bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Parallel Code for LES of Compressible Swirling Jet Flow Undergoing Vortex Breakdown
Authors: Luginsland T. , Bühler S. , Obrist D. , Kleiser L. 
Published: March 2011

AbstractSwirling jets undergoing vortex breakdown occur in many technical applications, e.g. vortex burners, turbines and jet engines. To simulate the highly nonlinear dynamics of the flow, it is necessary to use high‐order numerical methods, leading to increased computational cost. To be able to perform simulations in acceptable turn‐around time, an available LES code for solving the filtered compressible Navier‐Stokes equations in cylindrical coordinates using compact finite‐difference schemes was parallelized for massively‐parallel architectures. The parallelization was done following the ghost‐cell approach for filtering in the three spatial directions. The inter‐process communication is handled using the message passing interface (MPI). The weak and strong scaling properties of the code indicate that it can be used for massively parallel simulations using several thousand processors. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dynamical Friction Phenomena and Friction‐Induced Vibrations in Pneumatic Sealings
Authors: Wangenheim Matthias 
Published: March 2011

AbstractEspecially from dry sliding contacts between solids the description of the friction by the law of Coulomb is well‐known. This law describes the relation between normal force and tangential force via the proportional factor μ, the coefficient of friction. This coefficient has to be derived empirically by experiments and is considered as being dependent only on the solid bodies' materials and surfaces. On the contrary seals are usually lubricated contacts. A viscoelastic seal material interacts with a hard solid counterpart in the state of mixed friction, i.e. viscous friction, hysteresis friction, and adhesion take effect simultaneously. The result is a friction characteristic which shows strong dependence on the sliding velocity, described e.g. by Richard Stribeck with the ‘Stribeck‐curve’, which was initially describing the friction of a journal bearing. One particularity of this curve is a decreasing coefficient of friction for increasing sliding velocity in the range of small velocities. It can be shown, that this decrease can cause friction induced vibrations and other undesired dynamical effects for certain mechanical properties of a system with sliding contact.In this contribution the identification of friction induced dynamics and the development of a minimal model is carried out at the example of pneumatic sealing contacts in an industrial application. Furthermore model‐based measures are shown that prevent the application from performing undesired dynamical effects. The results are validated experimentally. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Promoting effects of urethane derivatives of phenols on the ring‐opening polymerization of 1,3‐benzoxazines
Authors: Sudo Atsushi , Mori Atsushi , Endo Takeshi 
Published: March 2011

AbstractFor the purpose of reducing the induction period of the ring‐opening polymerization ofN‐methyl‐1,3‐benzoxazines, several urethanes were examined as promoters. The examined promoters3a–dwere the adducts of resorcinol and phenyl isocyanate, that of bisphenol A and phenyl isocyanate, that of resorcinol and butyl isocyanate, and that of 1,3‐propanediol and phenyl isocyanate, respectively. The aromatic urethanes3aand3b, which were adducts of the phenolic compounds and phenyl isocyanate, exhibited significant promoting effects. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Screening for distress and supportive care needs during the initial phase of the care process: a qualitative description of a clinical pilot experiment in a French cancer center
Authors: Dolbeault Sylvie , Boistard Béatrice , Meuric Jocelyne , Copel Laure , Brédart Anne 
Published: March 2011

AbstractObjective: To provide a qualitative description of a clinical pilot experiment in a French cancer center, conducted by a nurse after the treatment decision consultation attended by new cancer patients during the initial phase of the care process.Methods: The Psychological Distress Thermometer (PDS) and a problem checklist were administered to 255 patients before nurse consultation, helping her to manage the clinical interview, explore patient's distress and supportive care needs, and finally refer the patients in need to the required Supportive Care units.Results: Patients were primarily referred to the social service unit (35% patients), followed by the physiotherapy unit (23.9%) and the psycho‐oncology unit (19.6% of patients). In cases of significant distress (43% patients with PDS>3), the percentage of patients referred to the psychosocial units increased (44% referred to the Social Unit, 35% to the Psycho‐Oncology Unit). However, the main interest of our screening procedure resides in its qualitative and didactic dimension, based on clinical training and cooperation with healthcare professionals during the process of investigating patients' distress and their supportive care needs. Difficulties and limitations are also described.Conclusions: This first clinical experiment conducted among dedicated nurses involved in a Therapeutic Decision Consultation in a French cancer center has provided evidence in support of the idea that non‐specialist professionals are able to identify patients' distress and their Supportive Care needs (particularly in the psychosocial field) provided that they have received appropriate training. Copyright © 2011 John Wiley & Sons, Ltd.
Perceived positive impact of cancer among long‐term survivors of childhood cancer: a report from the childhood cancer survivor study
Authors: Zebrack Brad J. , Stuber Margaret L. , Meeske Kathleen A. , Phipps Sean , Krull Kevin R. , Liu Qi , Yasui Yutaka , Parry Carla , Hamilton Rachel , Robison Leslie L. , Zeltzer Lonnie K. 
Published: March 2011

