociations are competitive with the N9H bond fission in the anionic guanine. The replacement of hydrogen in the ring of purine has a significant effect on the N9H bond fragmentation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
DFT study of rearrangements in cyclopentylheptenyl carbocations
Authors: Vrcek Valerije
Published: November 2006

Carbocation rearrangements relevant to sterol biosynthesis were investigated computationally by using the model cyclopentylheptenyl carbocations 1A and 1B. Five different rearrangement pathways of these equilibrating cations were located at the potential energy surface (PES), all calculated at the B3LYP/6‐31G(d) level of theory. Each of these five distinct pathways differs from previous mechanistic proposals, and each involves new and unusual intermediates. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
The W algorithm and the D transformation for the numerical evaluation of three‐center nuclear attraction integrals
Authors: Duret Stefan , Safouhi Hassan
Published: November 2006

Three‐center nuclear attraction integrals over exponential‐type functions are required for ab initio molecular structure calculations and density functional theory (DFT). These integrals occur in many millions of terms, even for small molecules, and they require rapid and accurate numerical evaluation. The use of a basis set of B functions to represent atomic orbitals, combined with the Fourier transform method, led to the development of analytic expressions for these molecular integrals. Unfortunately, the numerical evaluation of the analytic expressions obtained turned out to be extremely difficult due to the presence of two‐dimensional integral representations, involving spherical Bessel integral functions. % The present work concerns the development of an extremely accurate and rapid algorithm for the numerical evaluation of these spherical Bessel integrals. This algorithm, which is based on the nonlinear D transformation and the W algorithm of Sidi, can be computed recursively, allowing the control of the degree of accuracy. Numerical analysis tests were performed to further improve the efficiency of our algorithm. The numerical results section demonstrates the efficiency of this new algorithm for the numerical evaluation of three‐center nuclear attraction integrals. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Exact‐mass library for pesticides using a molecular‐feature database
Authors: Ferrer Imma , Fernandez‐Alba Amadeo , Zweigenbaum Jerry A. , Thurman E. Michael
Published: November 2006

An automated molecular‐feature database (MFD) consisting of the exact monoisotopic mass of 100 compounds, at least one exact mass product ion for each compound, and chromatographic retention time were used to identify pesticides in food and water samples. The MFD software compiles a list of accurate mass ions, excludes noise, and compares them with the monoisotopic exact masses in the database. The screening criteria consisted of ±5 ppm accurate mass window, ±0.2 min retention time window, and a minimum 1000 counts (signal‐to‐noise (S/N) ratio of ∼10:1). The limit of detection for 100 tested compounds varied from <0.01 mg/kg for 72% of the compounds to <0.1 mg/kg for 95% of the compounds. The MFD search was useful for rapid screening and identification of pesticides in food and water, as shown in actual samples. The combined use of accurate mass and chromatographic retention time eliminated false positives in the automated analysis. The major weakness of the MFD is matrix interferences and loss of mass accuracy. Strengths of the MFD include rapid screening of 100 compounds at sensitive levels compared with a manual approach and the ease of use of the library for any accurate mass spectrometer instrumentation capable of routine sub‐5‐ppm mass accuracy. Copyright © 2006 John Wiley & Sons, Ltd.
Improved matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry of carboxymethyl cellulose
Authors: Enebro Jonas , Karlsson Sigbritt
Published: November 2006

A refined sample preparation procedure for matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOFMS) was developed for the evaluation of the degree of substitution (DS) in partially depolymerised carboxymethyl cellulose (CMC). By adding ammonium sulphate to the sample mixture prior to the analysis, good quality mass spectra could be acquired. The usual time‐consuming search for ‘sweet‐spots’ at the crystalline rim of the MALDI target spot was also avoided. This quality improvement made it possible to investigate whether various positions on the target spot generated mass spectra in which the measured DS varied. The accuracy and reproducibility of the sample preparation procedure were tested by applying it on three commercial CMCs. The study shows that the DS values that were calculated from the spectra acquired from the centre region of the MALDI target spot were in better agreement with the DS provided by the supplier than were the values obtained from the large crystals at the target spot rim. This observation could be one reasonable explanation for the higher DS values reported in other publications. By applying our refined MALDI sample preparation procedure DS values that were in good agreement with the values provided by the manufacturer could be obtained. This indicates that MALDI‐TOFMS of partially depolymerised CMCs can be used for an estimation of the DS as a complement to the more established methods, e.g. NMR, titrimetry, and chromatographic techniques. Copyright © 2006 John Wiley & Sons, Ltd.
Dissipativity and stability of interconnections
Authors: Willems Jan C. , Takaba Kiyotsugu
Published: November 2006

