bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a novel ligand binding site in phosphoserine phosphatase from the hyperthermophilic archaeon Thermococcus onnurineus
Authors: Jung Tae‐Yang , Kim Yae‐Sel , Oh Byoung‐Ha , Woo Euijeon 
Published: January 2013

AbstractPhosphoserine phosphatase (PSP) catalyzes the final and irreversible step of L‐serine synthesis by hydrolyzing phosphoserine to produce L‐serine and inorganic phosphate. Developing a therapeutic drug that interferes with serine production is of great interest to regulate the pathogenicity of some bacteria and control D‐serine levels in neurological diseases. We determined the crystal structure of PSP from the hyperthermophilic archaeon Thermococcus onnurineus at 1.8 Å resolution, revealing an NDSB ligand bound to a novel site that is located in a fissure between the catalytic domain and the CAP module. The structure shows a half‐open conformation of the CAP 1 module with a unique protruding loop of residues 150–155 that possesses a helical conformation in other structures of homologous PSPs. Activity assays indicate that the enzyme exhibits marginal PSP activity at low temperature but a sharp increase in the kcat/KM value, approximately 22 fold, when the temperature is increased. Structural and biochemical analyses suggest that the protruding loop in the active site might be an essential component for the regulation of the activity of PSP from hyperthermophilic T. onnurineus. Identification of this novel binding site distantly located from the catalytic site may be exploited for the development of effective therapeutic allosteric inhibitors against PSP activity. © Proteins 2013. © 2012 Wiley Periodicals, Inc.
Assessment of 3D models for allergen research
Authors: Power Trevor D. , Ivanciuc Ovidiu , Schein Catherine H. , Braun Werner 
Published: January 2013

AbstractAllergenic proteins must crosslink specific IgE molecules, bound to the surface of mast cells and basophils, to stimulate an immune response. A structural understanding of the allergen–IgE interface is needed to predict cross‐reactivities between allergens and to design hypoallergenic proteins. However, there are less than 90 experimentally determined structures available for the approximately 1500 sequences of allergens and isoallergens cataloged in the Structural Database of Allergenic Proteins. To provide reliable structural data for the remaining proteins, we previously produced more than 500 3D models using an automated procedure, with strict controls on template choice and model quality evaluation. Here, we assessed how well the fold and residue surface exposure of 10 of these models correlated with recently published experimental 3D structures determined by X‐ray crystallography or NMR. We also discuss the impact of intrinsically disordered regions on the structural comparison and epitope prediction. Overall, for seven allergens with sequence identities to the original templates higher than 27%, the backbone root‐mean square deviations were less than 2 Å between the models and the subsequently determined experimental structures for the ordered regions. Further, the surface exposure of the known IgE epitopes on the models of three major allergens, from peanut (Ara h 1), latex (Hev b 2), and soy (Gly m 4), was very similar to the experimentally determined structures. For the three remaining allergens with lower sequence identities to the modeling templates, the 3D folds were correctly identified. However, the accuracy of those models is not sufficient for a reliable epitope mapping. © Proteins 2013. © 2012 Wiley Periodicals, Inc.
Enhanced polarization switching in ferroelectric Bi0.5Na0.5TiO3 single crystals by defect control
Authors: Yanai Ken , Kitanaka Yuuki , Noguchi Yuji , Miyayama Masaru , Moriyoshi Chikako , Kuroiwa Yoshihiro , Kurushima Kousuke , Mori Shigeo 
Published: January 2013

AbstractSingle crystals of ferroelectric (Bi,Na)TiO3 (BNT) were grown by the top‐seeded solution growth (TSSG) method at a high oxygen pressure of 0.9 MPa using Pt crucibles and their conductivity (leakage current) and polarization properties were investigated at 25 °C along 〈100〉cubic. The platinum concentration ([Pt]) in BNT crystals was controlled by using different kinds of Na salts in flux. It is shown that the conductivity of BNT crystals is governed by Bi vacancies for crystals with a [Pt] less than approximately 4000 ppm and by Pt impurities for ones with a higher [Pt]. magnified imagePhoto and polarization hysteresis of a high‐quality (Bi,Na)TiO3 ferroelectric single crystal. Enhanced polarization switching (a large remanent polarization and a low coercive field) was achieved by defect control during the crystal growth.
Néel order and the destruction of localized magnetic moments in the crossover from the Mott–Heisenberg to the Slater limit
Authors: Kopeć T. K. , Zaleski T. A. 
Published: January 2013

