bluuebunny/crossref_metadata_2025 huggingface dataset:
Flexible ligand docking using conformational ensembles
Authors: Lorber David M. , Shoichet Brian K.
Published: July 2010

Molecular docking algorithms suggest possible structures for molecular complexes. They are used to model biological function and to discover potential ligands. A present challenge for docking algorithms is the treatment of molecular flexibility. Here, the rigid body program, DOCK, is modified to allow it to rapidly fit multiple conformations of ligands. Conformations of a given molecule are pre‐calculated in the same frame of reference, so that each conformer shares a common rigid fragment with all other conformations. The ligand conformers are then docked together, as an ensemble, into a receptor binding site. This takes advantage of the redundancy present in differing conformers of the same molecule. The algorithm was tested using three organic ligand protein systems and two protein‐protein systems. Both the bound and unbound conformations of the receptors were used. The ligand ensemble method found conformations that resembled those determined in X‐ray crystal structures (RMS values typically less than 1.5 Å). To test the method's usefulness for inhibitor discovery, multi‐compound and multi‐conformer databases were screened for compounds known to bind to dihydrofolate reductase and compounds known to bind to thymidylate synthase. In both cases, known inhibitors and substrates were identified in conformations resembling those observed experimentally. The ligand ensemble method was 100‐fold faster than docking a single conformation at a time and was able to screen a database of over 34 million conformations from 117,000 molecules in one to four CPU days on a workstation.
A monomeric mutant of Clostridium symbiosum glutamate dehydrogenase: Comparison with a structured monomeric intermediate obtained during refolding
Authors: Millevoi Stefania , Chiaraluce Roberta , Consalvi Valerio , Giangiacomo Laura , Pasquo Alessandra , Linda Britton K. , Stillman Timothy J. , Rice David W. , Engel Paul C.
Published: July 2010

The refolding ofClostridium symbiosumglutamate dehydrogenase (GDH) involves the formation of an inactive structured monomeric intermediate prior to its concentration‐dependent association. The structured monomer obtained after removal of guanidinium chloride was stable and competent for reconstitution into active hexamers. Site‐directed mutagenesis ofC.symbiosum gdhgene was performed to replace the residues Arg‐61 and Phe‐187 which are involved in subunit‐subunit interactions, as determined by three‐dimensional structure analysis. Heterologous over‐expression inEscherichia coliof the double mutant (R61E/F187D) led to the production of a soluble protein with a molecular mass consistent with the monomeric form of clostridial GDH. This protein is catalytically inactive but cross‐reacts with an anti‐wild‐type GDH antibody preparation. The double mutant R61E/F187D does not assemble into hexamers. The physical properties and the stability toward guanidinium chloride and urea of R61E/F187D were studied and compared to those of the structured monomeric intermediate.
The dimerization motif of the glycophorin A transmembrane segment in membranes: Importance of glycine residues
Authors: Brosig Bettina , Langosch Dieter
Published: July 2010

The glycophorin A transmembrane segment homodimerizes to a right‐handed pair of α‐helices. Here, we identified the amino acid motif mediating this interaction within a natural membrane environment. Critical residues were grafted onto two different hydrophobic host sequences in a stepwise manner and self‐assembly of the hybrid sequences was determined with the ToxR transcription activator system. Our results show that the motif LIxxGxxxGxxxT elicits a level of self‐association equivalent to that of the original glycophorin A transmembrane segment. This motif is very similar to the one previously established in detergent solution. Interestingly, the central GxxxG motif by itself already induced strong self‐assembly of host sequences and the three‐residue spacing between both glycines proved to be optimal for the interaction. The GxxxG element thus appears to be the most crucial part of the interaction motif.
Treatment response criteria for prostatic cancer
Authors: Schroeder F. H.
Published: July 2010

Response criteria for phase II and phase III trials of prostate carcinoma patients of the EORTC Genito Urinary‐Group are described. These criteria, initially closely related to National Prostatic Cancer Project criteria, have gone through a development into the direction of more stringency. Admission of patients to phase II trials is now restricted to those showing objectively measurable lesions, excluding bone metastases. World Health Organization criteria are applied to these patients. For phase III trials, progression to Metastatic TNM system status, time to progression, and duration of survival are recommended as end points. Measurable marker lesions, as for phase II trials and subjective and nonspecific response criteria, are accepted as parameters for progression. Response usually is not evaluated in these studies.

Based on recent literature and personal experiences, the author suggests that serum acid phosphatase (SPAP) and volume changes of the primary tumor can be used as indicators for response under certain conditions.

There is obviously a great need for further development of objective response criteria for prostatic cancer patients.
Cryotherapy
Authors: Loening Stefan A. , Bonney William W. , Fallon Bernard , Gerber Walter L. , Hawtrey Charles E. , Lubaroff David M. , Narayana Ambati S. , Culp David A.
Published: July 2010

Since 1969 cryosurgical perineal destruction of the prostate has been developed at the University of Iowa for treatment of patients with prostatic cancer. The technique of this procedure has been the subject of previous reviews. This is a summary of our experience of patient survival and the effect on local prostatic cancer growth in those patients with various stages of the disease subjected to perineal cryosurgical destruction of their cancer. We also report briefly on our experience in the laboratory where the Dunning tumor model is used to study the effect of cryosurgery as well as combinations of immunological modifications.
Cytochrome P450 Inhibition Assay for Standardized Extract of Terminalia chebula Retz.
Authors: Ponnusankar S. , Pandit S. , Venkatesh M. , Bandyopadhyay A. , Mukherjee Pulok K.
Published: July 2010

