bluuebunny/crossref_metadata_2025 huggingface dataset:
Out‐of‐phase relationships between convection over northwest India and warm pool region during the winter season
Authors: Yadav R. K. , Rupa Kumar K. , Rajeevan M.
Published: December 2008

In this paper, we investigate the effect of convection over warm pool region of Indonesia on northwest India winter precipitation (NWIWP) using an analysis of latest available observed climate data. The analysis is based on correlations and composites performed using India Meteorological Department (IMD) records of station data. We find that there is an out‐of‐phase relationship between convection over warm pool region and northwest India during the winter season. In particular, a positive precipitation anomaly over northwest India is typically found in correspondence to subdued convection over warm pool region. A physical mechanism for such effect is proposed, by which during excess years of NWIWP the tropical cooling over the warm pool region due to suppressed convection generates an upper‐level convergence (cyclonic circulation) anomaly over south Asia which intensifies the westerly jet stream over Indian region. Also, the reduced convection over the warm pool may be due to reduced Madden‐Julian oscillation (MJO) activities on the intra‐seasonal timescale. The Rossby‐gyre dynamics with the strong vertical and westward meridional tilts in the tropical baroclinic atmosphere forms cyclonic circulation anomalies at the upper troposphere due to a weak MJO which intensifies the westerly jet stream over the Indian region. The jet stream guides the western disturbances (WDs) and hence increases precipitation over northwest India. The seasonal persistence in migration of convective maximum from south Asia (foothills of the Himalayas) to Indonesia during the peak months of boreal summer to winter increases the seasonal predictability of NWIWP. Copyright © 2008 Royal Meteorological Society
Intervertebral disc cell response to dynamic compression is age and frequency dependent
Authors: Korecki Casey L. , Kuo Catherine K. , Tuan Rocky S. , Iatridis James C.
Published: December 2008

The maintenance of the intervertebral disc extracellular matrix is regulated by mechanical loading, nutrition, and the accumulation of matrix proteins and cytokines that are affected by both aging and degeneration. Evidence suggests that cellular aging may lead to alterations in the quantity and quality of extracellular matrix produced. The aims of this study were to examine the role of loading and maturation (a subset of aging), and the interaction between these two factors in intervertebral disc cell gene expression and biosynthesis in a controlled 3D culture environment. Cells were isolated from young (4–6 months) and mature (18–24 months) bovine caudal annulus fibrosus and nucleus pulposus tissue. Isolated cells were seeded into alginate and dynamically compressed for 7 days at either 0.1, 1, or 3 Hz or maintained as a free‐swelling control. After 7 days, DNA and sulfated glycosaminoglycan contents were analyzed along with real time, quantitative reverse transcription‐polymerase chain reaction analysis for collagen types I and II, aggrecan, and matrix metalloproteinase‐3 gene expression. Results suggest that maturation plays an important role in intervertebral disc homeostasis and influences the cell response to mechanical loading. While isolated intervertebral disc cells responded to mechanical compression in 3D culture, the effect of loading frequency was minimal. Altered cellular phenotype and biosynthesis rates appear to be an attribute of the cell maturation process, potentially independent of changes in cellular microenvironment associated with lost nutrition and disc degeneration. Mature cells may have a decreased capacity to create or retain extracellular matrix components in response to mechanical loading compared to young cells. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 800–806, 2009
Elimination of oxidation and decomposition by SnCl2 in the SERS study of pyridoxine on a roughened Au electrode
Authors: Chu Youping , Chen Shu , Zheng Jufang , Li Zelin
Published: December 2008

Severe interference from the oxidation and laser carbonization was encountered in the measurements of surface‐enhanced Raman scattering (SERS) spectra of pyridoxine (PN) on the roughened gold electrode. However, we found that high‐quality SERS spectra of PN could be obtained by the introduction of SnCl2, which only has few Raman peaks at low wavenumbers. SnCl2, as a good reductive, is capable of removing the oxidative species on the gold substrate and the dissolved oxygen in solution, and as a result lowering the open circuit potential (OCP). Sn(II) can also strongly chemically adsorb on the gold surface and interact with PN through coordination/chelation, such that not only to prevent PN from damage by the giant electromagnetic field for the ‘first‐layer’ effect, but also to give rise to very strong Raman scattering signals of PN where chemical enhancement plays an important role. Those are the main reasons for the elimination of the oxidation and decomposition of PN and for the high‐quality SERS spectra of PN. The way the SnCl2 confines PN within the enhanced electromagnetic field by its ability of adsorption and coordination/chelation can be utilized to improve the routine SERS analysis of analogous type of reactive organic/biomolecules. In addition, this method has been successfully extended to the SERS measurements of PN on the substrates of roughened silver and copper. Copyright © 2008 John Wiley & Sons, Ltd.
Parametric amplification and processing in optical fibers
Authors: Radic S.
Published: December 2008

We review recent progress made in parametric amplification and signal processing using high confinement fibers. In contrast to crystalline and semiconductor devices, fiber parametric amplifiers offer interaction lengths that can vary from 10 m to 1 km and are not limited by waveguide losses. The operation, design and impairment physics of general fiber parametric devices are reviewed. The technology prospects for advanced signal processing are discussed.
In situ Growth of Pd Nanoparticles in Crosslinked Polymer Matrices
Authors: Aberg Christopher M. , Seyam Mohamed A. , Lassell Scott A. , Bronstein Lyudmila M. , Spontak Richard J.
Published: December 2008

