bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging considerations for in vivo 13C metabolic mapping using hyperpolarized 13C‐pyruvate
Authors: Yen Y‐F. , Kohler S.J. , Chen A.P. , Tropp J. , Bok R. , Wolber J. , Albers M.J. , Gram K.A. , Zierhut M.L. , Park I. , Zhang V. , Hu S. , Nelson S.J. , Vigneron D.B. , Kurhanewicz J. , Dirven H.A.A.M , Hurd R.E. 
Published: March 2009

AbstractOne of the challenges of optimizing signal‐to‐noise ratio (SNR) and image quality in 13C metabolic imaging using hyperpolarized 13C‐pyruvate is associated with the different MR signal time‐courses for pyruvate and its metabolic products, lactate and alanine. The impact of the acquisition time window, variation of flip angles, and order of phase encoding on SNR and image quality were evaluated in mathematical simulations and rat experiments, based on multishot fast chemical shift imaging (CSI) and three‐dimensional echo‐planar spectroscopic imaging (3DEPSI) sequences. The image timing was set to coincide with the peak production of lactate. The strategy of combining variable flip angles and centric phase encoding (cPE) improved image quality while retaining good SNR. In addition, two aspects of EPSI sampling strategies were explored: waveform design (flyback vs. symmetric EPSI) and spectral bandwidth (BW = 500 Hz vs. 267 Hz). Both symmetric EPSI and reduced BW trended toward increased SNR. The imaging strategies reported here can serve as guidance to other multishot spectroscopic imaging protocols for 13C metabolic imaging applications. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Legendre multiwavelet Galerkin method for solving the hyperbolic telegraph equation
Authors: Yousefi S. A. 
Published: March 2009

AbstractRecently, it is found that telegraph equation is more suitable than ordinary diffusion equation in modeling reaction diffusion for such branches of sciences. In this article a numerical method for solving the one‐dimensional hyperbolic telegraph equation is presented. The method is based upon Legendre multiwavelet approximations. The properties of Legendre multiwavelet are first presented. These properties together with Galerkin method are then utilized to reduce the telegraph equation to the solution of algebraic equations. Illustrative examples are included to demonstrate the validity and applicability of the technique. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2009
Effect of process variables on mechanical properties of polyurethane/clay nanocomposites
Authors: Joulazadeh Mehrnaz , Navarchian Amir. H. 
Published: March 2009

AbstractThis paper addresses the effects of operating variables on mechanical properties of polyurethane/clay nanocomposites including tensile strength, abrasion resistance, and hardness. The variables were prepolymer type, clay cation, clay content, and prepolymer–clay mixing time. The experiments were carried out based on the design of experiments using Taguchi methods. The nanocomposites were synthesized via in situ polymerization starting from two different types of prepolymers (polyether‐ and polyester‐types of polyol reacted with toluene diisocyanate), and methylene‐bis‐ortho‐chloroanilline (MOCA) as a chain extender/hardener. Montmorillonite with three types of cation (Na+, alkyl ammonium ion, and MOCA) were examined. Among the parameters studied, prepolymer type and clay cation have the most significant effects on mechanical properties. Polyester nanocomposites showed larger improvements in mechanical properties compared to polyether materials due to higher shear forces exerted by polymer matrix on clay aggregates during polymer–clay mixing. The original MMT with Na+ cation results in weak improvements in mechanical properties compared to organoclays. It is observed that the stress and elongation at break, and abrasion resistance of the nanocomposite samples can be optimized with 1.5% of clay loading. The morphology and chemical structure of the optimum sample were examined by X‐ray diffraction and FT‐IR spectroscopy, respectively. Copyright © 2009 John Wiley & Sons, Ltd.
Molecular orientation, crystallinity, and flexural modulus correlations in injection molded polypropylene/talc composites
Authors: Branciforti Marcia Cristina , Oliveira Carlos Amauri , de Sousa Jose Alexandrino 
Published: March 2009