The hydroalcoholic extract of fruit pulp of Terminalia chebula Retz. was standardized and evaluated for its safety through cytochrome P450 (CYP 450) inhibition assay. Standardization was performed through high performance thin layer chromatography (HPTLC) using gallic acid (GA) standard. Cytochrome P450‐CO complex microplate assay was performed using rat liver microsomes. The effect of standardized extract, its fraction and bioactive marker compound were comparatively evaluated for its effect on CYP P450 enzymes. The extract of fruit pulp was used for HPTLC, where the Rf value of the marker was found to be 0.43. The calibration plot was linear in the range of 2–14 µg of GA and correlation co‐efficient of 0.99965. The mean quantity of GA was found to be 2.5% w/w. The CYP P450 concentration of the rat liver microsome sample used in the study was found to be 0.417 nmol/mg protein. The in vitro effect of various concentrations of extracts and fractions showed a linear concentration‐dependent inhibition of cytochrome P450 up to 60 µL. The study showed more inhibition of fraction when compared to the extract and GA. Still, the inhibition showed by fraction is less when compared with standard Ketoconazole. Thus, this study indicated the in vitro cytochrome P450 inhibition potential of T. Chebula.
Anti‐allergic effects of total bakkenolides from Petasites tricholobus in ovalbumin‐sensitized rats
Authors: Zhang Fu‐Jin , Wang Qin , Wang Yan , Guo Mei‐Li
Published: July 2010

The anti‐allergic effect of total bakkenolides from the rhizome of Petasites tricholobus (BAPT) was evaluated in an ovalbumin‐induced allergic rhinitis model in male Wistar rats. The major components of the bakkenolide fraction are bakkenolide‐D, bakkenolide‐B, bakkenolide‐IIIa and bakkenolide‐IVa, which account for 60.04% of the total. The rats were treated with 40 mg/kg, 20 mg/kg, 10 mg/kg or 5 mg/kg BAPT, and 0.942 mg/kg loratadine and 0.5% gum tragacanth were used as positive and negative controls, respectively. The frequency of nose rubbing and sneezing was observed, the number of eosinophils infiltrating into the nasal tissue was counted, and serum levels of IL‐4 and histamine were determined by ELISA. The results showed that BAPT had a beneficial effect on allergic rhinitis in ovalbumin‐sensitized Wistar rats, which was evidenced by a significant decrease in the frequency of sneezing, the number of eosinophils infiltrating into the nasal tissue, and the serum levels of IL‐4 and histamine. BAPT may therefore be a potential antiallergic drug. Copyright © 2010 John Wiley & Sons, Ltd.
Cysteine‐reactive covalent capture tags for enrichment of cysteine‐containing peptides
Authors: Giron Priscille , Dayon Loïc , Mihala Nikolett , Sanchez Jean‐Charles , Rose Keith
Published: July 2010

Considering the tremendous complexity and the wide dynamic range of protein samples from biological origin and their proteolytic peptide mixtures, proteomics largely requires simplification strategies. One common approach to reduce sample complexity is to target a particular amino acid in proteins or peptides, such as cysteine (Cys), with chemical tags in order to reduce the analysis to a subset of the whole proteome. The present work describes the synthesis and the use of two new cysteinyl tags, so‐called cysteine‐reactive covalent capture tags (C3T), for the isolation of Cys‐containing peptides. These bifunctional molecules were specifically designed to react with cysteines through iodoacetyl and acryloyl moieties and permit efficient selection of the tagged peptides. To do so, a thioproline was chosen as the isolating group to form, after a deprotection/activation step, a thiazolidine with an aldehyde resin by the covalent capture (CC) method. The applicability of the enrichment strategy was demonstrated on small synthetic peptides as well as on peptides derived from digested proteins. Mass spectrometric (MS) analysis and tandem mass spectrometric (MS/MS) sequencing confirmed the efficient and straightforward selection of the cysteine‐containing peptides. The combination of C3T and CC methods provides an effective alternative to reduce sample complexity and access low abundance proteins. Copyright © 2009 John Wiley & Sons, Ltd.
Groundwater Remediation and Aquifer Clean‐Up: A Case Study
Authors: Memon Bashir A. , George Lois D. , Mumtaz Azmeh M.
Published: July 2010

Groundwater was being remediated with pump and treat technology at a facility where the groundwater was contaminated with commonly used degreaser solvents. Hydraulic conductivity of the heterogeneous residuum was beneficiated by applying pneumatic fracturing technology. The remedial system was controlled and monitored by a sophisticated remote telemetry system. A case history follows.
Remediation of MTBE‐Contaminated Water and Soil
Authors: Keller Arturo A. , Sirivithayapakorn Sanya , Kram Mark
Published: July 2010

