bluuebunny/crossref_metadata_2025_split huggingface dataset:
Socioeconomic conditions among long‐term gynaecological cancer survivors—a population‐based case–control study
Authors: Platou Toril Forbord , Skjeldestad Finn Egil , Rannestad Toril 
Published: May 2009

AbstractBackground: The population of gynaecological cancer survivors is growing, yet little is known about the effects of cancer and treatment on socioeconomic conditions well beyond the completion of therapy. The aim of this study was to investigate the socioeconomic conditions in long‐term survivors of gynaecological cancer compared with a representative group of women from the general population.Material and methods: The study comprises women aged 32–75 residing in central part of Norway and who were treated as primary cases of gynaecological cancer at the University Hospital in Trondheim, Norway (n=160), and a control group from the general population (n=493). All analyses were done by χ2 test and logistic regression.Results: Gynaecological cancer survivors scored lower on a Socioeconomic Condition Index than the control group. They had on the average a complete remission period of 12 years. Compared with the control group, they were more often disabled (p<0.01) and had lower annual household income (p<0.01). No difference was detected between the groups in ability to pay bills. More cases than controls had experienced problems assigning personal insurance (p<0.03).Conclusion: Long‐term gynaecological cancer survivors lived under poorer socioeconomic conditions, were more often disabled and had lower annual household income than the women in the control group, whereas no difference in ability to pay bills were found between the groups. In spite of poorer socioeconomic conditions, the gynaecological cancer survivors seem to adapt well to their financial situation. Copyright © 2009 John Wiley & Sons, Ltd.
A model for the interaction between NF‐kappa‐B and ASPP2 suggests an I‐kappa‐B‐like binding mechanism
Authors: Benyamini Hadar , Leonov Hadas , Rotem Shahar , Katz Chen , Arkin Isaiah T. , Friedler Assaf 
Published: May 2009

AbstractWe used computational methods to study the interaction between two key proteins in apoptosis regulation: the transcription factor NF‐κ‐B (NFκB) and the proapoptotic protein ASPP2. The C‐terminus of ASPP2 contains ankyrin repeats and SH3 domains (ASPP2ANK‐SH3) that mediate interactions with numerous apoptosis‐related proteins, including the p65 subunit of NFκB (NFκBp65). Using peptide‐based methods, we have recently identified the interaction sites between NFκBp65 and ASPP2ANK‐SH3 (Rotem et al., J Biol Chem 283, 18990–18999). Here we conducted a computational study of protein docking and molecular dynamics to obtain a structural model of the complex between the full length proteins and propose a mechanism for the interaction. We found that ASPP2ANK‐SH3 binds two sites in NFκBp65, at residues 236–253 and 293–313 that contain the nuclear localization signal (NLS). These sites also mediate the binding of NFκB to its natural inhibitor IκB, which also contains ankyrin repeats. Alignment of the ankyrin repeats of ASPP2ANK‐SH3 and IκB revealed that both proteins share highly similar interfaces at their binding sites to NFκB. Protein docking of ASPP2ANK‐SH3 and NFκBp65, as well as molecular dynamics simulations of the proteins, provided structural models of the complex that are energetically similar to the NFκB‐IκB determined structure. Our results show that ASPP2ANK‐SH3 binds NFκBp65 in a similar manner to its natural inhibitor IκB, suggesting a possible novel role for ASPP2 as an NFκB inhibitor. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Calcineurin regulatory subunit B is a unique calcium sensor that regulates calcineurin in both calcium‐dependent and calcium‐independent manner
Authors: Li Jing , Jia ZhiGuang , Zhou WenChang , Wei Qun 
Published: May 2009