AbstractWe study the antiferromagnetic phase of the three‐dimensional (3D) Hubbard model with nearest‐neighbor hopping on a bipartite cubic lattice. We use the quantum SU(2) × U(1) rotor approach that yields a fully self‐consistent treatment of the antiferromagnetic state that respects the symmetry properties of the model and satisfies the Mermin–Wagner theorem. As our theory describes the evolution from a Slater (U ≪ t) to a Mott–Heisenberg (U ≫ t) antiferromagnet, we present the phase diagram of the antiferromagnetic Hubbard model as a function of the crossover parameter U/t.
Specific features of sublimation growth of bulk AlN crystals on SiC wafers
Authors: Mokhov E. , Izmaylova I. , Kazarova O. , Wolfson A. , Nagalyuk S. , Litvin D. , Vasiliev A. , Helava H. , Makarov Yu. 
Published: January 2013

AbstractThe features of 2” AlN bulk crystal growth by the sublimation sandwich method (SSM) on SiC seeds in a graphite‐heated reactor are investigated. AlN growth conditions and crystal properties are compared with the results of SiC sublimation growth in the same reactor. The specifics of AlN sublimation growth, including insufficient reproducibility of results, are believed to be caused by the low sticking coefficient of molecular nitrogen and the high reactivity of Al vapors. The formation of pores in the AlN crystal is explained by selective sublimation etching of the growing surface. The negative effect of non‐optimal growth conditions and impurities on AlN crystal quality is discussed. The analysis of container materials, inert to Al vapors was carried out. Various types of TaC crucibles suitable for growth of bulk AlN crystals on SiC seeds were developed. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chemical labeling of electrochemically cleaved peptides
Authors: Roeser Julien , Alting Niels F. A. , Permentier Hjalmar P. , Bruins Andries P. , Bischoff Rainer P. H. 
Published: January 2013

RATIONALECleavage of peptide bonds C‐terminal to tyrosine and tryptophan after electrochemical oxidation may become a complementary approach to chemical and enzymatic cleavage. A chemical labeling approach specifically targeting reactive cleavage products is presented here and constitutes a promising first step towards the development of a new proteomics workflow.METHODSHexylamine was used to react with the spirolactone moieties generated after electrochemical oxidation and cleavage of tripeptides. The influence of pH and reaction time on the yield was determined and the excess of tagging reagent was optimized. Selective detection of the tagged cleavage products was achieved by precursor ion scanning in a triple quadrupole mass spectrometer.RESULTSOptimal labeling was reached under aqueous conditions when working at pH 10 with a reaction time of 0.5 min. The excess of hexylamine over spirolactone groups can be significantly decreased by working under non‐aqueous conditions in pure acetonitrile to prevent spirolactone hydrolysis. The specific formation of hexylamine‐containing y1 reporter ions generated by collision‐induced dissociation (CID) tandem mass spectrometry (MS/MS) allows for selective detection by precursor ion scanning of the cleaved and labeled peptides.CONCLUSIONSThis work presents a method for selective labeling and detection of electrochemically cleaved Tyr‐ and Trp‐containing peptides for which reaction conditions have been optimized with hexylamine as labeling agent. This workflow offers new possibilities for electrochemical oxidation, cleavage and labeling of peptides and proteins. Copyright © 2013 John Wiley & Sons, Ltd.
Does the analysis of the enantiomeric composition of clenbuterol in human urine enable the differentiation of illicit clenbuterol administration from food contamination in sports drug testing?
Authors: Thevis Mario , Thomas Andreas , Beuck Simon , Butch Anthony , Dvorak Jiri , Schänzer Wilhelm 
Published: January 2013