AbstractIn order to promote better understanding of the structure‐mechanical properties relationships of filled thermoplastic compounds, the molecular orientation and the degree of crystallinity of injection molded talc‐filled isotactic polypropylene (PP) composites were investigated by X‐ray pole figures and wide‐angle X‐ray diffraction (WAXD). The usual orientation of the filler particles, where the plate planes of talc particles are oriented parallel to the surface of injection molding and influence the orientation of the α‐PP crystallites was observed. The PP crystallites show bimodal orientation in which the c‐ and a*‐axes are mixed oriented to the longitudinal direction (LD) and the b‐axis is oriented to the normal direction (ND). It was found that the preferential b‐axis orientation of PP crystallites increases significantly in the presence of talc particles up to 20 wt% in the composites and then levels‐off at higher filler content. WAXD measurements of the degree of crystallinity through the thickness of injection molded PP/talc composites indicated an increasing gradient of PP matrix crystallinity content from the core to the skin layers of the molded plaques. Also, the bulk PP crystallinity content of the composites, as determined by DSC measurements, increased with talc filler concentration. The bulk crystallinity content of PP matrix and the orientation behavior of the matrix PP crystallites and that of the talc particles in composites are influenced by the presence of the filler content and these three composite's microstructure modification factors influence significantly the flexural moduli and the mechanical stiffness anisotropy data (ELD/ETD) of the analyzed PP/talc composites. Copyright © 2009 John Wiley & Sons, Ltd.
The concept of the marginally matched subject in propensity‐score matched analyses
Authors: Austin Peter C. , Lee Douglas S. 
Published: March 2009

AbstractPropensity‐score matching is increasingly being used to reduce the impact of treatment‐selection bias when estimating causal treatment effects using observational data. Matching on the propensity score creates sets of treated and untreated subjects who have a similar distribution of baseline covariates. Propensity‐score matching frequently relies upon calipers, such that matched treated and untreated subjects must have propensity scores that lie within a specified caliper distance of each other. We define the ‘marginally matched’ subject as a subject who would be matched using the specified caliper width, but who would not have been matched had calipers with a narrower width been employed. Using patients hospitalized with an acute myocardial infarction (or heart attack) and with exposure to a statin prescription at discharge, we demonstrate that the inclusion of marginally matched subjects can have both a quantitative and qualitative impact upon the estimated treatment effect. Furthermore, marginally matched treated subjects can differ from marginally matched untreated subjects to a substantially greater degree than the differences between non‐marginally matched treated and untreated subjects in the propensity‐score matched sample. The concept of the marginally matched subject can be used as a sensitivity analysis to examine the impact of the matching method on the estimates of treatment effectiveness. Copyright © 2009 John Wiley & Sons, Ltd.
Gender differences in the psychosocial experience of parents of children with cancer: a review of the literature
Authors: Clarke Naomi E. , McCarthy Maria C. , Downie Peter , Ashley David M. , Anderson Vicki A. 
Published: March 2009

AbstractObjective: To build a descriptive literature base of investigated and identified gender differences in the psychosocial experience of parents of children with cancer, in order to guide future research in this area.Methods: An extensive literature search was conducted using Medline, PsycINFO, CINAHL and EMBASE databases. Thirty papers were included in the review. Themes from these papers were identified, and on this basis, the review findings were grouped according to five main outcome categories: role perceptions, illness beliefs, psychological distress, coping strategies and perceptions of marital, family and child functioning.Results: Few gender differences were found in perceptions of marital, family and child functioning. There was a tendency toward traditional gender roles in the division of parental tasks. Findings in relation to parent psychological distress and preferred coping strategies were mixed, with trends toward increased distress, more emotion‐focused coping and greater social support‐seeking in mothers.Conclusions: Further studies using longitudinal designs with solid theoretical groundings will provide valuable information on the unique psychosocial experiences of mothers and fathers throughout the child's illness, which may in turn guide the development of evidence‐based interventions. Copyright © 2009 John Wiley & Sons, Ltd.
The role of companions in aiding older cancer patients to recall medical information
Authors: Jansen Jesse , van Weert Julia C. M. , Wijngaards‐de Meij Leoniek , van Dulmen Sandra , Heeren Thea J. , Bensing Jozien M. 
Published: March 2009