AbstractCalcineurin subunit B (CNB), a regulatory subunit of calcineurin, is a member of EF‐hand calcium (Ca2+)‐binding protein superfamily. In this study, we performed phosphatase activity, pull‐down, and circular dichroism analyses, which shows Ca2+‐free CNB (apo‐CNB) is able to bind CNA (Calcineurin subunit A) and regulate its phosphatase activity, albeit to a lesser extent than Ca2+‐saturated CNB (holo‐CNB). This is supported by subsequent molecular dynamics (MD) simulations which aimed to examine calcium‐induced conformational changes of CNB, using both holo‐CNB and apo‐CNB. Based on the trajectories of MD, we found that there were no drastic changes between holo‐CNB and apo‐CNB. The modest differences seen are mainly reflected in the interhelical angles of the four EF‐hand motifs and solvent accessible surface area of the hydrophobic groove which is responsible for CNA binding. Interestingly, this hydrophobic groove was largely retained in both holo‐CNB and apo‐CNB. Comparative analyses show that the calcium‐induced conformational change in CNB is remarkably different from that of the two prototypical EF‐hand calcium‐binding proteins, namely, calmodulin and recoverin. This is the first time that CNB is shown to activate CNA in the absence of Ca2+. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Thermodynamics of zinc binding to hepatitis C virus NS3 protease: A folding by binding event
Authors: Abian Olga , Neira Jose Luis , Velazquez‐Campoy Adrian 
Published: May 2009

AbstractThe hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease is responsible for the processing of the non‐structural region of the viral precursor polyprotein in infected hepatic cells. HCV NS3 is a zinc‐dependent serine protease. The zinc ion, which is bound far away from the active site and considered to have a structural role, is essential for the structural integrity of the protein; furthermore, the ion is required for the hydrolytic activity. Consequently, the NS3 zinc binding site has been considered for a long time as a possible target for drug discovery. As a first step towards this goal, the energetics of the NS3‐zinc interaction and its effect on the NS3 conformation must be established and discussed. The thermodynamic characterization of zinc binding to NS3 protease by isothermal titration calorimetry and spectroscopy is presented here. Spectroscopic and calorimetric results suggest that a considerable conformational change in the protein is coupled to zinc binding. The energetics of the conformational change is comparable to that of the folding of a protein of similar size. Therefore, zinc binding to NS3 protease can be considered as a “folding by binding” event. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Insight into the substrate length restriction of M32 carboxypeptidases: Characterization of two distinct subfamilies
Authors: Lee Marianne M. , Isaza Clara E. , White James D. , Chen Rita P.‐Y. , Liang George F.‐C. , He Hannah T.‐F. , Chan Sunney I. , Chan Michael K. 
Published: May 2009

AbstractM32 carboxypeptidases are a distinct family of HEXXH metalloproteases whose structures exhibit a narrow substrate groove that is blocked at one end. Structural alignments with other HEXXH metalloprotease‐peptide complexes suggested an orientation in which the substrate is directed towards the back of the groove. This led us to hypothesize, and subsequently confirm that the maximum substrate length for M32 carboxypeptidases is restricted. Structural and sequence analyses implicate a highly conserved Arg at the back of the groove as being critical for this length restriction. However, the Thermus thermophilus and Bacillus subtilis M32 members lack this conserved Arg. Herein, we present the biochemical and structural characterization of these two proteins. Our findings support the important role of the conserved Arg in maintaining the length restriction, and reveal a proline‐rich loop as an alternate blocking strategy. Based on our results, we propose that M32 carboxypeptidases from Bacilli belong to a separate subfamily. Proteins 2009. © 2009 Wiley‐Liss, Inc.
A novel audit model for assessing quality in non‐regulated research
Authors: Volsen S. G. , Masson M. M. 
Published: May 2009

AbstractThe need for Quality standards in non‐regulated research is a matter of considerable current debate. Whilst a number of such guidelines have been developed over recent years, their successful implementation remains a challenge to all. In order to assess whether research standards are indeed improving on the bench following the instigation of such a quality system, a question posed by both senior management and scientists alike, an independent compliance programme is required. However, given the lack of predicate rules, naivety to audit process and general sensitivity to external scrutiny within the scientific ranks, then work in this ‘Grey Area’ generates high exposure for the conventional GLP, GCP or GMP auditor. We have developed, tried, and tested a highly effective, novel audit model for assessing the quality of non‐regulated research. This simple system can be applied successfully irrespective of scientific discipline or field. Whilst common principles will always apply during any quality system audit, the refinements and idiosyncrasies we describe here will, as we have found, help underpin success. Our intentional assumption is that this is a first time endeavour for the quality professional. Copyright © 2009 John Wiley & Sons, Ltd.
Quantitative approach to the understanding of catalytic effect of metal oxides on the desorption reaction of MgH2
Authors: Hirate H. , Saito Y. , Nakaya I. , Sawai H. , Shinzato Y. , Yukawa H. , Morinaga M. , Baba T. , Nakai H. 
Published: May 2009