Polymer nanocomposites continue to receive considerable attention as multifunctional hybrid materials, with most nanocomposites fabricated by physical dispersion of surface‐functionalized nanoscale objects. In this study, we explore the viability of growing Pd‐containing nanoparticles from Na2PdCl4 in two different polymers: hypercrosslinked polystyrene (HPS) and an aromatic polyimide (PIm). In HPS, single Pd‐containing nanoparticles possessing a relatively narrow size distribution (ca. 1–4 nm) form upon reduction of the divalent PdCl ions. Single nanoparticles with a broad size distribution ranging from ≈2 to 16 nm develop in PIm, which simultaneously undergoes chemical crosslinking during ion reduction. Such hybrid materials hold promise in molecular catalysis and gas separation.

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Visual scanning and cognitive performance in prediagnostic and early‐stage Huntington's disease
Authors: Blekher Tanya , Weaver Marjorie R. , Marshall Jeanine , Hui Siu , Jackson Jacqueline Gray , Stout Julie C. , Beristain Xabier , Wojcieszek Joanne , Yee Robert D. , Foroud Tatiana M.
Published: December 2008

The objective of this study was to evaluate visual scanning strategies in carriers of the Huntington disease (HD) gene expansion and to test whether there is an association between measures of visual scanning and cognitive performance. The study sample included control (NC, n = 23), prediagnostic (PDHD, n = 21), and subjects recently diagnosed with HD (HD, n = 19). All participants completed a uniform clinical evaluation that included examination by neurologist and molecular testing. Eye movements were recorded during completion of the Digit Symbol Subscale (DS) test. Quantitative measures of the subject's visual scanning were evaluated using joint analysis of eye movements and performance on the DS test. All participants employed a simple visual scanning strategy when completing the DS test. There was a significant group effect and a linear trend of decreasing frequency and regularity of visual scanning from NC to PDHD to HD. The performance of all groups improved slightly and in a parallel fashion across the duration of the DS test. There was a strong correlation between visual scanning measures and the DS cognitive scores. While all individuals employed a similar visual scanning strategy, the visual scanning measures grew progressively worse from NC to PDHD to HD. The deficits in visual scanning accounted, at least in part, for the decrease in the DS score. © 2008 Movement Disorder Society
Online privacy and security practices of the 100 largest US nonprofit organizations
Authors: Hoy Mariea Grubbs , Phelps Joseph
Published: December 2008

Although online consumer privacy has been an important issue in the commercial realm for more than a decade, nonprofit organizations (NPOs, or nonprofits, for short) have just begun to address the topic recently. No published scholarly research has examined the online information practices of the largest NPOs with regard to privacy and security issues. The absence of data leaves one unable to empirically gauge the extent of NPO compliance with the Federal Trade Commissions (FTCs) suggested information practices. Such an investigation would be useful not only to US nonprofits but also non‐US nonprofits that are reaching US donors via their web sites.

This study examines the online information practices of The Nonprofit Times 100 web sites and compares their practices to that of their commercial counterparts. The NPO web sites were found to collect just as much, and in some cases even more, personally identifying information as the commercial sites. The NPO web sites were more likely to display a privacy disclosure and privacy seal. Of critical concern, and not assessed in the commercial samples, is that nearly all of the NPO sites post personally identifying information (of individuals who are not employees).

The current study provides benchmarks useful for assessing security issues pertaining to the collection, use, and even posting of personal information for NPO web sites. It also proposes actions for improving online security and privacy with the hope of encouraging more discussion of these important issues within the NPO community.

Copyright © 2008 John Wiley & Sons, Ltd.
The influence of cause marketing associations on product and cause brand value
Authors: Wymer Walter , Samu Sridhar
Published: December 2008

The purpose of the study presented in this paper is to add to our understanding of the added value, both monetary and non‐monetary, to a brand when supporting a cause in a cause marketing ad. The findings show that consumers do not perceive the brand to be worth more if it was shown to be supporting a cause. The study also failed to show a significant improvement in consumer brand attitudes for brands featured in cause marketing ads. However, there was an attitude improvement for the cause. Product type and consumer dispositional variables were also examined.

In summary, this study calls into question the value brands derive from being paired with a cause. This study discusses productive areas of future research and managerial implications.

Copyright © 2008 John Wiley & Sons, Ltd.
Retaining the visitor, enhancing the experience: identifying attributes of choice in repeat museum visitation
Authors: Burton Christine , Louviere Jordan , Young Louise
Published: December 2008

How people make choices in relation to cultural and leisure consumption has been explored from the viewpoint of motivation, lifestyle segmentation, and lifecycle. Little is known about the specific characteristics associated with choices to visit, re‐visit, or not to visit a museum. Understanding characteristics of choice, developing incentives, bundled packages, and levels of pricing is an essential element in marketing strategies for museums operating in a competitive leisure marketplace. However, determining what really matters to cultural consumers is complex and methodologies to assist in unraveling such complexities are not easily identified. This study aimed to address ways in which people respond to specific incentives as influences in choosing museum visitation. The study was conducted in two major museums in Australia to determine how useful choice modeling is in identifying features that matter to cultural consumers. The results suggest that choice modeling has much to offer in relation to understanding the benefits people are seeking from a museum experience as well as offering strategic insight into potential collaborative ventures and re‐combinations of existing museum products and services.