RATIONALEClenbuterol (4‐amino‐α‐[(tert‐butylamino)methyl]‐3,5‐dichlorobenzyl alcohol) is approved for human and veterinary use primarily for the treatment of pulmonary afflictions. Despite the authorized administration in cases of medical indications, the misuse of clenbuterol in animal husbandry as well as elite and amateur sport has frequently been reported, arguably due to growth‐promoting properties. Due to various recent incidences of doping control specimens containing clenbuterol, strategies towards the discrimination of a surreptitious application from unintended intake via animal‐derived edibles or dietary supplements were required.METHODSThe enantiomeric compositions of clenbuterol in human urine samples derived from administration studies with therapeutic amounts of the β2‐agonist and authentic doping control specimens were determined. Due to the facts that therapeutic clenbuterol consists of a racemic mixture of (+)‐ and (−)‐stereoisomers and that the first mentioned (dextrorotatory) stereoisomer is retained to a greater extent in edible animal tissue, the differentiation of a recent administration of therapeutic (and thus racemic) clenbuterol from food contamination (stereoisomerically depleted clenbuterol) was considered. Employing deuterated clenbuterol as internal standard, the target analytes were extracted from human urine by means of concerted liquid‐liquid and solid‐phase extractions and subjected to chiral liquid chromatography hyphenated to high resolution/high accuracy mass spectrometry with electrospray ionization.RESULTSBoth enantiomers of clenbuterol were baseline separated and relative abundances of corresponding labeled and unlabeled stereoisomers were determined, demonstrating that the therapeutic use of clenbuterol results in racemic mixtures in urine for at least 24 h while adverse analytical findings presumably originating from food contaminations can yield (−)‐clenbuterol‐depleted pairs of analytes.CONCLUSIONSThe determination of relative abundances of clenbuterol enantiomers can indicate the ingestion of clenbuterol via contaminated food; however, depletion of (−)‐clenbuterol in edible animal tissue is time‐dependent and thus results can still be inconclusive as to the inadvertent ingestion of clenbuterol when clenbuterol administration to animals was conducted until slaughter. Copyright © 2013 John Wiley & Sons, Ltd.
Grain‐stored energy and the propagation of intergranular corrosion in AA2xxx aluminium alloys
Authors: Zhou X. , Luo C. , Ma Y. , Hashimoto T. , Thompson G.E. , Hughes A.E. , Skeldon P. 
Published: January 2013

ABSTRACTIn the present study, intergranular corrosion (IGC) in AA2024 and AA2099 aluminium alloys was investigated. The IGC propagation path was examined using scanning and transmission electron microscopies. Further, electron backscatter diffraction was employed to investigate the relationship between the grain structure and the IGC susceptibility. It was found that IGC could occur at grain boundaries where second phase precipitates were absent. It was also revealed that IGC occurred at the grain boundaries that surround grains of relatively high‐stored energy, and corrosion was not confined within the region immediately adjacent to the grain boundaries but had developed into the grains of relatively high‐stored energy, suggesting that IGC propagated within the grains that have relatively high levels of defects. Copyright © 2013 John Wiley & Sons, Ltd.
Comparison of Nanotube–Protein Corona Composition in Cell Culture Media
Authors: Shannahan Jonathan H. , Brown Jared M. , Chen Ran , Ke Pu Chun , Lai Xianyin , Mitra Somenath , Witzmann Frank A. 
Published: January 2013

AbstractIn biological environments, nanomaterials associate with proteins forming a protein corona (PC). The PC may alter the nanomaterial's pharmacokinetics and pharmacodynamics, thereby influencing toxicity. Using a label‐free mass spectrometry‐based proteomics approach, the composition of the PC is examined for a set of nanotubes (NTs) including unmodified and carboxylated single‐ (SWCNT) and multi‐walled carbon nanotubes (MWCNT), polyvinylpyrrolidone (PVP)‐coated MWCNT (MWCNT‐PVP), and nanoclay. NTs are incubated for 1 h in simulated cell culture conditions, then washed, resuspended in PBS, and assessed by liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) for their associated PC. To determine those attributes that influence PC formation, the NTs are extensively characterized. NTs had negative zeta potentials in water (SWCNT‐COOH < MWCNT‐COOH < unmodified NTs) while carboxylation increases their hydrodynamic sizes. All NTs are also found to associate a common subset of proteins including albumin, titin, and apolipoproteins. SWCNT‐COOH and MWCNT‐COOH are found to bind the greatest number of proteins (181 and 133 respectively) compared to unmodified NTs (<100), suggesting covalent binding to protein amines. Modified NTs bind a number of unique proteins compared to unmodified NTs, implying hydrogen bonding and electrostatic interactions are involved in PC formation. PVP‐coating of MWCNT did not influence PC composition, further reinforcing the possibility of hydrogen bonding and electrostatic interactions. No relationships are found between PC composition and corresponding isoelectric point, hydropathy, or aliphatic index, implying minimal roles of hydrophobic interaction and pi‐stacking.
“Liver‐first” approach for synchronous colorectal liver metastases: is this a justifiable approach?
Authors: De Rosa A. , Gomez D. , Brooks A. , Cameron I.C. 
Published: January 2013