AbstractThe hydrogen desorption reaction of magnesium hydride (MgH2), MgH2→Mg+H2, is accelerated by mixing catalytic metal oxides (e.g., Nb2O5). This catalytic effect of metal oxides, MxOy, is theoretically estimated in a quantitative way using atomization energy concept. The atomization energies, ΔEM for metal ion and ΔEO for oxide ion in various metal oxides are evaluated using the energy density analysis of the total energy. It is shown that the hydrogen desorption rate increases monotonously with increasing y ×ΔEO values of metal oxides. This indicates that the oxide ion in MxOy interacts mainly with hydrogen atoms in MgH2. The y × ΔEO value is a measure of the magnitude of the OH interaction operating between MxOy and MgH2, and hence, it is indeed a good parameter to show the catalytic activities of metal oxides. This approach is useful for the analysis of other catalyst and catalytic reactions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
High‐resolution soft X‐ray spectral analysis in the CK region of titanium carbide using the DV‐Xα molecular orbital method
Authors: Shimomura Kenta , Muramatsu Yasuji , Denlinger Jonathan D. , Gullikson Eric M. 
Published: May 2009

AbstractWe used the discrete variational (DV) ‐Xα method to analyze the high‐resolution soft X‐ray emission and absorption spectra in the CK region of titanium carbide (TiC). The spectral profiles of the X‐ray emission and absorption can be successfully reproduced by the occupied and unoccupied density of states (DOS), respectively, in the C2p orbitals of the center carbon atoms in a Ti62C63 cluster model, suggesting that the center carbon atom in a large cluster model expanded to the cubic‐structured 53 (= 125) atoms provides sufficient DOS for the X‐ray spectral analysis of rock‐salt structured metal carbides. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Calculation of the electronic structure of AmO2 and Pr6O11 for XANES analysis with redox property
Authors: Suzuki Chikashi , Nishi Tsuyoshi , Nakada Masami , Akabori Mitsuo , Hirata Masaru , Kaji Yoshiyuki 
Published: May 2009

AbstractWe calculated X‐ray absorption near‐edge structure (XANES) of Am LIII of AmO2 and Pr LIII of Pr6O11 using the relativistic discrete‐variational (DV)‐Xα method based on the Dirac–Slater method, and compared it with the experimental spectra. These spectra were calculated on a model of AmO2 ([AmO8]12−) and Pr6O11 ([PrO8]12−). In spite of using small cluster models, the calculated spectra were in good agreement with the experiment ones. Besides, we calculated the electronic structure of AmO2 and Pr6O11 to analyze the peak structures of XANES. From this calculation, it was found that O s, p, and f components had influence on the specific peak structures but that O d component had influence on various peak structures for AmO2 and Pr6O11. From this result, it was suggested that the change of the electronic structure of actinide 6d and O d or f was important for actinide LIII XANES corresponding to oxygen to metal ratio in the oxide nuclear fuel. On the basis of these results, we calculated the fine structures of densities of states and the transition energy from the HOMO to the white line of AmO2, UO2, and Pr6O11 and investigated redox properties of Am and U in the oxide nuclear fuel with the evaluation of validity of Pr as simulant materials of Am. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Simultaneous determination of parabens, triclosan and triclocarban in water by liquid chromatography/electrospray ionisation tandem mass spectrometry
Authors: González‐Mariño Iria , Quintana José Benito , Rodríguez Isaac , Cela Rafael 
Published: May 2009