Copyright © 2008 John Wiley & Sons, Ltd.
Characterization of gelatin nanofibers electrospun using ethanol/formic acid/water as a solvent
Authors: Chen Hsin‐Chieh , Jao Win‐Chun , Yang Ming‐Chien
Published: December 2008

Gelatin nanofibers were prepared via electrospinning using aqueous solutions of formic acid and ethanol as the solvent instead of cytotoxic solvents. The resulting mat was further crosslinked with glutaraldehyde (GTA). The influence of the storing time on the viscosity and gel point of the solution was investigated. The gelatin nanofibers were examined using a field emission scanning electron microscope (FESEM) for the fiber size and morphology. The lowest diameter of gelatin fiber (85 nm, without beads) was achieved when the gelatin concentration was 20 wt% and electrospinning was conducted with a voltage of 20 kV over a distance of 10 cm at ambient temperature. The results from differential scanning calorimetry (DSC) showed that the softening temperature of gelatin nanofibers crosslinked with GTA was elevated. In addition, GTA‐crosslinked gelatin nanofibers exhibited cell compatibility for mouse mesangial cells (CRL 1927). Copyright © 2008 John Wiley & Sons, Ltd.
Preparation and characterization of phosphorus‐containing Mannich‐type bases as curing agents for epoxy resin
Authors: Liu Huan , Xu Kai , Ai Hao , Zhang Liangliang , Chen Mingcai
Published: December 2008

Two novel phosphorus‐containing Mannich‐type bases, [(2‐{[(diethoxy‐phosphoryl)‐phenyl‐methyl]‐amino}‐ ethylamino)‐phenyl‐methyl]‐phosphonic acid diethyl ester (PEDA) and ({2‐[2‐(2‐{[(diethoxy‐phosphoryl)‐phenyl‐methyl]– amino}‐ethylamino)‐ethylamino]‐ethylamino}‐phenyl‐methyl)‐phosphonic acid diethyl ester (PTTA) were prepared and employed as curing agents in an attempt to prepare flame retardant epoxy systems. Through a curing reaction, phosphorus was incorporated in the backbone of the epoxy polymer. The processing characteristic of these systems was studied in terms of gel time at different temperatures. Thermal and flame retardancy properties of the cured epoxy thermosets were characterized by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and flammability test. The degradation activation energy was calculated by Kissinger's model. The results showed that the gel time of the phosphorus‐containing epoxy systems was prolonged; the glass transition temperature (Tg) was increased due to the introduction of phosphorus and the initial degradation activation energy of phosphorus‐containing epoxy systems was lower than phosphorus‐free epoxy systems. High char yield (23–27 wt%) and limiting oxygen index (LOI) values of 28–30 were observed for the phosphorus‐containing epoxy thermosets, indicating their improvement in flame retardancy. Copyright © 2008 John Wiley & Sons, Ltd.
Ccl2/Mcp‐1 blockade reduces glomerular and interstitial macrophages but does not ameliorate renal pathology in collagen4A3‐deficient mice with autosomal recessive Alport nephropathy
Authors: Clauss Sebastian , Gross Oliver , Kulkarni Onkar , Avila‐Ferrufino Alejandro , Radomska Ewa , Segerer Stephan , Eulberg Dirk , Klussmann Sven , Anders Hans‐Joachim
Published: December 2008

Lack of the α3 or α4 chain of type IV collagen (COL4) causes autosomal recessive Alport nephropathy in humans and mice that is characterized by progressive glomerulosclerosis and tubulointerstitial disease. Renal pathology is associated with chemokine‐mediated macrophage infiltrates but their contribution to the progression of Alport nephropathy is unclear. We found Ccl2 to be expressed in increasing amounts during the progression of nephropathy in Col4a3‐deficient mice; hence, we blocked Ccl2 with anti‐Ccl2 Spiegelmers, biostable L‐enantiomeric RNA aptamers suitable for in vivo applications. Ccl2 blockade reduced the recruitment of ex vivo‐labelled macrophages into kidneys of Col4a3‐deficient mice. We therefore hypothesized that a prolonged course of Ccl2 blockade would reduce renal macrophage counts and prevent renal pathology in Col4a3‐deficient mice. Groups of Col4a3‐deficient mice received subcutaneous injections of either an anti‐mCcl2 Spiegelmer or non‐functional control Spiegelmer on alternate days, starting from day 21 or 42 of age. Glomerular and interstitial macrophage counts were found to be reduced with Ccl2 blockade by 50% and 30%, respectively. However, this was not associated with an improvement of glomerular pathology, interstitial pathology, or of overall survival of Col4a3‐deficient mice. We conclude that Ccl2 mediates the recruitment of glomerular and interstitial macrophages but this mechanism does not contribute to the progression of Alport nephropathy in Col4a3‐deficient mice. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Proteomic analysis of Aspergillus nidulans cultured under hypoxic conditions
Authors: Shimizu Motoyuki , Fujii Tatsuya , Masuo Shunsuke , Fujita Kensaku , Takaya Naoki
Published: December 2008