AbstractObjectives: This study investigates information recall in unaccompanied and accompanied older cancer patients and their companions.Methods: One hundred cancer patients (aged ⩾65 years) and 71 companions completed a recall questionnaire after a nursing consultation preceding chemotherapy treatment. Recall was checked against the actual communication in video‐recordings of the consultations. Patients also completed measures of anxiety and memory‐related beliefs.Results: Findings revealed that recall in patient and companion couples together was higher than their separate recall scores (both proportional and absolute), indicating that they supplement each other. Proportionally, unaccompanied patients recalled almost as much as couples, whereas their absolute recall scores were lower. Younger age and higher education were associated with higher recall in both patients and companions. Patients' memory‐related beliefs predicted the recall scores of their companions rather than their own recall score. When patients reported memory complaints, recall was lower in their companion. In contrast, when patients indicated that they did not understand all information, their companion recalled more.Conclusions: These findings indicate that, although an interrelationship exists between recall in patients and their companions, accompanied patients are likely to benefit from the extra information that their companions remember. Copyright © 2009 John Wiley & Sons, Ltd.
Improving patient outcomes through the routine use of patient‐reported data in cancer clinics: future directions
Authors: Luckett T. , Butow P. N. , King M. T. 
Published: March 2009

AbstractObjectives: Recent reviews suggest that the routine use of patient‐reported outcome measures (PROMs) in cancer clinics improves the processes of care but not patient outcomes such as quality of life or satisfaction. We set out to identify future strategies for (1) interventions to impact patient outcomes and (2) trials to identify treatment effects.Methods: MEDLINE and PsycINFO were systematically searched to identify reports of relevant randomized controlled trials. Intervention and trial designs were compared and contrasted along the parameters identified by previous reviews and the rationales reported in each article. Results were cross‐referenced with evidence for impact to develop recommendations.Results: Six articles were identified. Evidence for impact on patient outcomes was limited. Interventions varied according to the PROMs used, the frequency, content and presentation of feedback, and the training offered to medical teams. Trials varied in their unit of randomization, outcome measures, control of contamination, monitoring of PROM use, and length of follow‐up. Our analysis identified the need for future interventions to ensure that PROM data are used to optimum effect and for trials to control for contamination and monitor use of PROMs to link this with outcomes.Conclusions: Future interventions should motivate and equip health professionals to use PROM data in managing patients, train patients in self‐efficacy, use more specific PROMs in clinic, improve the interpretability of feedback for both medical staff and patients, and monitor the use of PROMs to intervene when problems arise. Future trials should use a cluster‐randomized design to control for contamination and enable systems‐based interventions. Copyright © 2009 John Wiley & Sons, Ltd.
Sexual function, depressive symptoms and marital status in nonseminoma testicular cancer patients: a longitudinal study
Authors: Tuinman Marrit A. , Hoekstra Harald J. , Vidrine Damon J. , Gritz Ellen R. , Sleijfer Dirk Th. , Fleer Joke , Hoekstra‐Weebers Josette E. H. M. 
Published: March 2009

AbstractGoal: To longitudinally investigate sexual functioning in testicular cancer patients during the first year, and examine the effect of relationship status (with a partner or single) and depressive symptoms on sexual functioning.Patients and methods: 93 testicular cancer patients (39% single) treated in two large referral centers for testicular cancer filled in the International Index of Erectile Function (IIEF) and CES‐D after orchiectomy (T1) and 3 (T2) and 12 (T3) months later.Results: Orgasmic functioning, overall satisfaction and total sexual functioning decreased between T1 and T2 and increased to an above T1 level at T3. Levels of erectile functioning and intercourse satisfaction were higher at T3 than at T1 and T2. Desire remained stable. Type of treatment did not affect sexual functioning. Singles reported worse sexual functioning at all measurement times than committed patients, and comparable desire. One year after surgery, singles also reported worse sexual functioning on three domains when compared with norms. Depressive symptoms were highest and significantly but weakly related to one domain of sexual functioning at T1, to three domains at T2, and to none at T3. Early depressive symptoms had small to moderate predictive power on sexual functioning at T2, but not at T3.Conclusion: Sexual functioning, but not desire, fluctuates during the first year after testicular cancer. Type of treatment and depressive symptoms were no risk factors for sexual dysfunction in the longer term. Singles reported more sexual problems than patients in a relationship and norms, they may need more information and guidance concerning their sexuality. Copyright © 2009 John Wiley & Sons, Ltd.
Computational protein design as a tool for fold recognition
Authors: Schmidt am Busch Marcel , Mignon David , Simonson Thomas 
Published: March 2009