AbstractBackgroundTo review the outcomes of patients with synchronous colorectal liver metastases (CRLM) treated by the “liver‐first” approach.MethodsRelevant articles were reviewed from the published literature using the Medline database. The search was performed using the keywords “colorectal cancer”, “liver‐first”, “reverse strategy”, “liver metastases”, “liver resection”, and “hepatectomy”ResultsThere have been four retrospective studies that have reported the outcomes of patients with synchronous CRLM following the reverse strategy. The number of patients included ranged from 16 to 27. One study included patients with advanced rectal cancer and synchronous liver metastases only. None of the studies defined resectability for the CRLM. Overall, the morbidity and mortality rates were low. The recurrence rate ranged from 25 to 70 %. One study did not report survival data, and the overall 5 year survival ranged from 31 to 41 %.ConclusionThe “liver‐first” approach may be beneficial to a selected group of patients with synchronous CRLM. Patient selection is likely to be determined by their response to down‐staging chemotherapy with or without biological agents.
The Multisurface Obstacle Test for Older Adults (MSOT): development and reliability of a novel test for older adults
Authors: Morat Tobias , Kroeger Daniela , Mechling Heinz 
Published: January 2013

Abstract
Locomotion is an essential component of independence and well-being at old age. Performance deficits in the gait of older adults most often become evident on multisurface and varying terrains. Research results substantiate that falls occur in everyday movement situations that are characterized by instability. A test track, the Multisurface Obstacle Test for Older Adults (MSOT), was developed to diagnose individual performance. The 10-m track consists of different obstacles and varying surfaces, which represent everyday movement situations in a compact way. Twenty-nine untrained, healthy older adults (11 men, 18 women) were tested on three different days at 1-week intervals in a test–retest design by the same conductor. Mean age of the participants was 68.8 ± 5.3 years with a mean body mass index of 24.4 ± 2.5 kg/m2. The measured outcome variable was the required time (seconds) on the MSOT. The feasibility for the tested sample of untrained older adults was very good. The MSOT was undertaken safely by the participants, and no falls occurred. The range of the mean for time was between 8.12 ± 1.53 s and 9.00 ± 1.62 s. Regarding intertrial reliability, mean differences (MD) of −3.39 to −5.52 % and coefficients of variation (CV) of 2.72 to 4.19 % between the first and second trials and MD of −0.69 to −0.85 % and CV of 2.57 to 4.54 % over the three test sessions were observed. The correlation coefficients between the sessions were .92–.98. There were significant differences (p < .05) between the first and second trials of each session and between the first and second sessions. The smallest detectable differences (SDD) revealed that a small improvement is enough to detect changes in performance in the MSOT. Selecting tasks from real-life situations of older adults contributes to substantiate practical usability of the MSOT. The measured time on the MSOT showed high relative and absolute reliability in the target group of older adults between 60 and 80 years.
Rheological Behavior of Selected Water‐Nonionic–Anionic Surfactant Quasi‐ternary Systems
Authors: Chruściel Arkadiusz 
Published: January 2013

AbstractThe results of studies on the rheological behavior of ternary mixtures comprising water, linear alkylbenzenesulfonic acid, and a non‐ionic surfactant from a group comprising ethoxylated fatty acid methyl esters are presented in this paper. In the latter group, those examined include ethoxylated rapeseed and coconut fatty acid methyl esters, and ethoxylated lauryl acid methyl ester. The flowing curves, effect of temperature on viscosity, as well as the relationship between viscosity and composition of the examined ternary systems were studied. As a practical objective, the studies were intended to utilize the findings for optimizing unit operations which are applied in the process of technology to make washing powder formulations.
Fatty Acid Composition of Irvingia gabonensis and Treculia africana Seed Lipids and Phospholipids
Authors: Ifeduba Ebenezer A. , Awachie Mabel N. , Sabir Jamal S. M. , Akoh Casimir C. 
Published: January 2013