The fungus Aspergillus nidulans reduces nitrate to ammonium and simultaneously oxidizes ethanol to acetate to generate ATP under hypoxic conditions in a mechanism called ammonia fermentation (Takasaki, K. et al.. J. Biol. Chem. 2004, 279, 12414–12420). To elucidate the mechanism, the fungus was cultured under normoxic and hypoxic (ammonia fermenting) conditions, intracellular proteins were resolved by 2‐DE, and 332 protein spots were identified using MALDI MS after tryptic digestion. Alcohol and aldehyde dehydrogenases that play key roles in oxidizing ethanol were produced at the basal level under hypoxic conditions but were obviously provoked by ethanol under normoxic conditions. Enzymes involved in gluconeogenesis, as well as the tricarboxylic and glyoxylate cycles, were downregulated. These results indicate that the mechanism of fungal energy conservation is altered under hypoxic conditions. The results also showed that proteins in the pentose phosphate pathway as well as the metabolism of both nucleotide and thiamine were upregulated under hypoxic conditions. Levels of xanthine and hypoxanthine, deamination products of guanine and adenine were increased in DNA from hypoxic cells, indicating an association between hypoxia and intracellular DNA base damage. This study is the first proteomic comparison of the hypoxic responses of A. nidulans.
Adaptation of the rat cardiac proteome in response to intensity‐controlled endurance exercise
Authors: Burniston Jatin G.
Published: December 2008

Endurance training improves cardiac function and protects against heart disease. The rodent intensity‐controlled running model replicates endurance exercise in humans and can be used to investigate molecular adaptations in the heart. Rats (n = 6, 280 ± 3 g) performed exercise tests to measure their peak oxygen uptake ($\ { \dot V} { O}_{ 2} { peak}$) and training was prescribed at 70–75% $\ { \dot V} { O}_{ 2} { peak}$ for 30 min, 4 days/wk. Hearts were isolated 4 h after a final $\ { \dot V} { O}_{ 2} { peak}$ test and left ventricle proteomes compared to weight‐matched control animals (n = 6, 330 ± 2 g) using differential analysis of 2‐D gels. Proteins were identified by searching MS and MS/MS spectra against Swiss‐Prot using MASCOT (www.matrixscience.com). Average $\ { \dot V} { O}_{ 2} { peak}$ increased 23% (p = 0.008) over the 6‐week regimen and 23 gel spots differed (p<0.05) between exercised and control hearts. Expression of myofibrillar proteins (e.g. α‐myosin heavy chain and cardiac α‐actin) and proteins associated with fatty acid metabolism (e.g. heart fatty acid binding protein, acetyl coenzyme A dehydrogenase and mitochondrial thioesterase‐1) increased. In addition, this work discovered a novel increase in phosphorylation of heat shock protein 20 at serine 16. Previously this modification has been associated with improved cardiomyocyte contractility and protection against apoptosis.
On the estimation of false positives in peptide identifications using decoy search strategy
Authors: Shen Changyu , Sheng Quanhu , Dai Jie , Li Yixue , Zeng Rong , Tang Haixu
Published: December 2008

False positive control/estimate in peptide identifications by MS is of critical importance for reliable inference at the protein level and downstream bioinformatics analysis. Approaches based on search against decoy databases have become popular for its conceptual simplicity and easy implementation. Although various decoy search strategies have been proposed, few studies have investigated their difference in performance. With datasets collected on a mixture of model proteins, we demonstrate that a single search against the target database coupled with its reversed version offers a good balance between performance and simplicity. In particular, both the accuracy of the estimate of the number of false positives and sensitivity is at least comparable to other procedures examined in this study. It is also shown that scrambling while preserving frequency of amino acid words can potentially improve the accuracy of false positive estimate, though more studies are needed to investigate the optimal scrambling procedure for specific condition and the variation of the estimate across repeated scrambling.
Proteomic analysis of membrane proteins expressed specifically in pluripotent murine embryonic stem cells
Authors: Intoh Atsushi , Kurisaki Akira , Yamanaka Yuko , Hirano Hisashi , Fukuda Hiroyuki , Sugino Hiromu , Asashima Makoto
Published: December 2008

Embryonic stem cells (ESCs) are established from the inner cell mass of preimplantation embryos, are capable of self‐renewal, and exhibit pluripotency. Given these unique properties, ESCs are expected to have therapeutic potential in regenerative medicine and as a powerful tool for in vitro differentiation studies of stem cells. Various growth factors and extracellular matrix components regulate the pluripotency and differentiation of ESC progenies. Thus, the cell surface receptors that bind these regulatory factors are crucial for the precise regulation of stem cells. To identify membrane proteins that are involved in the regulation of pluripotent stem cells, the membrane proteins of murine ESCs cultured with or without leukemia inhibitory factor (LIF) were purified and analyzed by quantitative proteomics. 2‐D PAGE‐based analysis using fluorescently labeled proteins and shotgun‐based analysis with isotope‐labeled peptides identified 338 proteins, including transmembrane, membrane‐binding, and extracellular proteins, which were expressed specifically in pluripotent or differentiated murine ESCs. Functions of the identified proteins revealed cell adhesion molecules, channels, and receptors, which are expected to play important roles in the maintenance of murine ESC pluripotency. Membrane proteins that are expressed in pluripotent ESCs but not in differentiated cells such as Slc16a1 and Bsg could be useful for the selection of the stem cells in vitro.
Dopamine agonists and impulse control disorders in Parkinson's disease
Authors: MacMahon Douglas G , Macphee Graeme JA
Published: December 2008