A new definition of dissipativity is proposed. It is purely in terms of the rate of supply that goes in and out of a dynamical system. It is proven that dissipativity is equivalent to the existence of a non‐negative storage. Several results regarding the dissipativity of systems defined by quadratic differential forms are given, and some open questions are mentioned. These ideas are applied to the question of stability of interconnected systems. Copyright © 2006 John Wiley & Sons, Ltd.
A random‐effects Markov transition model for Poisson‐distributed repeated measures with non‐ignorable missing values
Authors: Li Jinhui , Yang Xiaowei , Wu Yingnian , Shoptaw Steven
Published: November 2006

In biomedical research with longitudinal designs, missing values due to intermittent non‐response or premature withdrawal are usually ‘non‐ignorable’ in the sense that unobserved values are related to the patterns of missingness. By drawing the framework of a shared‐parameter mechanism, the process yielding the repeated count measures and the process yielding missing values can be modelled separately, conditionally on a group of shared parameters. For chronic diseases, Markov transition models can be used to study the transitional features of the pathologic processes. In this paper, Markov Chain Monte Carlo algorithms are developed to fit a random‐effects Markov transition model for incomplete count repeated measures, within which random effects are shared by the counting process and the missing‐data mechanism. Assuming a Poisson distribution for the count measures, the transition probabilities are estimated using a Poisson regression model. The missingness mechanism is modelled with a multinomial‐logit regression to calculate the transition probabilities of the missingness indicators. The method is demonstrated using both simulated data sets and a practical data set from a smoking cessation clinical trial. Copyright © 2006 John Wiley & Sons, Ltd.
The statistical performance of an MCF‐7 cell culture assay evaluated using generalized linear mixed models and a score test
Authors: Rey deCastro B. , Neuberg Donna
Published: November 2006

Biological assays often utilize experimental designs where observations are replicated at multiple levels, and where each level represents a separate component of the assay's overall variance. Statistical analysis of such data usually ignores these design effects, whereas more sophisticated methods would improve the statistical power of assays. This report evaluates the statistical performance of an in vitro MCF‐7 cell proliferation assay (E‐SCREEN) by identifying the optimal generalized linear mixed model (GLMM) that accurately represents the assay's experimental design and variance components. Our statistical assessment found that 17β‐oestradiol cell culture assay data were best modelled with a GLMM configured with a reciprocal link function, a gamma error distribution, and three sources of design variation: plate‐to‐plate; well‐to‐well, and the interaction between plate‐to‐plate variation and dose. The gamma‐distributed random error of the assay was estimated to have a coefficient of variation (COV) = 3.2 per cent, and a variance component score test described by X. Lin found that each of the three variance components were statistically significant. The optimal GLMM also confirmed the estrogenicity of five weakly oestrogenic polychlorinated biphenyls (PCBs 17, 49, 66, 74, and 128). Based on information criteria, the optimal gamma GLMM consistently out‐performed equivalent naive normal and log‐normal linear models, both with and without random effects terms. Because the gamma GLMM was by far the best model on conceptual and empirical grounds, and requires only trivially more effort to use, we encourage its use and suggest that naive models be avoided when possible. Copyright © 2006 John Wiley & Sons, Ltd.
In Situ Organization of Gold Nanorods on Mixed Self‐Assembled‐Monolayer Substrates
Authors: Zareie M. Hadi , Xu Xiaoda , Cortie Michael B.
Published: November 2006