AbstractComputationally designed protein sequences have been proposed as a basis to perform fold recognition and homology searching. To investigate this possibility, an automated procedure is used to completely redesign 24 SH3 proteins and 22 SH2 proteins. We use the experimental backbone coordinates as fixed templates in the folded state and a molecular mechanics model to compute the pairwise interaction energies between all sidechain types and conformations. Energy calculations are done with the Proteins@Home volunteer computing platform. A heuristic algorithm is then used to scan the sequence and conformational space for optimal solutions. We produced 200,000—450,000 sequences for each backbone template. The designed sequences ressemble moderately‐distant, natural homologues of the initial templates, according to their identity scores and their similarity with respect to the Pfam sets of SH2 and SH3 domains. Standard homology detection tools document their native‐like character: the Conserved Domain Database recognizes 61% (52%) of our low‐energy sequences as SH3 (SH2) domains; the SUPERFAMILY, Hidden‐Markov Model library recognizes 81% (84%). Conversely, position specific scoring matrices (PSSMs) derived from our designed sequences can be used to detect natural homologues in sequence databases. Within SwissProt, a set of natural SH3 PSSMs detects 772 SH3 domains, for example; our designed PSSMs detect 67% of these, plus one additional sequence and two false positives. If six amino acids involved in substrate binding (a selective pressure not accounted for in our design) are reset to their experimental types, then 77% of the experimental SH3 domains are detected. Results for the SH2 domains are similar. Several directions to improve the method further are discussed. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies
Authors: Sun Weitao , He Jing 
Published: March 2009

AbstractSecondary structure topology in this article refers to the order and the direction of the secondary structures, such as helices and strands, with respect to the protein sequence. Even when the locations of the secondary structure Cα atoms are known, there are still (N!2N)(M!2M) different possible topologies for a protein withNhelices andMstrands. This work explored the question if the native topology is likely to be identified among a large set of all possible geometrically constrained topologies through an evaluation of the residue contact energy formed by the secondary structures, instead of the entire chain. We developed a contact pair specific and distance specific multiwell function based on the statistical characterization of the side chain distances of 413 proteins in the Protein Data Bank. The multiwell function has specific parameters to each of the 210 pairs of residue contacts. We illustrated a general mathematical method to extend a single well function to a multiwell function to represent the statistical data. We have performed a mutation analysis using 50 proteins to generate all the possible geometrically constrained topologies of the secondary structures. The result shows that the native topology is within the top 25% of the list ranked by the effective contact energies of the secondary structures for all the 50 proteins, and is within the top 5% for 34 proteins. As an application, the method was used to derive the structure of the skeletons from a low resolution density map that can be obtained through electron cryomicroscopy. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Identification of trypsin‐inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor
Authors: Chen Ting , Lee Tian‐Ren , Liang Wei‐Guang , Chang Wun‐Shaing Wayne , Lyu Ping‐Chiang 
Published: March 2009