As the number of leaking underground fuel tank sites with methyl tertiary butyl ehter (MTBE) contamination continues to grow, there is a need to develop cost‐effective solutions for treatment of soil and water contamination. MTBE poses special challenges because of its physicochemical properties, in particular high solubility and low Henry's constant, low affinity for sorption, and very slow rate of microbial degradation. Advanced oxidation processes tend to generate undesirable by‐products. Based on laboratory studies with hollow fiber membranes (HFM), a field‐scale unit was constructed and tested at a number of sites, to determine the effectiveness of this technology in dealing with MTBE contamination. In addition, to treat the soil contamination, the HFM unit was coupled with a Spray Aeration Vapor Extraction (SAVE) unit, which is based on an internal combustion engine. The engine provides the means to treat soil vapors, as well as organic vapors from the spray aeration and HFM units. The overall treatment objectives of 5μg/l for MTBE and 1 μg/l for benzene were achieved with a treatment train consisting of an ion exchange unit, a spray aeration system, a hollow fiber membrane module and two granular activated carbon (GAC) units, for flowrates ranging from 3.8 to 30 l/min (1 to 8 gal/min). The ion exchange unit sewed to reduce water hardness and avoid scaling in the subsequent treatment units, extending the run‐time of the entire system. Overall removal efficiencies for the spray aeration system and hollow fiber membrane module ranged from 85 to over 99 percent. High removal efficiencies (> 97%) were obtained at elevated water temperatures (54°C) or lower flowrates (up to 11 l/min). The GAC units were used only to polish the effluent and meet the discharge requirements. Soil, water, and gas phases are treated with this system. Cost estimates are provided for similar treatment processes, for water flowrates up to 38 l/min (10 gal/min). © 1999 John Wiley & Sons, Inc.
An Improved Technique for Determining Abundance of Polycyclic Aromatic Hydrocarbon Degrading Microbial Populations
Authors: Guerin Turlough F.
Published: July 2010

The current study describes an improved method for estimating the abundance of polycyclic aramatic hydrocarbon (PAH) degraders in contaminated soil and groundwater. Since the method is a simple incremental improvement to a commonly used approach, it can be easily introduced into the remediation practitioner's testing protocols by simply changing growth indicator dyes. The procedure described is relatively easy to conduct and provides an important addition to laboratories that are using conventional, nonmolecular techniques for microbial enumeration in their bioremediation programs. © 1999 John Wiley & Sons, Inc.
Excluding induced subgraphs: quadrilaterals
Authors: Prömel Hans JüRgen , Steger Angelika
Published: July 2010

In this note we determine the structure of “almost all” graphs not containing a quadrilateral (i.e., a cycle of length four) as an induced subgraph. In particular, it turns out that there are asymptotically twice as many graphs not containing an induced quadrilateral than there are bipartite graphs.
Regularity lemmas for hypergraphs and quasi‐randomness
Authors: Chung Fan R.K.
Published: July 2010

We give a simple proof for Szemerédi's Regularity Lemma and its generalization for k‐uniform hypergraphs. For fixed k, there are altogether k ‐1 different versions of the regularity lemma for k‐uniform hypergraphs. The connection between regularity lemmas for hypergraphs and quasi‐random classes of hypergraphs is also investigated.
The dimension of random ordered sets
Authors: Erdos P. , Kierstead H. A. , Trotter W. T.
Published: July 2010

Let P = (X, <) be a finite ordered set and let |P| denote the cardinality of the universe X. Also let Δ(P) denote the maximum degree of P, i.e., the maximum number of points comparable to any one point of P. Füredi and Kahn used probabilistic methods to show that the dimension of P satisfies dim(P)≦ c1 Δ(P)log|P| and dim(P) ≦ c2Δ(P) log2Δ(P) where c, and c2 are positive absolute constants. In this article, we consider the probability space Ω(n, p) of bipartite ordered sets having n minimal elements and n maximal elements, where the events that any minimal element is less than any maximal element are independently distributed and each has probabilityp =p(n). We show that for every ϵ >0, there exist δ, c > 0 so that: (1) if (log1+ϵn)/n
n‐ cnlp log n for almost all P ∈Ω(n, p). The first inequality is best possible up to the value of the constant δ when p > (log2+en)/n. As to the accuracy of the second inequality, we have the trivial upper bound dim(P)≦n for all P∈Ω(n, p). We then develop a nontrivial upper bound which holds for almost all P ∈Ω(n, p), when p ≧ 1 /log n. This upper bound has the same form as the lower bound when p is constant. We also study the space ℒ︁(n) of all labelled ordered sets on n points and show that there exist positive constants c1, c2 so that n/4 ‐ c1n/log n < dim(P) <c2 n/4 ‐ c2n/log n for almost all P ∈ ℒ︁(n).
Stability properties of a flow process in graphs
Authors: Van Den Berg J. , Meester R. W. J.
Published: July 2010

We study a flow process in infinite graphs where vertices with large resources tend to attract resources from neighbors. The initial resources are random. An interesting question is whether in each finite region all motion stops after a finite time. Under certain assumptions, we prove that this is true. For some other cases, we prove a weaker stability result. We pay attention mostly to the case of Z2, but several results can be easily generalized to Zd.
An algorithmic approach to the Lovász local lemma. I
Authors: Beck József
Published: July 2010

The Lovász Local Lemma is a remarkable sieve method to prove the existence of certain structures without supplying any efficient way of finding these structures. In this article we convert some of the applications of the Local Lemma into polynomial time sequential algorithms (at the cost of a weaker constant factor in the “exponent”). Our main example is the following: assume that in an n‐uniform hypergraph every hyperedge intersects at most 2n/48 other hyperedges, then there is a polynomial time algorithm that finds a two‐coloring of the points such that no hyperedge is monochromatic.
Cycles in a random graph near the critical point
Authors: Luczak Tomasz
Published: July 2010

Let G(n, M) be a graph chosen at random from the family of all labelled graphs with n vertices and M(n) = 0.5n + s(n) edges, where s3(n)n−2→∞ but s(n) = o(n). We find the limit distribution of the length of shortest cycle contained in the largest component of G(n, M), as well as of the longest cycle outside it. We also describe the block structure of G(n, M) and derive from this result the limit probability that G(n, M) contains a cycle with a diagonal. Finally, we show that the probability tending to 1 as n‐→∞ the length of the longest cycle in G(n, M) is of the order s2(n)/n.
A critical point for random graphs with a given degree sequence
Authors: Molloy Michael , Reed Bruce
Published: July 2010