A method is described for assembling gold nanorods, end‐to‐end, into long chains attached on top of a mixed self‐assembled monolayer that has been functionalized with streptavidin. Methods to prepare chains of nanorods in colloidal suspension have been reported by others, but our protocol offers a way to directly form such structures on a substrate. The rods are spaced ≈5 nm apart in the resulting chains, which extend for over a micrometer in length. The assembly and morphology of the nanorod structures were characterized by surface plasmon resonance spectroscopy, as well as by scanning electron microscopy and scanning probe microscopy. Structures of this type could conceivably serve as plasmonic waveguides in future nanodevices.
Uncertainty in computer application and its control through the engineering of software
Authors: Lehman M. M.
Published: November 2006

Computers are being applied more and more broadly to address applications in all areas of human activity, penetrating ever deeper into the very fabric of society. As a consequence, mankind is becoming, collectively and individually, ever more dependent on software and on the integrity of that software. In this context the term software includes both the systems software that constitutes a fundamental part of the operational configuration and the programs that implement each individual application. Integrity is a many faceted concept that has to do with the availability of programs whenever they are needed and their correctness in relation to the circumstances at the moment of execution or, more precisely, when the results of computation are applied. A program must produce a solution that is correct and relevant when used. It must continue to do so whenever required over the lifetime of an application and of the systems that realize and support it. All this is required despite continuing change in a dynamic world.

This paper discusses some properties of software and of software technology and identifies fundamental issues that must be addressed if program integrity is to be achieved initially, and if a program is to be maintained as satisfactory in a continuously changing operational environment. The discussion leads to formulation of a ‘Principle of Uncertainty’ that applies, in general, to all computer applications in the real world.

The principle follows from the fact that any program is a model, albeit many times removed by abstraction and reification from the real world it reflects and addresses. The consequences of this basic fact lead to a need for a disciplined technology associated with a controlled process for definition of each application, its operational domain, the envisaged system and software, and for its development, application and evolution (maintenance).

This paper concludes with a brief mention of the implications of the analysis on relevant technological issues. Fundamental concepts and observations that underlie the development of a software engineering discipline and its supporting technology are introduced. Software engineering is seen as the discipline that permits one to limit uncertainty and its consequences through the introduction and control of appropriate development processes and the systematic and disciplined applications of methods and tools. The emergence of such tools, of computer assisted software engineering (CASE) and of programming and project support environments (IPSEs) is briefly discussed. Finally the paper addresses issues that arise in transferring this still developing technology to industry and introducing it into practice, outlining briefly how this may be approached.
Organizational foundations for maintenance
Authors: Swanson E. B. , Beath C. M.
Published: November 2006

Maintaining application software for information systems in organizations poses managerial problems. Among these are: How should maintenance be planned? How should the maintenance staff be organized? What information is needed to manage maintenance? In a recent field study, in which we developed twelve cases, we explored the answers to these and other related questions. We found that organizational issues in maintenance may be comprehended in terms of a Relational Foundations Model involving the application systems, the IS staff and the system users. Vignettes from the cases illustrate. A new, organizational view of maintenance is suggested, one which departs from the traditional view of maintenance as a technical, individual programming task.
Dynamic program updating: A software maintenance technique for minimizing software, downtime
Authors: Segal M. E. , Frieder O.
Published: November 2006

When a new version of a software system is created, the current version of the system must be shut down while the new version is installed, resulting in software ‘downtime’. There are application domains where such downtime is undesirable if not wholly unacceptable. A dynamic program updating system replaces, or updates, a computer program with a new version while the program continues to run. A dynamic program updating system for programs written in conventional procedural languages such as Pascal and C is described. The proposed system updates programs without causing substantial performance degradation and requires minimal user intervention to initiate the update. A fully functional prototype updating system is presented and a sample program, namely an internet packet router called the ‘Packet Pumper’, is updated. The performance of the updating system and the Packet Pumper is discussed.
Lurking within COBOL PERFORMs
Authors: Crawford M. A.
Published: November 2006