AbstractObjectiveInvestigations examining psychosocial adjustment among childhood cancer survivors have focused primarily on negative effects and psychopathology. Emergent literature suggests the existence of positive impact or adjustment experienced after cancer, as well. The purpose of this study is to examine the distribution of Perceived Positive Impact (PPI) and its correlates in young adult survivors of childhood cancer.Methods6425 survivors and 360 siblings completed a comprehensive health survey, inclusive of a modified version of the Post‐traumatic Growth Inventory (PTGI) as a measure of PPI. Linear regression models were used to examine demographic, disease and treatment characteristics associated with PPI.ResultsSurvivors were significantly more likely than siblings to report PPI. Endorsement of PPI was significantly greater among female and non‐white survivors, and among survivors exposed to at least one intense therapy, a second malignancy or cancer recurrence. Survivors diagnosed at older ages and fewer years since diagnosis were more likely to report PPI. Income, education and marital/relationship status appeared to have varied relationships to PPI depending upon the subscale being evaluated.ConclusionsThe existence and variability of PPI in survivors in this study suggest that individual characteristics, inclusive of race, gender, cancer type, intensity of treatment, age at diagnosis and time since diagnosis, have unique and specific associations with different aspects of perceived positive outcomes of childhood cancer.Copyright © 2011 John Wiley & Sons, Ltd.
Physical and Microbiological Characterisation of Staphylococcus epidermidis Inactivation by Dielectric Barrier Discharge Plasma
Authors: Helmke Andreas , Hoffmeister Dennis , Berge Frank , Emmert Steffen , Laspe Petra , Mertens Nina , Vioel Wolfgang , Weltmann Klaus‐Dieter 
Published: March 2011

AbstractThe inactivation of the Gram‐positive bacteria Staphylococcus epidermidis (ATCC 12228) in its vegetative state was studied in vitro after exposure to cold atmospheric pressure plasma generated by direct dielectric barrier discharge (DBD). Compared to UV radiation at 254 nm, plasma UV emission yielded no significant contribution to bacterial inactivation. Analysis of bacterial growth inhibition revealed a pH dependency on growth media. Yet, measurements combined with numerical simulations excluded the pH shift induced by plasma generated reactive species as the main cause of bacterial inactivation. Scanning electron microscopy (SEM) images showed no alteration of cell walls, while fluorescence microscopy revealed lethal damage to cell membranes even after 1 s treatment. When the cell membrane was already severely damaged, also degradation of the bacterial DNA by plasma treatment was found. We conclude that membrane damage due to reactive oxygen species (ROS) and DNA degradation are the main mechanisms of plasma‐induced bacterial death that is aggregated by milieu acidification. magnified image
Insulin‐like growth factor‐2 (IGF2) loss of imprinting marks a field defect within human prostates containing cancer
Authors: Bhusari Sachin , Yang Bing , Kueck Jessica , Huang Wei , Jarrard David F. 
Published: March 2011