Given a sequence of nonnegative real numbers λ0, λ1… which sum to 1, we consider random graphs having approximately λi n vertices of degree i. Essentially, we show that if Σ i(i ‐ 2)λi > 0, then such graphs almost surely have a giant component, while if Σ i(i ‐2)λ. < 0, then almost surely all components in such graphs are small. We can apply these results to Gn,p,Gn.M, and other well‐known models of random graphs. There are also applications related to the chromatic number of sparse random graphs.
Connectivity properties of random subgraphs of the cube
Authors: Bollobás B. , Kohayakawa Y. , Luczak T.
Published: July 2010

The n‐dimensional cube Qn is the graph whose vertices are the subsets of {1, n} where two such vertices are adjacent if and only if their symmetric difference is a singleton. Clearly Qn is an n‐connected graph of diameter and radius n. Write M = n2n−1 = e(Qn) for the size of Qn. Let Q̃ = (Qt)M0 be a random Q̃‐process. Thus Qt is a spanning subgraph of Qn of size t, and Qt is obtained from Qt‐1 by the random addition of an edge of Qn not in Qt‐1. Let t(k) = τ(Q̃ δ ≧ k) be the hitting time of the property of having minimal degree at least k. It is shown in [5] that, almost surely, at time t(1) the graph Qt becomes connected and that in fact the diameter of Qt at this point is n + 1. Here we generalize this result by showing that, for any fixed k≧2, almost surely at time t(k) the graph Qt acquires the extremely strong property that any two of its vertices are connected by k internally vertex‐disjoint paths each of length at most n, except for possibly one, which may have length n + 1. In particular, the hitting time of k‐connectedness is almost surely t(k). © 1995 John Wiley & Sons, Inc.
Maximal full subspaces in random projective spaces—thresholds and Poisson approximation
Authors: Kordecki Wojciech
Published: July 2010

Let Gn, pdenote a random graph onnvertices. It is an interesting problem when small cliques arise and what distributions of the number of small cliques may occur. Matroids are natural generalization of graphs; therefore, we can try to investigate maximal flats of a small rank in random matroids. The most studied and most interesting seem to be “random projective geometries” introduced by Kelly and Oxley. Many of the theorems in our paper are based on the results published in a long paper of Barbour, Janson, Karoski, and Ruciski. However, proofs for projective geometries generally are more complicated.
The shape of stretched planar trees
Authors: Maier Robert S.
Published: July 2010

We study the asymptotics of a “stretched” model of unlabeled rooted planar trees, in which trees are not taken equiprobable but are weighted exponentially, according to their height. By using standard methods for computing the probabilities of large deviations of random processes, we show that, as the number of vertices tends to infinity, the normalized shape of a random tree converges in distribution to a deterministic limit. We compute this limit explicitly. © 1995 John Wiley & Sons, Inc.
Designing project‐based instruction to foster generative and mechanistic understandings in genetics
Authors: Duncan Ravit Golan , Tseng Katie Ann
Published: July 2010

The acquisition of scientific knowledge is fraught with difficulties and challenges for the learner. The very nature of some scientific domains contributes to the learning difficulties students' experience. Phenomena in these domains are composed of multiple organization levels featuring complicated interactions within and across these levels. Molecular genetics is a compelling example of such a domain. Current instructional practices in genetics leave students ill prepared to benefit from technological advances in genetics or to participate in public discussions about genetic issues. We argue that instruction in genetics needs to be refocused such that it promotes generative understandings of the genetic mechanisms that are at the core of modern genetics. This paper presents the early stages of design‐based research involving the development and study of a curriculum unit in genetics for high school students. We employed several design strategies to make the structure and mechanisms of genetic phenomena salient in the activities of the unit. Our findings suggest that the curriculum does, to a large extent, engender a deeper understanding of genetic phenomena. Specifically, we observed gains in students' understanding of the genetic information and the mechanisms that link genes to traits. © 2010 Wiley Periodicals, Inc. Sci Ed 95: 21–56, 2011
Exploring subcellular imaging on the buncher‐ToF J105 3D chemical imager
Authors: Rabbani S. , Fletcher J. S. , Lockyer N. P. , Vickerman J. C.
Published: July 2010

Imaging Mass Spectrometry is emerging as a promising technique to further the understanding of disease and treatment. ToF‐SIMS is also uniquely placed to become a powerful tool in this field due to its chemical specificity and the ability to perform high spatial resolution imaging. In this paper advances in single cell imaging at a sub‐cellular level in 2D and 3D are explored using a novel SIMS instrument based on a buncher‐ToF configuration, the J105 3D Chemical Imager. The data shows molecular localisation on a sub‐cellular scale, over a suitable timeframe, whilst sustaining high mass resolution. The cells are imaged using a 40 keV C60+ dc beam and a clear differentiation between the material within the nuclei and lipid membrane can be made. In addition challenges in data manipulation and interpretation are discussed. Investigation of cell preparation suggests that the frozen hydrated approach may be beneficial. Copyright © 2010 John Wiley & Sons, Ltd.
SIMS with highly excited primary beams for molecular depth profiling and imaging of organic and biological materials
Authors: Matsuo Jiro , Ninomiya Satoshi , Yamada Hideaki , Ichiki Kazuya , Wakamatsu Yoshinobu , Hada Masaki , Seki Toshio , Aoki Takaaki
Published: July 2010