COBOL‐implemented systems commonly rely on the PERFORM verb to provide structure and iteration in the software. Because of that key role, shortfalls in the use of PERFORM can lead to challenging difficulties in both enhancive and corrective maintenance. This paper explains the source of many of the symptoms by examining the way the compiler‐generated object code executes. Then it classifies the symptoms by their pattern and relates the classes to the normally hidden generated code. In closing, the paper offers six positive actions to improve COBOL software using the PERFORM verb, and points to their contribution in enhancive and corrective maintenance, software quality assurance, systems improvement, and the management of software maintenance.
Practice case study
Authors: Calow H.
Published: November 2006

This case study demonstrates how simple changes in the way maintenance is managed can result in significant benefits, improving productivity and performance.

It describes the work carried out by a major U.K. services organization and was contracted to provide support and maintenance services for one of their key business systems.
Software metrics and software maintenance
Authors: Leach Ronald J.
Published: November 2006

The term “software crisis” refers to the huge amount of resources needed for the development and maintenance of software. A major problem with research in these areas is the lack of solid data. In particular, there is little data that can be used to predict the types of problems that are likely to occur during the software's maintenance.

This paper describes the results of an analysis of a software system that underwent several revisions. Maintenance of the system was performed by distinct programming teams. At each revision of the software system, the analysis was performed by doing measurements of module complexity based on three quantities: Halstead's Software Science Effort, McCabe's cyclomatic complexity, and coupling analyses. The relationships of Software Science Effort to unchangeability of modules, of cyclomatic complexity to path coverage, and coupling analysis to measurement of modularity and coherence during the maintenance are given.
Problems of maintenance of JSP structures
Authors: Davies C. G.
Published: November 2006

A JSP oriented program design environment has been produced at UMIST (known as MAJIC), which computerizes the whole of the JSP methodology. This computerization of JSP has shown some shortcomings of the method with regard to the maintenance of the finished programs. The method imposes restrictions on the modification of program and data structures which reduces the effectiveness of using the method to maintain existing structures. This paper investigates some of those restrictions in the light of the work done to produce the MAJIC system. The restrictions are centred on the JSP mechanism for data structure correspondences, which are crucial to the use of JSP. Rules are proposed by which controlled modifications may be made to Jackson structures without, as is otherwise the case, of the need to reprocess large parts of the method. The rules were made in order to make a tool based on JSP more flexible, but they may equally be applied to maintenance of structures produced manually.
Characteristics of empirical software maintenance studies: 1980–1989
Authors: Sharpe Shane , Haworth Dwight A. , Hale David
Published: November 2006

This study examines empirical software maintenance research during the decade of the 1980s and categorizes the research according to placement, origin, and nature of research to determine what has been done in the past. To aid in the investigation, an exhaustive electronic keyword search was made of abstracts found in Computer Database Abstracts and INSPEC's Computer and Control Abstracts. Once candidate articles were identified, their full abstracts were scrutinized to determine whether the entire article should be reviewed. Based on a review of the full articles, summary statistics and research trends were established for software maintenance research published during the decade of the 1980s. The discussion that follows is partially based on an interpretation of the findings by an expert panel of information systems professionals actively working in the software maintenance area or engaged in management activities associated with software maintenance. Conclusions concerning the form and direction of future software maintenance publications are then advanced.
Decision‐based software development
Authors: Wild Chris , Maly Kurt , Liu Lianfang
Published: November 2006

Current software development paradigms focus on the products of the development process. Much of the decision‐making process which produces these products is outside the scope of these paradigms. The decision‐based software development (DBSD) paradigm views the design process as a series of interrelated decisions which involve the identification and articulation of problems, alternatives, solutions and justifications. Decisions made by programmers and analysts are recorded in a project database. Unresolved problems are also recorded and resources for their resolution are allocated by management according to the overall development strategy. This decision structure is linked to the products affected by the relevant decisions and provides a process‐oriented view of the resulting system. Software maintenance uses this decision view of the system to understand the rationale behind the decisions affecting the part of the system to be modified. The relationships between decisions help assess the impact of changing one or more decisions. We describe D‐HyperCase, a prototype Decision‐Based Hypermedia System and give results of applying the DBSD approach during its development.
Predicting maintainability with software quality metrics
Authors: Henry Sallie , Wake Steve
Published: November 2006