This issue of Progress features two case reports of patients who developed impulse control disorders following treatment with a dopamine agonist for Parkinson's disease, each with serious and lasting consequences. Here, Dr MacMahon and Dr Macphee shed more light on this group of medication‐related disorders, the risk factors for their development and management strategies for both prevention and treatment. Copyright © 2008 Wiley Interface Ltd
A solvatochromic study of silicates and borate containing 4‐nitrocatechol ligands
Authors: Riedel Franziska , Spange Stefan
Published: December 2008

Solvatochromism of 4‐nitrocatechol (1), tetra‐n‐butylammonium 2‐hydroxy‐4‐nitrophenolate (2), sodium tris(4‐nitrobenzene‐1,2‐diolato)silicate (3a), tetra‐n‐butylammonium tris(4‐nitrobenzene‐1,2‐diolato)silicate (3b), pyrrolidinium tris(4‐nitrobenzene‐1,2‐diolato)silicate (3c), (3‐amino‐1‐propyl)‐bis(4‐nitrobenzene‐1,2‐diolato)silicate (4a), and (N,N‐diethyl‐3‐amino‐1‐propyl)‐bis(4‐nitrobenzene‐1,2‐diolato)silicate (4b) as well as potassium bis(4‐nitrobenzene‐1,2‐diolato)borate (5) has been studied in a set of common solvents. The origin of the solvent‐induced UV/vis band shifts of 1–3c, and 5 has been determined by means of Linear Solvation Energy Relationship (LSER) using the empirical Kamlet–Taft and Catalán solvent parameter sets, respectively. The solvent‐induced UV/vis band shift of the negatively charged moiety of all solvatochromic dyes studied is mainly a function of the hydrogen‐bond donor (HBD) strength and the dipolarity/polarizability of the solvent as shown by multiple regression analyses. HBD solvents cause a hypsochromic shift of the UV/vis band due to specific solvation of the anion site. Oppositely, increasing dipolarity/polarizability of the solvent induces a bathochromic shift of the UV/vis absorption band. The donor strength of the solvent has an influence on the UV/vis band shift since ion pair formation occurs in solvents of low relative permittivity. This is shown by the impact of the counter ion of sodium tris(4‐nitrobenzene‐1,2‐diolato)silicate (3a) compared to tetra‐n‐butylammonium tris(4‐nitrobenzene‐1,2‐diolato)silicate (3b). The influence of the counter ion on the position of the UV/vis absorption band occurs in the same way as HBD solvents do. Na+ and the pyrrolidinium ion, respectively, have a stronger influence than the tetra‐n‐butylammonium ion on the solvatochromic band shift due to the stronger cation–anion interaction. Copyright © 2008 John Wiley & Sons, Ltd.
Clinical utility of five genetic variants for predicting prostate cancer risk and mortality
Authors: Salinas Claudia A. , Koopmeiners Joseph S. , Kwon Erika M. , FitzGerald Liesel , Lin Daniel W. , Ostrander Elaine A. , Feng Ziding , Stanford Janet L.
Published: December 2008

BACKGROUND

A recent report suggests that the combination of five single‐nucleotide polymorphisms (SNPs) at 8q24, 17q12, 17q24.3 and a family history of the disease may predict risk of prostate cancer. The present study tests the performance of these factors in prediction models for prostate cancer risk and prostate cancer‐specific mortality.

METHODS

SNPs were genotyped in population‐based samples from Caucasians in King County, Washington. Incident cases (n = 1,308), aged 35–74, were compared to age‐matched controls (n = 1,266) using logistic regression to estimate odds ratios (OR) associated with genotypes and family history. Cox proportional hazards models estimated hazard ratios for prostate cancer‐specific mortality according to genotypes.

RESULTS

The combination of SNP genotypes and family history was significantly associated with prostate cancer risk (ptrend = 1.5 × 10−20). Men with ≥5 risk factors had an OR of 4.9 (95% CI 1.6–18.5) compared to men with none. However, this combination of factors did not improve the ROC curve after accounting for known risk predictors (i.e., age, serum PSA, family history). Neither the individual nor combined risk factors was associated with prostate cancer‐specific mortality.

CONCLUSION

Genotypes for five SNPs plus family history are associated with a significant elevation in risk for prostate cancer and may explain up to 45% of prostate cancer in our population. However, they do not improve prediction models for assessing who is at risk of getting or dying from the disease, once known risk or prognostic factors are taken into account. Thus, this SNP panel may have limited clinical utility. Prostate 69:363–372, 2009. © 2008 Wiley‐Liss, Inc.
Role of side chains in collagen triple helix stabilization and partner recognition
Authors: Berisio Rita , De Simone Alfonso , Ruggiero Alessia , Improta Roberto , Vitagliano Luigi
Published: December 2008