AbstractA method for the determination of several household biocides in water by liquid chromatography/electrospray ionisation tandem mass spectrometry (LC/ESI‐MS/MS) is presented. It permits the simultaneous determination of triclosan (TCS), triclocarban (TCC) and seven parabens, including the distinction between branched and linear isomers of propyl (i‐PrP and n‐PrP) and butyl parabens (i‐BuP and n‐BuP). Prior to LC/MS/MS, analytes are preconcentrated by solid‐phase extraction (SPE) on Oasis HLB (60 mg) cartridges at natural sample pH and subsequently eluted with 4 mL of methanol. This simple SPE procedure provides extraction recoveries above 85% except for raw wastewater, where it falls to 65% for TCC. The performance of the method was tested with two triple‐quadrupole LC/MS instruments from a low/mid and mid/high market range: a Varian 1200L and an API‐4000. The latter system provided between 3 and 80 times lower limits of quantification (LOQs) than the first one, in the 0.08–0.44 ng/L range for surface water. Moreover, a comparison of matrix effects on both instruments showed a very different behaviour, particularly in the case of parabens. For these compounds signal suppression was observed in the 1200L instrument and signal enhancement with the 4000 instrument. As a result, different calibration approaches were chosen for them and this pointed to the need of matrix effect re‐evaluation in method transfer between different LC/MS systems. The application of the method to real samples showed the ubiquity of methyl paraben (MeP) and n‐PrP (at the 1–6 µg/L in raw wastewater) and the coexistence of i‐BuP and n‐BuP at similar levels (ca. 100–200 ng/L in raw wastewater). Copyright © 2009 John Wiley & Sons, Ltd.
Determination of urine melamine by validated isotopic ultra‐performance liquid chromatography/tandem mass spectrometry
Authors: Cheng Wei‐Chih , Chen Shu‐Kong , Lin Tien‐Jen , Wang I‐Jen , Kao Ya‐Min , Shih Daniel Yang‐Chih 
Published: May 2009

AbstractLittle is known about melamine (MEL) analysis in children's urine. In this study, an isotopic ultra‐performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) method was developed and systematically validated for the analysis of MEL in urine. The method is easily performed and comprises acidification, solid‐phase extraction (SPE) and UPLC/MS/MS analysis.13C3N3(15NH2)3was used as the internal standard (IS) for calibration. Transition ionsm/z127 > 85 of MEL andm/z133 > 89 of the IS were used for quantification andm/z127 > 68 of MEL was used for quantitative confirmation. Recovery and precision were assessed to guarantee the applicability of the method. The limit of quantification (LOQ) was 0.01 µg/mL while the calculated method detection limit was 0.006 µg/mL. The mean recoveries ranged from 96–99%. The method was then applied to analyze urine samples from children who had potentially consumed MEL‐tainted dairy products during screening in Taiwan. Ten nephrolithiasis cases and 20 age‐ and gender‐matched controls were selected for this study. Three out of the 10 nephrolithiasis cases had elevated levels of MEL. Comparatively, twenty age‐ and gender‐matched non‐nephrolithiasis controls consuming Taiwan brand milk powder all showed MEL levels lower than the detection limit except for two children with background levels of 0.02 µg/mL. The background level in these children urine samples was established by UPLC/MS/MS analysis. Positive results of urine MEL tests might be associated with nephrolithiasis in these candidates. Measurement of urine MEL concentration can be helpful in confirming MEL‐related nephrolithiasis, but its clinical application needs further clarification. Copyright © 2009 John Wiley & Sons, Ltd.
Unknown input reconstruction for LPV systems
Authors: Kulcsár Balázs , Bokor József , Shinar Josef 
Published: May 2009

AbstractDetection and invariant subspaces of unknown inputs' signals for linear parameter‐varying systems are examined in the paper. For a class of nonlinear system like this, the effect of unmeasured signals in parameter‐varying measurement equation at the plant output is investigated.The main contributions of the paper are the parameter‐varying extension of the pseudo‐actuation of the possible and generic unknown sensor signal and the proposition of parameter‐dependent similarity transformation. The general parameter‐varying measurement equation is casted into a parameter‐independent form by the similarity transformation, if any. Moreover, it showed that the nonlinear state transformation does not modify the output subspace spanned by the equivalent pseudo‐actuator directions.The proposed methods are illustrated by a numerical example. Copyright © 2009 John Wiley & Sons, Ltd.
Principal component analysis and dimensional analysis as materials informatics tools to reduce dimensionality in materials science and engineering
Authors: Rajan Krishna , Suh Changwon , Mendez Patricio F. 
Published: May 2009