AbstractBACKGROUNDLoss of imprinting (LOI) is an epigenetic alteration involving loss of parental origin‐specific expression at normally imprinted genes. A LOI for IGF2, a paracrine growth factor, has been implicated in the development of prostate and other cancers. In the current study, we define IGF2 LOI in histologically normal prostate tissues in relationship to tumor foci and gene expression.METHODSMicrodissected tumor associated (TA) adjacent (2 mm) and distant (10 mm) tissues surrounding tumor foci were generated. IGF2 imprinting in informative prostate tissue sets was quantitated using a fluorescent primer extension assay and expression analyzed utilizing quantitative PCR. DNA methylation analyses were performed using quantitative pyrosequencing.RESULTSA marked IGF2 LOI was found in adjacent TA tissues (39 ± 3.1%) and did not significantly decrease in tissues distant (38 ± 5.3%) from tumor foci (45 ± 2.9%; P = 0.21). IGF2 imprinting correlated with IGF2 expression in TA tissues, but not within the tumor foci. Hypomethylation of the IGF2 DMR0 region correlated with decreased IGF2 expression in tumors (P < 0.01). The expression of IGF2 and its adjacent imprinted gene H19 were increased in adjacent and distant tissues compared to tumors (P < 0.05) indicating the importance of factors other than LOI in driving IGF2 expression.CONCLUSIONSLOI of IGF2 occurs not only adjacent to prostate tumor foci, but is widely prevalent even in distant areas within the peripheral zone. These data provide evidence for a widespread epigenetic field defect in histologically normal tissues that might be employed to identify prostate cancer in patients. Prostate 71:1621–1630, 2011. © 2011 Wiley‐Liss, Inc.
The effect of demographic and clinical factors on the relationship between BMI and PSA levels
Authors: Wright Jonathan L. , Lin Daniel W. , Stanford Janet L. 
Published: March 2011

AbstractINTRODUCTIONStudies have reported lower prostate specific antigen (PSA) levels in men with a higher body mass index (BMI). Additional factors such as diabetes mellitus, benign prostatic hyperplasia (BPH) and certain medications may also affect PSA levels and confound the PSA–BMI association. In this study we evaluated the potential confounding effect of these factors on the obesity–PSA relationship and evaluated the association between these factors and PSA level.METHODSThe study cohort consisted of 770 population‐based controls without a history of prostate cancer (PCa) who participated in a prior PCa study. Demographic, anthropometric, and medical history data were obtained, and PSA level was determined from blood drawn at the time of interview. Linear regression was performed to evaluate the PSA–BMI relationship, adjusting for potential confounders. Finally, a forward stepwise algorithm was used to determine which factors were independently associated with PSA values.RESULTSWith increase in BMI (<25, 25–29, ≥30), the geometric mean PSA level declined (1.18, 1.13, and 0.94, respectively); obese men had a 17% (95% CI 0.70–0.99) lower age‐adjusted PSA level compared to normal weight men. However, this relationship was non‐significant (P = 0.17) in the multivariate model. Independent predictors of PSA level included age (β = 1.03, 95% CI 1.02–1.04), history of BPH (β = 1.48, 95% CI 1.27–1.72), current statin (β = 0.85, 95% CI 0.74–0.98), and NSAID use (β = 0.84, 95% CI 0.72–0.98).CONCLUSIONThe relationship between obesity and PSA is confounded by a number of factors, which likely explain the observed inverse association previously reported. These results should help in interpreting PSA values in men screened for PCa. Prostate 71:1631–1637, 2011. © 2011 Wiley‐Liss, Inc.
Low AZGP1 expression predicts for recurrence in margin‐positive, localized prostate cancer
Authors: Yip Po Yee , Kench James G. , Rasiah Krishan K. , Benito Ruth Pe , Lee C.‐Soon , Stricker Phillip D. , Henshall Susan M. , Sutherland Robert L. , Horvath Lisa G. 
Published: March 2011