Collagen is a widespread protein family involved in a variety of biological processes. The complexity of collagen and its fibrous nature prevent detailed investigations on the full‐length protein. Reductionist approaches conducted by dissecting the protein complexity through the use of model peptides have proved to be quite effective. There are, however, several issues regarding structure–stability relationships, aggregation in higher‐order assemblies, and partner recognition that are still extensively investigated. In this review, we discuss the role that side chains play in triple helix stabilization and in partner recognition. On the basis of recent literature data, we show that collagen triple helix stability is the result of the interplay of different factors. As a general trend, interactions established by amino/imino acid side chains within the triple helix scaffold effectively modulate the intrinsic residue propensity for this common structural motif. The use of peptide models has also highlighted the role that side chains play in collagen self‐association and in its interactions with receptors. Valuable examples in these fields are illustrated. Finally, future actions required to obtain more detailed information on the structure and the function of this complex protein are also delineated. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Near‐field laser ablation inductively coupled plasma mass spectrometry: a novel elemental analytical technique at the nanometer scale
Authors: Zoriy Myroslav V. , Becker J. Sabine
Published: December 2008

An analytical technique utilizing a near‐field effect (to enhance the incident light energy on the thin tip of an Ag needle) in a laser ablation inductively coupled plasma mass spectrometry (NF‐LA‐ICP‐MS) procedure was developed. To produce the thin needles with a tip diameter in the hundreds of nm range a robust needle etching procedure was established. The ‘sample‐to‐tip’ distance was controlled via the measurement of a tunnel current between the needle and sample surface. The NF‐LA‐ICP‐MS technique thus developed was applied for the analysis of copper isotopic standard reference material NIST SRM 976 and tungsten‐molybdenum alloy NIST SRM 480 in the nm resolution range. The observed craters ranged from 200 nm to about 2 µm in diameter and were dependent on the needle used as well as on the ‘sample‐to‐tip’ distance. The mass spectrometric measurements of 63Cu+ ion intensity on NIST SRM 976 showed that using near‐field enhancement in laser ablation allowed a roughly 6‐fold increase in the ion intensity of the analyte when the needle was about 100 nm (and below) from the surface, in contrast to when it was far away (e.g. 10 µm) from the sample. The relative standard deviation (RSD) of the 65Cu+/63Cu+ isotopic ratio measurements by NF‐LA‐ICP‐MS was 3.9% (n = 9). The detection efficiencies obtained for the compared LA‐ICP‐MS and NF‐LA‐ICP‐MS methods were found to be 4.6 * 10−3 counts per second (cps)/ablated atom and 2.7 * 10−5 cps/ablated atom, respectively. Copyright © 2008 John Wiley & Sons, Ltd.
Electron capture dissociation of peptide hormone changes upon opening of the tocin ring and complexation with transition metal cations
Authors: van der Burgt Yuri E. M. , Palmblad Magnus , Dalebout Hans , Heeren Ron M. A. , Deelder André M.
Published: December 2008

Electron capture dissociation (ECD) is an analytical technique in mass spectrometry (MS) that allows detailed structural study of biomolecules to gain insight in their function. In this work the ECD behavior of two peptide hormones oxytocin (OT1) and vasopressin (VP1) was studied. The results of OT1 and VP1 were compared to structural analogues OT2 and VP2, which have similar amino acid sequences but lack the tocin ring. The ECD results showed that both the fragment type (c/z versus b/y) and the cleavage sites (ring versus tail) changed upon opening of the tocin ring. All four peptides were complexed with three different transition metal cations (Zn2+, Ni2+ and Cu2+) and the ECD results were compared to those obtained from the doubly protonated species. The use of various metal ions yielded different cleavages sites within the same peptide. This can be an effect of the metal ion itself, or a consequence of a change in conformation as was suggested earlier. In addition, the type of fragment ion varied for each metal‐complexed peptide, which is in agreement with previous observations. Copyright © 2008 John Wiley & Sons, Ltd.
IsoScore: automated localization of biotransformations by mass spectrometry using product ion scoring of virtual regioisomers
Authors: Leclercq Laurent , Mortishire‐Smith Russell J. , Huisman Maarten , Cuyckens Filip , Hartshorn Michael J. , Hill Alastair
Published: December 2008

We describe a novel approach for the automated localization of biotransformations, which we term IsoScore. Accurate mass measurement spectra of a parent drug and its metabolites are acquired. All virtual regioisomers of a given biotransformation are generatedin silicoby iterating over all plausible sites of oxidation around the parent drug. Each is then fragmented virtually using an exhaustive approach supplemented with chemical intelligence. Each fragment is scored based on the likelihood that it can be formed from the precursor structure. The fragment library of each virtual isomer is then compared with the experimentally observed ions. The likelihood that a regioisomer explains the observed fragmentation data is contained in its cumulated score. We include additional weightings, which take into account the level of similarity between the mass spectra of the metabolite and the parent compound.

This concept was tested on a variety of metabolites from different chemical platforms formed via single biotransformations. For a very large proportion of the metabolites, IsoScore correctly located the biotransformation to the expected position. All ions above a defined threshold in the spectrum are used to contribute to the score with no predisposition to ignore minor ions or to weight conclusions based on readily interpretable fragments. The approach is found to be most successful when differential scoring is observed between related ions in the parent and the metabolite. Further improvements in the scoring function will result in increased differentiation between likely and unlikely structures, even when the parent and the metabolite spectra show little similarity. Copyright © 2008 John Wiley & Sons, Ltd.
Comparison of collision‐ versus electron‐induced dissociation of sodium chloride cluster cations
Authors: Feketeová Linda , O'Hair Richard A. J.
Published: December 2008