AbstractHuman serine proteinase inhibitor Kazal‐type 2 (SPINK2) functions as a trypsin/acrosin inhibitor and is synthesized mainly in the testis and seminal vesicle where its activity is engaged in fertility. The SPINK2 protein contains a typical Kazal domain composed by six cysteine residues forming three disulfide bridges. The expression of SPINK2 is closely related to cancer such as lymphomas, in that a high transcript level of SPINK2 in patients with primary cutaneous follicle center cell lymphomas have better prognosis with lower mortality. To clarify the role of SPINK2 in cancer, we performed quantitative real‐time PCR and showed that the expression level of SPINK2 is significantly elevated in most leukemia cell lines except B‐lymphoblast TK‐6 cells. The molecular function and structural features of SPINK2 were also investigated by employing the recombinant active and mutant inactive SPINK2 proteins to determine its key P2‐P2' (Pro23‐Arg24‐His25‐Phe26) active site. The inhibition assay results demonstrated that Arg24 at the P1 site is crucial for the specificity of SPINK2 on target enzyme. Although His25 at the P1' and Phe26 at the P2' residues are also involved in trypsin‐SPINK2 interaction, Pro23 at the P2 site may not be directly participated in interacting with trypsin. In addition, we determined the 3D solution structure of SPINK2 and used this structure to predict the SPINK2‐proteinase complex structure and binding properties. These studies not only provide critical information about the structural properties and biophysical features of the SPINK2 proteinase inhibitor, but also suggest its important role in tumor progression and response to treatment. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Modular coenzyme specificity: A domain‐swopped chimera of glutamate dehydrogenase
Authors: Sharkey Michael A. , Engel Paul C. 
Published: March 2009

AbstractDomain‐swopped chimeras of the glutamate dehydrogenases from Clostridium symbiosum (CsGDH) (NAD+‐specific) and Escherichia coli (EcGDH) (NADP+‐specific) have been produced, with the aim of testing the localization of determinants of coenzyme specificity. An active chimera consisting of the substrate‐binding domain (Domain I) of CsGDH and the coenzyme‐binding domain (Domain II) of EcGDH has been purified to homogeneity, and a thorough kinetic analysis has been carried out. Results indicate that selectivity for the phosphorylated coenzyme does indeed reside solely in Domain II; the chimera utilizes NAD+ at 0.8% of the rate observed with NADP+, similar to the 0.5% ratio for EcGDH. Positive cooperativity toward L‐glutamate, characteristic of CsGDH, has been retained with Domain I. An unforeseen feature of this chimera, however, is that, although glutamate cooperativity occurs only at higher pH values in the parent CsGDH, the chimeric protein shows it over the full pH range explored. Also surprising is that the chimera is capable of catalysing severalfold higher reaction rates (Vmax) in both directions than either of the parent enzymes from which it is constructed. Proteins 2009. © 2009 Wiley‐Liss, Inc.
The behavior of clomazone in the soil environment
Authors: Gunasekara Amrith S , dela Cruz Imma Donna P , Curtis Matthew J , Claassen Victor P , Tjeerdema Ronald S 
Published: March 2009

AbstractBACKGROUND: Clomazone is a herbicide used to control broadleaf weeds and grasses. Clomazone use in agriculturally important crops and forests for weed control has increased and is a potential water contaminant given its high water solubility (1100 µg mL−1). Soil sorption is an environmental fate parameter that may limit its movement to water systems. The authors used model rice and forest soils of California to test clomazone sorption affinity, capacity, desorption, interaction with soil organic matter and behavior with black carbon.RESULTS: Sorption of clomazone to the major organic matter fraction of soil, humic acid (HA) (Kd = 29–87 L kg−1), was greater than to whole soils (Kd = 2.3–11 L kg−1). Increased isotherm non‐linearity was observed for the whole soils (N = 0.831–0.893) when compared with the humic acids (N = 0.954–0.999). Desorption isotherm results showed hysteresis, which was greatest at the lowest solution concentration of 0.067 µg mL−1 for all whole soils and HA extracts. Aliphatic carbon content appeared to contribute to increased isotherm linearity.CONCLUSION: The results indicate that clomazone does not sorb appreciably to sandy or clay soils. Its sorption affinity and capacity is greater in humic acid, and consequently clomazone has difficulty desorbing from soil organic matter. Sorption appears to follow processes explained by the dual‐mode model, the presence of fire residues (black carbon) and a recently proposed sorption mechanism. Copyright © 2009 Society of Chemical Industry