AbstractBACKGROUNDMen with positive margins after radical prostatectomy (RP) for localized prostate cancer (PC) have a 40–50% biochemical relapse rate at 5 years. Adjuvant radiotherapy improves biochemical progression‐free and overall survival in men with positive margins, but is associated with increased toxicity. There is an urgent need to identify new prognostic markers to define the group of patients who would benefit from multimodality therapy.METHODSNuclear β‐catenin, membranous secreted frizzled‐related protein 4 (sFRP4), zinc‐alpha 2‐glycoprotein (AZGP1), and macrophage inhibitory cytokine‐1 (MIC‐1) have previously been identified as molecular markers of outcome in localized PC. From these published studies, we identified a subset of patients with positive margins. The aim of this study was to assess the association between these four molecular markers and outcome in men with margin‐positive, localized PC.RESULTSWe identified 186 men with positive margins from 330 men with localized PC; 53% had preoperative PSA >10 ng/ml, 72% extraprostatic extension (EPE), 24% seminal vesicles involvement (SVI), and 57% RP Gleason score ≥ 7. AZGP1 (P = 0.009), membranous sFRP4 (P = 0.03) and MIC‐1 (P = 0.04) expression predicted for biochemical relapse on univariate analysis. Only absent/low AZGP1 expression (P = 0.01) was an independent predictor of recurrence in margin‐positive, localized PC when modeled with preoperative PSA (P = 0.2), EPE (P = 0.2), SVI (P = 0.4), Gleason score ≥ 7 (P = 0.5) and adjuvant treatment (P = 0.4). Furthermore, there was an association between absent/low AZGP1 expression and clinical recurrence (P = 0.007).CONCLUSIONSAZGP1 is a potential molecular marker for biochemical relapse in men with margin‐positive, localized PC. Routine assessment of this biomarker may lead to better selection of patients who will benefit from post‐RP radiotherapy. Prostate 71:1638–1645, 2011. © 2011 Wiley‐Liss, Inc.
The calcium sensor STIM1 is regulated by androgens in prostate stromal cells
Authors: Berry Paul A. , Birnie Richard , Droop Alastair P. , Maitland Norman J. , Collins Anne T. 
Published: March 2011

AbstractBACKGROUNDProstate development and maintenance in the adult results from an interaction of stromal and glandular components. Androgens can drive this process by direct action on the stroma. We investigated whether there was a direct link between androgens and another key regulator of stromal cells, intracellular Ca2+ ([Ca2+]i).METHODSProstate stromal cells were freshly obtained and cultures derived from patients with benign prostatic hyperplasia. Gene expression in dihydrotestosterone treated and untreated cells was compared using Affymetrix gene expression arrays and Ca2+ regulated features were identified by Gene Ontology (GO). Changes in [Ca2+]i were determined in Fluo‐4 loaded cells. Androgen regulation was confirmed by chromatin immunoprecipitaion.RESULTSStromal cell cultures were sorted for expression of integrin α1β1, which enriched for cells expressing the androgen receptor (AR). We identified key functional categories, within the androgen‐induced gene expression signature, focusing on genes involved in calcium signaling. From this analysis, stromal interaction molecule‐1 (STIM1) was identified as a significantly differentially expressed gene with four relevant associated GO terms. DNA sequence analysis showed that the promoter region of STIM1 contained putative androgen response element sequences in which AR binding ability of STIM1 was confirmed. Androgens directly regulated STIM1 expression and STIM1 effects on store‐operated calcium entry were inhibited by STIM1 knock‐down. Reduced STIM1 expression in prostate stromal cells led to a reduction in basal Ca2+ levels, the amount of Ca2+ released by thapsigargin and a reduction in store filling following TG‐induced store depletion.CONCLUSIONSThese results indicate that androgens modulate [Ca2+]i through the direct regulation of the STIM1 gene by AR binding to the STIM1 promoter. Prostate 71:1646–1655, 2011. © 2011 Wiley‐Liss, Inc.
Analysis of water patterns in protein kinase binding sites
Authors: Barillari Caterina , Duncan Anna L. , Westwood Isaac M. , Blagg Julian , van Montfort Rob L. M. 
Published: March 2011

AbstractDeregulation of protein kinases is associated with numerous diseases, making them important targets for drug discovery. The majority of drugs target the catalytic site of these proteins, but due to the high level of similarity within the ATP binding sites of protein kinases, it is often difficult to achieve the required pharmacological selectivity. In this study, we describe the identification and subsequent analysis of water patterns in the ATP binding sites of 171 protein kinase structures, comprising 19 different kinases from various branches of the kinome, and demonstrate that structurally similar binding sites often have significantly different water patterns. We show that the observed variations in water patterns of different, but structurally similar kinases can be exploited in the structure‐based design of potent and selective kinase inhibitors. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Structural memory of natively unfolded tau protein detected by small‐angle X‐ray scattering
Authors: Shkumatov Alexander V. , Chinnathambi Subashchandrabose , Mandelkow Eckhard , Svergun Dmitri I. 
Published: March 2011