Maintenance of software makes up a large fraction of the time and money spent in the software life‐cycle. By reducing the need for maintenance these costs can also be reduced. Predicting where maintenance is likely to occur can help to reduce maintenance by prevention. In this paper, maintenance is defined as correction of errors in the program. This paper details a study of the use of software quality metrics to determine high‐complexity components in a software system. By the use of a history of maintenance done on a particular system, it is shown that a predictor equation can be developed to identify components which needed maintenance activities. This same equation can also be used to determine which components are likely to need maintenance in the future. Through the use of these predictions and software metric complexities, it should be possible to reduce the likelihood of a component needing maintenance. This might be accomplished by reducing the complexity of that component through further decomposition. Even though this is only one study, this methodology of developing maintenance predictors could be applied in any environment.
Economics of software re‐engineering
Authors: Sneed Harry M.
Published: November 2006

There is a pressing need to be able to calculate and to justify the costs of software re‐engineering. The purpose of the paper is to address that need by establishing a framework for the economics of re‐engineering. The objective of re‐engineering is to reduce maintenance costs. This objective is served by increasing quality and reducing complexity. Both of these goals are examined here in the light of software maintainability metrics. The costs of re‐engineering are driven by the size and interdependency of the software as well as by the degree of automation available. The paper presents a method of estimating the costs of re‐engineering, and presents some figures acquired through practical experience. Finally, a method is defined for weighing estimated costs against expected benefits in order to support decisions on whether to renovate existing software or replace it by a new development. This is a major decision faced by many industrial managers today.
The role of symbolic execution in software maintenance
Authors: Coward P. D. , Ince D. C.
Published: November 2006

Two major problems facing the software maintenance programmer are avoiding the introduction of unexecutable code and coping with the large volume of regression tests that are often required during maintenance. In preparing program changes, staff who carry out maintenance often have to spend time on ascertaining the constraints which govern the variables at the proposed points of insertion of the new code. This effort is required to avoid the introduction of unexecutable code which can so easily happen when maintenance staff are unaware of the prevailing constraints. This often means that many of the paths executed during regression testing are executed more than once in an attempt to overcome the risk of coincidental correctness camouflaging an error. This paper describes how symbolic execution, and in particular the SYM‐BOL system, can be used to reduce the likelihood of introducing unexecutable code, to speed up the process of determining the constraints on variables at a given point in a program and to reduce the volume of regression testing.
Design metrics and software maintainability: An experimental investigation
Authors: Shepperd Martin , Ince Darrel
Published: November 2006

An empirical study was conducted into the relationship between various design metrics and software maintainability. This was based upon maintenance changes made to four different versions of a project management tool carried out by a total of 60 programmers. The overall conclusion from the investigation, was that accurate prediction of quality characteristics for single maintenance changes is extremely difficult. This is due to the many sources of variation—principally change type and programmer ability. Nevertheless, we show that measures of information flow local to specific modifications are significantly related to error rates, with a 600% greater probability of a residual error as a consequence of a change in a module with a high level of information flow‐based coupling, than a module with a low level of coupling. Furthermore, we show that different types of change reveal marked variations in their relationships with the design metrics. Consequently, we argue that using robust statistical techniques and theoretically well‐founded design metrics, engineering approximations are possible.
A conceptual design for a code analysis knowledge base
Authors: Dietrich Suzanne W. , Calliss Frank W.
Published: November 2006

A knowledge base system for inter‐module code analysis is presented. Inter‐module code analysis is a technique that a programmer can use to analyse programs written in languages that contain a clustering construct called a module (or package). A module allows a programmer to control the visibility of a component within a program. The knowledge base for inter‐module code analysis is designed using the enhanced entity‐relationship conceptual data model, which is a graphical representation of the data and its relationships. The conceptual design for a code analysis enterprise is mapped into a knowledge base system, which uses a declarative logic‐based language to represent data as both facts and rules. The use of this knowledge base in an inter‐module code analysis application is demonstrated.