Recent developments in SIMS with both Ar cluster ions and swift heavy ions are presented. With these primary beams, the analysis of organic semiconductors and animal cells shows that one of the key factors to realizing the SIMS analysis of organic materials is high‐energy deposition near the surface. Molecular depth profiling and images of organic materials were demonstrated by using SIMS. Copyright © 2010 John Wiley & Sons, Ltd.
Surface studies of halloysite nanotubes by XPS and ToF‐SIMS
Authors: Ng Kai‐Mo , Lau Yiu‐Ting R. , Chan Chi‐Ming , Weng Lu‐Tao , Wu Jingshen
Published: July 2010

This report provides detailed experimental results of thermal and surface characterization on untreated and surface‐treated halloysite nanotubes (HNTs) obtained from two geographic areas. Surface characterization techniques, including XPS and time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) were used. ToF‐SIMS surface analysis experiments were performed with both atomic and cluster ion beams. Higher ion yields and more high‐mass ions were obtained with the cluster ion beams. Static ToF‐SIMS spectra were analyzed with principal component analysis (PCA). Morphological diversities were observed in the samples although they mainly contained tubular structures. Thermogravimetric data indicated that aqueous hydrogen peroxide solution could remove inorganic salt impurities, such as alkali metal salts. The amount of grafting of benzalkonium chloride of HNT surface was determined by thermogravimetic analysis. PCA of ToF‐SIMS spectra could distinguish the samples mined from different geographical locations as well as among surface‐treated and untreated samples. Copyright © 2010 John Wiley & Sons, Ltd.
The chemical composition and bonding structure of amorphous hydrogenated carbon nitride film on aluminum surface deposited by electrodeposition
Authors: Yu Yuanlie , Zhang Junyan
Published: July 2010

Amorphous hydrogenated carbon nitride films with excellent adhesion to the substrates were deposited on the surfaces of aluminum plates by electrodeposition with acetonitrile as carbon source. The as‐obtained films were detailed characterized by Raman, XPS and FTIR. The results show that the as‐obtained films are mainly made up of sp2 C, sp3 C, CN, CN bonds and a spot of sp3CH2, sp3CH3, sp3CH and sp2CH bonds. The atomic ratio of N/C is evaluated to be about 2.98 at.% by XPS. Raman analysis indicated that ID/IG ratios decreased from 0.827 to 0.675 when the deposition time increased from 10 to 20 h. At the end, on the basis of the detailed analysis, results of Raman, FTIR and XPS, the possible deposition mechanism was discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Complex interface and growth analysis of single crystalline epi‐Si(111)/Y2O3/ Pr2O3/Si(111) heterostructures: Strain engineering by oxide buffer control
Authors: Wilke A. , Yang J.‐M. , Kim J. W. , Seifarth O. , Dietrich B. , Giussani A. , Zaumseil P. , Storck P. , Schroeder T.
Published: July 2010

Complex oxide heterostructures on Si gain in the field of engineered Si wafers increasing interest as flexible buffer systems for developing virtual Si substrates. Strain engineering of thin epitaxial Si thin films on insulating oxide buffers is of special interest to boost charge carrier mobility for Silicon‐on‐Insulator (SOI) technologies. The single crystalline Si(111)/Y2O3 (111)/Pr2O3 (111)/Si(111) heterostructure offers, in principle, the opportunity to grow strain‐engineered epitaxial Si(111) layers, realizing compressed, fully relaxed, as well as tensile‐strained Si films. This flexibility is based on a thickness‐dependence of the Y2O3 lattice constant in the oxide bi‐layer buffer: In theory, the Y2O3 buffer lattice constant on Pr2O3/Si(111) can change from pseudomorphism (bigger than Si) over the Si lattice constant towards a fully relaxed status (smaller than Si). By a detailed interface analysis, using TEM‐EELS in combination with an in‐situ RHEED–XPS study of the isomorphic Y2O3 growth on Pr2O3/Si(111), the physical origin of this Y2O3 buffer lattice constant variation is identified. It is possible to discriminate between the contributions from chemical mixing effects between the isomorphic oxides Y2O3 and Pr2O3 on the one hand and true misfit strain relaxation mechanisms in stoichiometric Y2O3 on the other hand. Copyright © 2010 John Wiley & Sons, Ltd.
Energy resolved XPS depth profile of (IrO2, RuO2, Sb2O5, SnO2) electrocatalyst powder to reveal core‐shell nanoparticle structure
Authors: Haverkamp Richard G. , Marshall Aaron T. , Cowie Bruce C. C.
Published: July 2010

Synchrotron‐based energy resolved XPS was used to characterize the structure of IrO2RuO2‐coated Sb2O5SnO2 nanoparticles. Samples were heat treated at 300, 350, 400, 450 and 500 °C after chloride Ir and Ru precursors were added to Sb2O5SnO2. Photoelectron kinetic energies of 100, 350 and 1400 eV were employed to obtain an indication of the depth of elemental distributions and chemical shifts. It was shown that the electrocatalyst consists of a core of Sb2O5SnO2 enriched with Sb2O5 towards the surface, with a shell of IrO2RuO2 deposited on this core, and an outer layer of Sb2O5SnO2 over this shell. No significant chemical interaction occurs between IrO2RuO2 and Sb2O5SnO2. The energy resolved XPS depth profile technique is effective for studying core‐shell materials. Copyright © 2010 John Wiley & Sons, Ltd.
Tailoring the surface chemistry of carbon fiber and E‐glass composites for improved adhesion
Authors: Gilbert M. J. , Awaja F. , Kelly G. L. , Fox B. L. , Brynolf R. , Pigram P. J.
Published: July 2010