AbstractLipid compositions of two non‐conventional oilseeds (Irvingia gabonensis and Treculia africana) were studied. Total lipids were extracted by the Folch method and phospholipids were isolated by solid phase extraction. Fatty acid compositions of total lipids and phospholipids were determined by gas chromatography. Phospholipid classes and tocopherols were quantified by HPLC. The major fatty acids in I. gabonensis seed total lipids were myristic (41.4–48.9 %) and lauric (39.8–46.8 %) while those in T. africana seed were linoleic (29.1–31.4 %) and oleic (22.9–25.9 %). The principal fatty acid at the sn‐2 position of I. gabonensis seed triacylglycerols was myristic (49.5 %) while that of T. africana was linoleic (50.6 %). Phospholipid content of crude T. africana seed oil was 3.3 % and that of I. gabonensis was 0.1–0.3 %. The composition and distribution of saturated fatty acids in I. gabonensis seed lipids suggest that it may contribute to cardiovascular disease risk factors among the Igbo people in Nigeria that use the seed as food ingredient.
Associations among bullying, cyberbullying, and suicide in high school students
Authors: Bauman Sheri , Toomey Russell B. , Walker Jenny L. 
Published: January 2013

ABSTRACTThis study examined associations among depression, suicidal behaviors, and bullying and victimization experiences in 1491 high school students using data from the 2009 Youth Risk Behavior Survey. Results demonstrated that depression mediated the association between bullying/victimization and suicide attempts, but differently for males and females. Specifically, depression mediated the link between traditional victimization and suicide attempts similarly across gender, whereas depression mediated the link between cyber victimization and suicide attempts only for females. Similarly, depression mediated the link between traditional bullying and suicide attempts for females only. Depression did not mediate the link between cyberbullying and suicide attempts for either gender. Implications of the findings are discussed, including the importance of greater detection of depression among students involved in bullying, and the need for a suicide prevention and intervention component in anti‐bullying programs. Findings suggest that bullying prevention efforts be extended from middle school students to include high school students.
Dynamics of homeomorphisms of the torus homotopic to Dehn twists
Authors: ADDAS-ZANATA SALVADOR , TAL FÁBIO A. , GARCIA BRÁULIO A. 
Published: January 2013

AbstractIn this paper, we consider torus homeomorphisms $f$ homotopic to Dehn twists. We prove that if the vertical rotation set of $f$ is reduced to zero, then there exists a compact connected essential ‘horizontal’ set $K$, invariant under $f$. In other words, if we consider the lift $\hat {f}$ of $f$ to the cylinder, which has zero vertical rotation number, then all points have uniformly bounded motion under iterates of $\hat {f}$. Also, we give a simple explicit condition which, when satisfied, implies that the vertical rotation set contains an interval and thus also implies positive topological entropy. As a corollary of the above results, we prove a version of Boyland’s conjecture to this setting: if $f$ is area preserving and has a lift $\hat {f}$ to the cylinder with zero Lebesgue measure vertical rotation number, then either the orbits of all points are uniformly bounded under $\hat {f}$, or there are points in the cylinder with positive vertical velocity and others with negative vertical velocity.
Some properties of positive entropy maps
Authors: ARBIETO A. , MORALES C. A. 
Published: January 2013

AbstractWe prove that the stable classes for continuous maps on compact metric spaces have measure zero with respect to any ergodic invariant measure with positive entropy. Then, every continuous map with positive topological entropy on a compact metric space has uncountably many stable classes. We also prove that every continuous map with positive topological entropy of a compact metric space cannot be Lyapunov stable on its recurrent set. For homeomorphisms on compact metric spaces we prove that the sets of heteroclinic points, and sinks in the canonical coordinates case, have zero measure with respect to any ergodic invariant measure with positive entropy. These results generalize those of Fedorenko and Smital [Maps of the interval Ljapunov stable on the set of nonwandering points. Acta Math. Univ. Comenian. (N.S.)60 (1) (1991), 11–14], Huang and Ye [Devaney’s chaos or 2-scattering implies Li–Yorke’s chaos. Topology Appl.117 (3) (2002), 259–272], Reddy [The existence of expansive homeomorphisms on manifolds. Duke Math. J.32 (1965), 627–632], Reddy and Robertson [Sources, sinks and saddles for expansive homeomorphisms with canonical coordinates. Rocky Mountain J. Math.17 (4) (1987), 673–681], Sindelarova [A counterexample to a statement concerning Lyapunov stability. Acta Math. Univ. Comenian. 70 (2001), 265–268], and Zhou [Some equivalent conditions for self-mappings of a circle. Chinese Ann. Math. Ser. A12(suppl.) (1991), 22–27].