bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation of the rat cardiac proteome in response to intensity‐controlled endurance exercise
Authors: Burniston Jatin G. 
Published: December 2008

AbstractEndurance 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

AbstractFalse 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

AbstractEmbryonic 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

AbstractThis 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

AbstractSolvatochromism 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

AbstractBACKGROUNDA 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.METHODSSNPs 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.RESULTSThe 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.CONCLUSIONGenotypes 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

AbstractCollagen 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

AbstractAn 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

AbstractElectron 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

AbstractWe 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

AbstractThe 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

AbstractProper 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

AbstractDue 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

AbstractGold 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

AbstractThe 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.