The collision‐induced dissociation (CID) and electron‐induced dissociation (EID) spectra of the [(NaCl)m(Na)n]n+ clusters of sodium chloride have been examined in a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer. For singly charged cluster ions (n = 1), mass spectra for CID and EID of the precursor exhibit clear differences, which become more pronounced for the larger cluster ions. Whereas CID yields fewer product ions, EID produces all possible [(NaCl)xNa]+ product ions. In the case of doubly charged cluster ions, EID again leads to a larger variety of product ions. In addition, doubly charged product ions have been observed due to loss of neutral NaCl unit(s). For example, EID of [(NaCl)11(Na)2]2+ leads to formation of [(NaCl)10(Na)2]2+, which appears to be the smallest doubly charged cluster of sodium chloride observed experimentally to date. The most abundant product ions in EID spectra are predominantly magic number cluster ions. Finally, [(NaCl)m(Na)2]+. radical cations, formed via capture of low‐energy electrons, fragment via the loss of [(NaCl)n(Na)]. radical neutrals. Copyright © 2008 John Wiley & Sons, Ltd.
Evaluation of equine urine reactivity towards phase II metabolites of 17‐hydroxy steroids by liquid chromatography/tandem mass spectrometry
Authors: Fidani M. , Gamberini M.C. , Pasello E. , Palazzoli F. , De Iuliis P. , Montana M. , Arioli F.
Published: December 2008

Proper storage conditions of biological samples are fundamental to avoid microbiological contamination that can cause chemical modifications of the target analytes. A simple liquid chromatography/tandem mass spectrometry (LC/MS/MS) method through direct injection of diluted samples, without prior extraction, was used to evaluate the stability of phase II metabolites of boldenone and testosterone (glucuronides and sulphates) in intentionally poorly stored equine urine samples. We also considered the stability of some deuterated conjugated steroids generally used as internal standards, such as deuterated testosterone and epitestosterone glucuronides, and deuterated boldenone and testosterone sulphates. The urines were kept for 1 day at room temperature, to mimic poor storage conditions, then spiked with the above steroids and kept at different temperatures (−18°C, 4°C, room temperature). It has been possible to confirm the instability of glucuronide compounds when added to poorly stored equine urine samples. In particular, both 17β‐ and 17α‐glucuronide steroids were exposed to hydrolysis leading to non‐conjugated steroids. Only 17β‐hydroxy steroids were exposed to oxidation to their keto derivatives whereas the 17α‐hydroxy steroids were highly stable. The sulphate compounds were completely stable. The deuterated compounds underwent the same behaviour as the unlabelled compounds. The transformations were observed in urine samples kept at room temperature and at a temperature of 4°C (at a slower rate). No modifications were observed in frozen urine samples. In the light of the latter results, the immediate freezing at −18°C of the collected samples and their instant analysis after thawing is the proposed procedure for preventing the transformations that occur in urine, usually due to microbiological contamination. Copyright © 2008 John Wiley & Sons, Ltd.
An anonymous on‐demand source routing in MANETs
Authors: Zou Chao , Chigan Chunxiao
Published: December 2008

Due to the unique features of mobilead hocnetworks (MANETs), traditional wired anonymous protocols cannot be directly adopted in MANETs. On the other hand, skillful as they are, existing MANET anonymous routing protocols are often inherited from traditional routing protocols by modifying the content of routing packets of the baseline MANET routing protocols, which causes themselves subjected to certain inherent defects. This paper proposes a novel anonymous on‐demand source routing (AODSR) protocol, which is a scalable distributed solution to achieve sender, receiver, and sender–receiver relation anonymity in MANETs. In AODSR, the route discovery process is not controlled by the initiator/target node, but controlled by a series of random residual‐hop numbers. This not only eliminates different protocol behaviors between the initiator/target node and intermediate nodes, but also avoids the flooding of routing packets. With the aid of the ‘buddy’ group strategy, the anonymity is further reinforced. Based on our security analysis, the peculiar reachability attack caused by the broadcast nature of wireless networks and the shielding attack caused by the hidden‐terminal problem, which are often ignored by existing anonymous MANET routing protocols, are also countered against by AODSR. Theoretical analysis and simulation shows that AODSR achieves high degree of anonymity while requiring low computational complexity and communication overhead. Copyright © 2008 John Wiley & Sons, Ltd.
HAADF‐STEM observation of Au nanoparticles on TiO2
Authors: Akita T. , Tanaka K. , Kohyama M. , Haruta M.
Published: December 2008

Gold nanoparticles deposited on a TiO2 single‐crystalline substrate as model structure of Au/TiO2 catalysts were observed by HAADF‐STEM (high‐angle annular dark field scanning transmission electron microscope) to investigate the interface structure. The atomic columns of Au and Ti were clearly identified, and the distance between the Au and Ti layers at the interface with the relationship of Au(111)[1–10]//TiO2(110)[001] was estimated as 0.33 nm. The interface structure was discussed from the viewpoint of the status of oxygen atoms. Copyright © 2008 John Wiley & Sons, Ltd.
Sample size determination for constrained longitudinal data analysis
Authors: Lu Kaifeng , Mehrotra Devan V. , Liu Guanghan
Published: December 2008