AbstractSmall‐angle X‐ray scattering (SAXS) is a universal low‐resolution method to study size and shape of globular proteins in solution but recent developments facilitate the quantitative characterization of the structure and structural transitions of metastable systems like partially or completely unfolded proteins. We present here a study of temperature induced transitions in tau, a natively unfolded protein involved in Alzheimer's disease. Previous studies on full length tau and several disease‐related mutants provided information about the residual structure in different domains revealing a specific role and extended conformations of the so‐called repeat domains, which are considered to be responsible for the formation of amyloid‐like fibrils (“paired helical filaments”). Here, we employ SAXS to investigate the temperature dependent properties of tau. Slow heating/cooling of the full length protein from 10°C to 50°C did not lead to detectable changes in the overall size. Surprisingly, quick heating/cooling caused tau to adopt a significantly more compact conformation, which was stable over up to 3 h and represents a structural “memory” effect. This compaction is not observed for the shorter tau constructs containing largely the repeat domains. The structural and functional implications of the observed unusual behavior of tau under nonequilibrium conditions are discussed. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides
Authors: Wagoner Victoria A. , Cheon Mookyung , Chang Iksoo , Hall Carol K. 
Published: March 2011

AbstractWe simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113–120 (AGAAAAGA) and the mouse prion protein MoPrP 111–120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)4, A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV The first two peptides are thought to act as the Velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves. Kinetic events along the fibrillization pathway influence the types of structures that occur and variations in the sequence affect aggregation kinetics and fibrillar structure. Discontinuous molecular dynamics simulations using the PRIME20 force field are performed on systems containing 48 peptides starting from a random coil configuration. Depending on the sequence, fibrillar structures form spontaneously over a range of temperatures, below which amorphous aggregates form and above which no aggregation occurs. AGAAAAGA forms well organized fibrillar structures whereas VAGAAAAGAV forms less well organized structures that are partially fibrillar and partially amorphous. The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV. The ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. However as the hydrophobicity of the sequence increases, the ability to form well‐ordered structures decreases. Thus, longer hydrophobic sequences form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Crystal structure of a metal‐dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity
Authors: Han Gye Won , Ko Jaeju , Farr Carol L. , Deller Marc C. , Xu Qingping , Chiu Hsiu‐Ju , Miller Mitchell D. , Sefcikova Jana , Somarowthu Srinivas , Beuning Penny J. , Elsliger Marc‐André , Deacon Ashley M. , Godzik Adam , Lesley Scott A. , Wilson Ian A. , Ondrechen Mary Jo 
Published: March 2011

AbstractThe crystal structures of an unliganded and adenosine 5′‐monophosphate (AMP) bound, metal‐dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis are reported at 2.4 and 1.94 Å, respectively. Functional characterization of this enzyme was guided by computational analysis and then confirmed by experiment. The structure consists of a polymerase and histidinol phosphatase (PHP, Pfam: PF02811) domain with a second domain (residues 105‐178) inserted in the middle of the PHP sequence. The insert domain functions in binding AMP, but the precise function and substrate specificity of this domain are unknown. Initial bioinformatics analyses yielded multiple potential functional leads, with most of them suggesting DNA polymerase or DNA replication activity. Phylogenetic analysis indicated a potential DNA polymerase function that was somewhat supported by global structural comparisons identifying the closest structural match to the alpha subunit of DNA polymerase III. However, several other functional predictions, including phosphoesterase, could not be excluded. Theoretical microscopic anomalous titration curve shapes, a computational method for the prediction of active sites from protein 3D structures, identified potential reactive residues in YP_910028.1. Further analysis of the predicted active site and local comparison with its closest structure matches strongly suggested phosphoesterase activity, which was confirmed experimentally. Primer extension assays on both normal and mismatched DNA show neither extension nor degradation and provide evidence that YP_910028.1 has neither DNA polymerase activity nor DNA‐proofreading activity. These results suggest that many of the sequence neighbors previously annotated as having DNA polymerase activity may actually be misannotated. Proteins 2011. © 2011 Wiley‐Liss, Inc.