The main challenges in the manufacture of composite materials are low surface energy and the presence of silicon‐containing contaminants, both of which greatly reduce surface adhesive strength. In this study, carbon fiber (CF) and E‐glass epoxy resin composites were surface treated with the Accelerated Thermo‐molecular adhesion Process (ATmaP). ATmaP is a multiaction surface treatment process where tailored nitrogen and oxygen functionalities are generated on the surface of the sample through the vaporization and atomization of n‐methylpyrrolidone solution, injected via specially designed flame‐treatment equipment. The treated surfaces of the polymer composites were analyzed using XPS, time of flight secondary ion mass spectrometry (ToF‐SIMS), contact angle (CA) analysis and direct adhesion measurements. ATmaP treatment increased the surface concentration of polar functional groups while reducing surface contamination, resulting in increased adhesion strength. XPS and ToF‐SIMS showed a significant decrease in silicon‐containing species on the surface after ATmaP treatment. E‐glass composite showed higher adhesion strength than CF composite, correlating with higher surface energy, higher concentrations of nitrogen and CO functional groups (from XPS) and higher concentrations of oxygen and nitrogen‐containing functional groups (particularly C2H3O+ and C2H5NO+ molecular ions, from ToF‐SIMS). Copyright © 2010 John Wiley & Sons, Ltd.
Characterization of β‐cyclodextrin modified SiO2
Authors: Nielsen Ronnie , Kingshott Peter , Uyar Tamer , Hacaloglu Jale , Larsen Kim L.
Published: July 2010

Silica particles containing a layer of β‐cyclodextrins were synthesized using a modified method of Armstrong (1985). The modified silica particles were extensively characterized to both the presence and amount of β‐cyclodextrin introduced onto the surface. Raman confirmed that β‐cyclodextrin was introduced onto the particle. The combination of thermogravmetric analysis (TGA) and direct pyrolysis mass spectroscopy were used to determine the amount and the chemical composition of organic material present on the silica, respectively. The two methods confirmed that β‐cyclodextrin was successfully introduced in amounts comparable to earlier literature values. The values obtained by TGA were compared to amounts found by elemental analysis and XPS. The elemental analysis and TGA found the same amount of β‐cyclodextrin, while the XPS values were in the region of 1.5 times higher. This suggests a heterogeneous distribution of the β‐cyclodextrin on the silica particles. Copyright © 2010 John Wiley & Sons, Ltd.
Incorporation and migration of phosphorus species within anodic films on an Al‐W alloy
Authors: Garcia‐Vergara S. J. , Molchan I. S. , Zhou F. , Habazaki H. , Kowalski D. , Skeldon P. , Thompson G. E.
Published: July 2010

The effect of tungsten species on the incorporation and migration of phosphorus species within anodic alumina is investigated. The study employs barrier anodic films, formed on a sputtering‐deposited Al‐15at.%W alloy in phosphate electrolytes. The films consist of either an outer tungsten‐containing region and an inner tungsten‐free region, or a tungsten‐containing region only. Phosphorus species are shown to migrate inward in the tungsten‐containing alumina more slowly than in the tungsten‐free alumina. In contrast, the outward migration of tungsten species is relatively unaffected by the presence of phosphorus species. The relevance of the results to the use of tungsten tracers for the study of porous film growth is discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Preparation and characterization of flame‐retardant lamellar Mg(OH)2 thin films on citric acid‐treated cotton fabrics
Authors: Mao Qinghui , Zhang Linping , Huang Dehui , Wang Dan , Huang Yang , Xu Hong , Cao Huantian , Mao Zhiping
Published: July 2010

Preparation and characterization of lamellar magnesium hydroxide (Mg(OH)2) thin films on cotton fabrics are reported in this paper. Mercerized cotton fabrics were treated with citric acid, so carboxyl groups were introduced to the surface of the fabrics. Mg(OH)2 seeds were first adsorbed on the citric acid‐treated cotton fabrics and then Mg(OH)2 thin films grew on the fabric through secondary growth method. Kinetics and isotherm studies found that the adsorption of Mg(OH)2 seeds on citric acid‐treated cotton fabrics followed pseudo second‐order kinetic model and Langmuir isotherm. This indicated that Mg(OH)2 seeds adsorption was monolayer chemical adsorption driven by electric attraction between positively charged Mg(OH)2 seeds and COO− ions on the cotton fiber surface. The X‐ray diffraction (XRD) and SEM characterizations of the Mg(OH)2 thin films covered cotton fabrics found that standing flaky Mg(OH)2 crystals formed a shell of porous but continuous network on cotton fabric surface. Owing to the Mg(OH)2 thin film covering, the fabric had fireproof property, lower thermal conductivity and higher optical absorbance in the UV, Vis and IR regions. Copyright © 2010 John Wiley & Sons, Ltd.
Comparative study of microstructure and tribological behavior of TiC/a‐C:H and a‐C:H coatings in a sand‐dust environment
Authors: Qi Jianwei , Wang Liping , Yan Fengyuan , Xue Qunji
Published: July 2010