The longitudinal data analysis model proposed by Liang and Zeger (Sankhyā: Indian J. Stat. Ser. B 2000; 62:134–148) uses the baseline as well as postbaseline values as the dependent variables, and the baseline mean responses are constrained to be the same across treatment groups due to randomization. Compared with the conventional longitudinal analysis of covariance, this approach can correctly estimate the variance of within‐group mean changes and achieve the specified coverage probabilities. General results on the sample size and power calculations for this model in the presence of missing data are obtained. The sample size relationship between the constrained and unconstrained longitudinal data analysis is established. Simple expressions for sample size calculation are obtained for the compound symmetry and first‐order autoregressive correlation structures. The sensitivity of the sample size requirement to the configuration of correlation structure and retention pattern is assessed. The performance of several ad hoc approximations for longitudinal data analysis sample size calculation is evaluated. Simulation studies are conducted to assess the validity of the proposed sample size formulas with deviation from normality. The sample size formulas are also illustrated in detail using real clinical trial data. Copyright © 2008 John Wiley & Sons, Ltd.
Particle Size, Surface Coating, and PEGylation Influence the Biodistribution of Quantum Dots in Living Mice
Authors: Schipper Meike L. , Iyer Gopal , Koh Ai Leen , Cheng Zhen , Ebenstein Yuval , Aharoni Assaf , Keren Shay , Bentolila Laurent A. , Li Jianquing , Rao Jianghong , Chen Xiaoyuan , Banin Uri , Wu Anna M. , Sinclair Robert , Weiss Shimon , Gambhir Sanjiv S.
Published: December 2008

This study evaluates the influence of particle size, PEGylation, and surface coating on the quantitative biodistribution of near‐infrared‐emitting quantum dots (QDs) in mice. Polymer‐ or peptide‐coated64Cu‐labeled QDs 2 or 12 nm in diameter, with or without polyethylene glycol (PEG) of molecular weight 2000, are studied by serial micropositron emission tomography imaging and region‐of‐interest analysis, as well as transmission electron microscopy and inductively coupled plasma mass spectrometry. PEGylation and peptide coating slow QD uptake into the organs of the reticuloendothelial system (RES), liver and spleen, by a factor of 6–9 and 2–3, respectively. Small particles are in part renally excreted. Peptide‐coated particles are cleared from liver faster than physical decay alone would suggest. Renal excretion of small QDs and slowing of RES clearance by PEGylation or peptide surface coating are encouraging steps toward the use of modified QDs for imaging living subjects.
Comparative mechanisms of zearalenone and ochratoxin A toxicities on cultured HepG2 cells: Is oxidative stress a common process?
Authors: El Golli Bennour Emna , Bouaziz Chayma , Ladjimi Moncef , Renaud Flore , Bacha Hassen
Published: December 2008

Zearalenone (ZEN) and Ochratoxin A (OTA) are structurally diverse fungal metabolites that can contaminate feed and foodstuff and can cause serious health problems for animals as well as for humans. In this study, we get further insight of the molecular aspects of ZEN and OTA toxicities in cultured human HepG2 hepatocytes. In this context, we have monitored the effects of ZEN and OTA on (i) cell viability, (ii) heat shock protein (Hsp) 70 and Hsp 27 gene expressions as a parameter of protective and adaptive response, (iii) oxidative damage, and (iv) cell death pathways. Our results clearly showed that both ZEN and OTA inhibit cell proliferation. For ZEN, a significant induction of Hsp 70 and Hsp 27 was observed. In the same conditions, ZEN generated an important amount of reactive oxygen species (ROS). Antioxidant supplements restored the major part of cell mortality induced by ZEN. However, OTA treatment downregulated Hsp 70 and Hsp 27 protein and mRNA levels and did not induce ROS generation. Antioxidant supplements did not have a significant effect on OTA‐induced cell mortality. Using another cell system (Vero monkey kidney cells), we demonstrated that OTA downregulates three members of HSP 70 family: Hsp 70, Hsp 75, and Hsp 78. Our findings showed that oxidative damage seemed to be the predominant toxic effect for ZEN, while OTA toxicity seemed to be rather because of the absence of Hsps protective response. Furthermore, the two mycotoxins induced an apoptotic cell death. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Malathion‐induced alteration of the antioxidant defence system in kidney, gill, and intestine of Carassius auratus gibelio
Authors: Huculeci Radu , Dinu Diana , Staicu Andreea Cristina , Munteanu Maria Cristina , Costache Marieta , Dinischiotu Anca
Published: December 2008

Pesticides such as malathion, commonly used in agriculture and households, are toxic substances that lead to reactive oxygen species generation, which harms organisms. Ecotoxicological consequences of malathion, particularly its effects on antioxidants in fish, are not well understood. Thus, we investigated the effects of malathion (0.05 mg/L) on lipid peroxidation and antioxidant systems in Carassius auratus gibelio kidney, intestine, and gills following exposure times of 1, 2, 3, and 6 days. The lipid peroxidation and antioxidative defense mechanisms display different responses in investigated tissues. The lipid peroxidation was increased in all investigated tissues, especially after 1 day of malathion administration. Changes in reduced glutathione levels have been registered, mainly after 6 days of pesticide exposure. The modulation in the activities of antioxidant enzymes, catalase, gluthatione peroxidase, glutathione reductase, and glutathione‐S‐transferase was time and tissue specific. The investigated parameters can be used as biomarkers of fish exposure to malathion. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.