AbstractIn engineering design, we are constantly faced with the need to describe the behavior of complex engineered systems for which there is no closed‐form solution. There is rarely a single multiscale theory or experiment that can meaningfully and accurately capture such information primarily due to the inherently multivariate nature of the variables influencing materials behavior. Seeking structure‐property relationships is an accepted paradigm in materials science, yet these relationships are often not linear, and so the challenge is to seek patterns among multiple length and time scales. In this paper, we present two separate but complementary examples of addressing the issue of high‐dimensional data in materials science in the spirit of the intellectual focus of this new journal. The first example uses principal component analysis and the second example uses statistical analysis coupled to dimensional analysis. Copyright © 2009 Wiley Periodicals, Inc., A Wiley Company
Doppler flow velocity waveforms in the embryonic chicken heart at developmental stages corresponding to 5–8 weeks of human gestation
Authors: Oosterbaan A. M. , Ursem N. T. C. , Struijk P. C. , Bosch J. G. , van der Steen A. F. W. , Steegers E. A. P. 
Published: May 2009

AbstractObjectivesTo obtain Doppler velocity waveforms from the early embryonic chicken heart by means of ultrasound biomicroscopy and to compare these waveforms at different stages of embryonic development.MethodsWe collected cardiac waveforms using high‐frequency Doppler ultrasound with a 55‐MHz transducer at Hamburger–Hamilton (HH) stages 18, 21 and 23, which are comparable to humans at 5 to 8 weeks of gestation. Waveforms were obtained at the inflow tract, the primitive left ventricle, the primitive right ventricle and at the outflow tract in 10 different embryos per stage. M‐mode recordings were collected to study opening and closure of the cushions. By exploring the temporal relationship between the waveforms, using a secondary Doppler device, cardiac cycle events were outlined.ResultsOur results demonstrate that stage‐ and location‐dependent intracardiac blood flow velocity waveforms can be obtained in the chicken embryo. The blood flow profiles assessed at the four locations in the embryonic heart demonstrated an increase in peak velocity with advancing developmental stage. In the primitive ventricle the ‘passive’ (P) filling peak decreased whereas the ‘active’ (A) filling peak increased, resulting in a decrease in P to A ratio with advancing developmental stage. M‐mode recordings demonstrated that the fractional closure time of the atrioventricular cushions increased from 20% at stage HH 18 to 60% at stage HH 23.ConclusionHigh‐frequency ultrasound biomicroscopy can be used to define flow velocity waveforms in the embryonic chicken heart. This may contribute to an understanding of Doppler signals derived from valveless embryonic human hearts at 5 to 8 weeks of gestation, prior to septation. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Tomographic ultrasound imaging of the pelvic floor: which levels matter most?
Authors: Dietz H. P. , Shek K. L. 
Published: May 2009

AbstractObjectivesTomographic ultrasound imaging has greatly simplified pelvic floor assessment. Abnormalities of the insertion of the levator ani can be documented in a single frame. In this study we aimed to determine which levels of the levator hiatus are associated with alterations in ultrasound parameters of pelvic organ support.MethodsThis was a subanalysis of a study conducted in 296 women seen before and after their first delivery. We analyzed postpartum changes in bladder neck descent and hiatal area as indicators of altered pelvic organ support. Tomographic ultrasound examination was performed on volumes obtained at maximal pelvic floor muscle contraction, at 2.5‐mm slice intervals, from 5 mm below to 12.5 mm above the plane of minimal hiatal dimensions.ResultsTwo hundred and eight recruits (70%) returned for a postnatal appointment. Of these, 130 had delivered vaginally and 26 (20%) were diagnosed with an avulsion injury. An abnormality in slices 3–8 was associated with increased bladder neck descent postpartum (P = 0.038 to P = 0.001) and increased hiatal area on Valsalva maneuver (P = 0.029 to P < 0.001). This was not the case for the two most distal slices.ConclusionsWe found no association between levator ani defects observed on tomographic ultrasound imaging below the plane of minimal hiatal dimensions and indices of increased hiatal distension or bladder neck descent on Valsalva maneuver. This implies that defects observed below this plane are either irrelevant for pelvic organ support or artifactual. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.