TiC/a‐C:H and a‐C:H nanocomposite coatings were prepared on AISI 440C steel substrates using magnetron sputtering process. A comparative study was made on their composition and microstructure by Raman spectroscopy and high‐resolution transmission electron microscopy (HRTEM). The tribological properties of two types of carbon‐based coatings were investigated by pin‐on‐disc tribometer under the sand‐dust conditions concerning the influence of applied load, amount of sand and sand particle sizes. The results show that these carbon‐based coatings exhibited high tribological performance with low friction coefficient and wear rate under the sand‐dust environments. However, the TiC/a‐C:H coatings exhibit relatively higher fluctuant friction coefficient as well as higher wear rate in comparison with the a‐C:H coatings under sand‐dust environments. The formation of nanocrystalline hard TiC phase distributed in amorphous carbon matrix decreased the residual stress but significantly increased the hardness and Young's modulus of TiC/a‐C:H coatings, and consequently caused a relatively higher abrasive and fatigue wear loss under the sand‐dust conditions. Copyright © 2010 John Wiley & Sons, Ltd.
Ageing of vinyl emulsion paints—an atomic force microscopy study
Authors: de Sá M. H. , Eaton Peter , Ferreira Joana L. , Melo M. J. , Ramos Ana M.
Published: July 2010

This paper presents a morphological study of poly(vinyl acetate) (PVAc) based films, either cast from polymer solutions or aqueous emulsions, which are widely used in modern and contemporary art, namely as binding media. Different vinyl films were prepared: single polymer, unpigmented and TiO2‐pigmented emulsion films, and subjected to accelerated light ageing. The evaluation of the surface changes of these films, over 3500 hours irradiation under a Xenon lamp (λ≥ 300 nm), was characterized by atomic force microscopy (AFM). The samples studied have suffered minor surface changes and revealed pronounced photostability. The AFM results obtained indicate that the most relevant morphological changes that occurred over time were primarily related to the exudation of surfactants, present in the vinyl emulsions. Copyright © 2010 John Wiley & Sons, Ltd.
Micro/nanotribological behaviors of ionic liquid nanofilms with different functional cations
Authors: Zhao Wenjie , Wang Liping , Bai Mingwu , Xue Qunji
Published: July 2010

Four kinds of molecularly thin films of room temperature ionic liquids (RTILs) with different functional cations were prepared on silicon substrates by dip‐coating method. Thermal stability of the RTILs was evaluated using Mettler thermal gravity analysis (TGA) in a nitrogen atmosphere. Chemical compositions of the RTIL nanofilms were examined by means of multifunctional XPS. Nanoscaled adhesion and friction forces between the films and AFM tip were measured by FFM whereas the morphologies of the films were also investigated. Microscaled friction and wear behaviors between the films and Si3N4 ball were further measured by the microtribometer. The micro/nanotribological behaviors of different RTIL films were comparatively investigated and discussed in terms of functional cations of the RTILs molecules. Results in this paper revealed that the functional cations of the RTIL films significantly affected their tribological behaviors both in micro‐ and nanoscales. The corresponding micro/nanotribological mechanism of the tested ultrathin RTIL films under the test conditions was consequently proposed based on the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.
D & TOF‐SIMS failure analysis of P‐buried layer from BiCMOS transistors
Authors: Budri Thanas , Sehgal Akshey , Arsenault Scott , Klatt Jeffrey , Noort Wibo Van , Ruby Scott , Ramdani Jamal , Allard Paul , Schnieders Albert
Published: July 2010

D & TOF‐SIMS instruments are used in conjunction with other analytical techniques in order to identify the sources of metallic contamination and particle‐type defects. In this paper D & ToF‐SIMS are used to identify metals in the P‐type buried layer of BiCMOS transistors and eliminate them in order to improve the overall device performance and process yield. Copyright © 2010 John Wiley & Sons, Ltd.
Considerations of the intermediate oxides via XPS elemental quantitative analysis for the thickness measurements of ultrathin SiO2 on Si
Authors: Liu Fen , Zhao Zhijuan , Zhao Liangzhong , Wang Hai
Published: July 2010

The thicknesses of intermediate oxides at the interface between ultrathin SiO2 and Si substrates have been measured via XPS elemental quantitative analysis for some SiO2/Si(100) and SiO2/Si(111) samples with the silicon oxide thickness less than 2 nm. The measurements involve XPS determination of the Si relative atomic ratio, calculation of Si atomic densities for the intermediate oxide, etc. and then the intermediate oxide thicknesses and the number of monolayers are obtained by referencing the thickness data from two international comparisons for these samples. The results show that the thickness of the intermediate oxides is in the range 0.14–0.16 nm with an average value of 0.15 nm. The number of monolayers for the intermediate oxides at the interface is less than one monolayer with an average value of 0.60. In the present work, there are a series of approximations. By making these approximations many parameters, including L and R0, used in the conventional calculation method are removed to give a simpler equation, which is valid when the thicknesses of SiO2 overlayer and the intermediate oxides are very small. This, therefore, appears to be a simple and quick method to obtain approximate oxide thicknesses of modest accuracy. The present work does not in any way replace or improve on Eqns (2–6) cited in the text. Copyright © 2010 John Wiley & Sons, Ltd.
Evaluating health risk models
Authors: Whittemore Alice S.
Published: July 2010

Interest in targeted disease prevention has stimulated development of models that assign risks to individuals, using their personal covariates. We need to evaluate these models and quantify the gains achieved by expanding a model to include additional covariates. This paper reviews several performance measures and shows how they are related. Examples are used to show that appropriate performance criteria for a risk model depend upon how the model is used. Application of the performance measures to risk models for hypothetical populations and for US women at risk of breast cancer illustrate two additional points. First, model performance is constrained by the distribution of risk‐determining covariates in the population. This complicates the comparison of two models when applied to populations with different covariate distributions. Second, all summary performance measures obscure model features of relevance to its utility for the application at hand, such as performance in specific subgroups of the population. In particular, the precision gained by adding covariates to a model can be small overall, but large in certain subgroups. We propose new ways to identify these subgroups and to quantify how much they gain by measuring the additional covariates. Those with largest gains could be targeted for cost‐efficient covariate assessment. Copyright © 2010 John Wiley & Sons, Ltd.
Evaluating diagnostic accuracy of genetic profiles in affected offspring families
Authors: Carayol Jerome , Tores Frédéric , König Inke R. , Hager Jörg , Ziegler Andreas
Published: July 2010

Diagnostic accuracy of a genetic test involving multiple disease genes is evaluated using sensitivity and specificity. For estimation, data from both affected and unaffected subjects are required. For early onset diseases, such as autism spectrum disorder (ASD), only data from families with affected offspring are available. To enable estimation of specificity when no data for unaffected offspring are available (single affected offspring, SAO, data), we combine the pseudocontrol method of Cordell and Clayton (Am. J. Hum. Genet. 2002; 70:124–141) with the approach of DeLong et al. (Biometrics 1985; 41:947–958) in a logistic regression model for disease outcome with a risk score (RS) constructed from genotype information as prognostic variable. The area under the receiver operating characteristic curve (AUC) is then computed using the non‐parametric Mann–Whitney method. Extensive simulation studies show that, analogous to other approaches utilizing pseudocontrols, the resulting estimates of AUC using SAO data are slightly conservative when compared with the estimates computed using the full population‐based data. The method is illustrated using data from a study of ASD. Copyright © 2010 John Wiley & Sons, Ltd.
Burnout and risk of regional musculoskeletal pain—a prospective study of apparently healthy employed adults
Authors: Melamed Samuel
Published: July 2010

Musculoskeletal pain (MP) is highly prevalent in the working population, often resulting in chronic disability. Work stress has been shown to be important in the aetiology of MP. Burnout is a unique affective response to chronic exposure to stress and might predict subsequent development of MP. To date, however, all studies in this area have been based on a cross‐sectional design, which prevents determining the direction of causality. This prospective study tested the extent to which baseline levels of burnout predict the onset of regional neck/shoulder and/or low back pain, in apparently healthy individuals. The participants were composed of 650 employed men and women who underwent follow‐up for 3–5 years. During the follow‐up period, 116 workers (17.8%) developed musculoskeletal pain. Logistic regression results indicated that burnout symptoms were associated with a 1.67‐fold increased risk of MP [95% confidence interval (CI) = 1.14–1.87], even after adjusting for possible confounding variables (such as white‐ or blue‐collar jobs). Those exhibiting high burnout levels, compared with others, showed higher relative risk of MP [odds ratio (OR) = 2.45, 95%CI = 1.35–4.45]. It was concluded that burnout might be a risk factor for the development of musculoskeletal pain in apparently healthy individuals. Copyright © 2009 John Wiley & Sons, Ltd.
Do burnout and insomnia predict each other's levels of change over time independently of the job demand control–support (JDC–S) model?
Authors: Armon Galit
Published: July 2010

In past research, the job demand control–support (JDC–S) model was found to predict both burnout and insomnia. Recent evidence suggests that burnout and insomnia are reciprocally associated with each other across time. The objective of this study was to test whether there is an additive effect of burnout on subsequent changes in insomnia over and above the effect of the JDC–S model, and the reverse causation hypothesis expecting insomnia to have an additive effect on subsequent levels of burnout. Subjects were 3,235 apparently healthy employed adults who completed questionnaires during a periodic health examination at two points of time, Time 1 (T1) and Time 2 (T2), about 18 months apart. Depressive symptomatology, body mass index, age, gender, follow‐up duration and T1 levels of the criterion were controlled. As hypothesized, the results indicate that T1 insomnia predicts the T1–T2 change in burnout over and above the influence of the T1 JDC–S model, and further that T1 burnout predicts the T1–T2 change in insomnia over and above the influence of the T1 JDC–S model. The results suggest that burnout and insomnia may adversely affect one another even in workers with low job strain. Several possible mechanisms of the link between JDC–S model, burnout and insomnia are suggested. Copyright © 2009 John Wiley & Sons, Ltd.
Burnout versus work engagement in their effects on 24‐hour ambulatory monitored cardiac autonomic function
Authors: van Doornen Lorenz J. P. , Houtveen Jan H. , Langelaan Saar , Bakker Arnold B. , van Rhenen Willem , Schaufeli Wilmar B.
Published: July 2010

Burnout has been associated with increased risk of cardiovascular disease. This relationship may be mediated by a stress‐related disruption in cardiac autonomic activity. The aim of the present study was to assess cardiac autonomic activity (sympathetic and parasympathetic) during a working day in burned out managers. Thirty burned out, 29 healthy control and 29 engaged managers (a psychologically contrasting group) were identified using the Maslach Burnout Inventory‐General Survey (MBI‐GS) and the Utrecht Work Engagement Scale (UWES). Twenty‐four‐hour ambulatory measurements were carried out during a regular workday and the subsequent night. Pre‐ejection period (PEP) and respiratory sinus arrhythmia (RSA) were used as measures of cardiac sympathetic and parasympathetic activity, respectively. Contrary to expectations, the burned out, engaged and control groups did not differ in cardiac sympathetic and cardiac parasympathetic activity, or heart rate. Thus, burnout does not seem to be associated with an unfavourable cardiac autonomic profile. Copyright © 2009 John Wiley & Sons, Ltd.