bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survival after relapse in children with solid tumors: A follow‐up study from the Italian off‐therapy registry
Authors: Ceschel Stefano , Casotto Veronica , Valsecchi Maria Grazia , Tamaro Paolo , Jankovic Momcilo , Hanau Guia , Fossati Franca , Pillon Marta , Rondelli Roberto , Sandri Alessandro , Silvestri Daniela , Haupt Riccardo , Cuttini Marina 
Published: January 2006

AbstractBackgroundDespite the increased survival of children with solid tumors, a significantproportion of cases still relapse following treatment discontinuation, and knowledge about the long‐term outcome of this selected group of patients remains incomplete.ObjectiveTo describe the long‐term outcome of children treated for a solid tumor who relapsed after the elective end of therapy, and to explore factors associated with survival.MethodsAll patients with the selected diagnoses—Hodgkin disease (HD), neuroblastoma (NB), tumor of the central nervous system (CNS), Wilms tumor (WT), or soft tissue sarcoma (STS)‐enrolled in the Italian Pediatric Off‐Therapy Registry in the period 1980–1998 were evaluated. Out of 3,927 patients, 694 had relapsed after treatment suspension; 639 were available for analysis. Survival and event‐free survival were estimated by the Kaplan–Meier method. The log‐rank test was used to assess differences in survival among the various types of cancer considered. Multivariate Cox proportional hazards analysis was adopted to explore possible prognostic factors.ResultsThere were 335 deaths: most of them (93%) were related to the primary cancer. The overall survival rate after relapse was 38% (95% CI 33–42) at 5 years, and 32% (95% CI 27–36%) at 15 years, while event free survival was 31% (95% CI 26–35) and 26% (95% CI 22–30%), respectively. There were significant differences according to the original diagnosis, with patients with HD doing better, and those with NB, CNS, and STS worse. No improvement of prognosis was evident over time. Post‐relapse stem cell transplantation was associated with decreased risk of death only in the first year, not thereafter.ConclusionsOverall, patients with solid tumors who relapse after treatment discontinuation have a poor outcome, but significant differences exist according to the tumor types. Pediatr Blood Cancer 2006; 47:560–566. © 2006 Wiley‐Liss, Inc.
Evaluation of plasma tissue factor and tissue factor pathway inhibitor levels in childhood hemangiomas
Authors: Türker Meral , İrken Gülersu , Ören Hale , Yılmaz Şebnem , Yüksel Faize , Olgun Nur 
Published: January 2006

AbstractBackgroundThe purpose of the study was to evaluate the plasma levels of tissue factor (TF), an angiogenic marker, and tissue factor pathway inhibitor (TFPI), an antiproliferative protein, in the childhood hemangiomas at proliferative and regressive stages.ProcedureThe study included 30 patients with hemangiomas and 30 healthy children. Localization, number, stage, type, duration of growth, and complications of the hemangiomas were determined. Venous blood samples from all individuals were collected into citrated tubes and centrifuged. Supernatant plasma was separated, aliquated, and stored at −70°C until samples could be assayed. Plasma levels of TF and TFPI were measured with quantitative ELISA kits.ResultsPlasma TF and TFPI levels did not show any significant difference between the study and control groups. When plasma TF and TFPI levels of the children in the control group and in the study group who were in proliferative and regressive stage were compared to each other, no statistically significant difference could be detected.ConclusionsPlasma TF and TFPI levels of our patients with hemangiomas were not different from healthy children and they did not show any significant difference in proliferative and regressive stages. © 2006 Wiley‐Liss, Inc.
Daily subcutaneous amifostine administration during irradiation of pediatric head and neck cancers
Authors: Anacak Yavuz , Kamer Serra , Haydaroglu Ayfer 
Published: January 2006

AbstractFive pediatric patients with head and neck cancers were treated with radiotherapy. Subcutaneous injections of 200 mg flat dose amifostine were given 30 min prior to radiation fractions. A total of 129 amifostine injections were done. Grade 3 nausea occurred three times and emesis only once. Hypotension, hypocalcemia, or allergic reactions following injections were not recorded. No grade 3 or 4 mucosal or skin reactions occurred. After 16 months, all patients were alive and disease‐free. There were no grade 3 or 4 side effects of radiotherapy on follow‐up. Further studies with more patients are required to determine the role of amifostine in pediatric radiation oncology, but these data should contribute to the clinical spectrum of amifostine use in pediatric oncology. Pediatr Blood Cancer 2007;48:579–581. © 2006 Wiley‐Liss, Inc.
Rational use of drugs: prescribing and dispensing practices at public health facilities in Lao PDR
Authors: Keohavong Bounxou , Syhakhang Lamphone , Sengaloundeth Sivong , Nishimura Akio , Ito Katsuki 
Published: January 2006

AbstractPurposeTo evaluate the rational use of drug (RUD) patterns with a focus on prescribing and dispensing practices for providing information to the policy makers for further planning and identifying intervention strategies.MethodA cross‐sectional study conducted by interviewing 370 presenting outpatients, checking records of 900 out‐ patients with any cases and 798 outpatients with tracer diseases such as simple diarrhea, pneumonia and non‐pneumonia (Flu) within 30 public health facilities (HFs) of five geographical areas with different socio‐economic statuses grouped into high, middle and low. The WHO Operational Package for Monitoring and Assessing Country Pharmaceutical Situations indicators were used for data collection.ResultsAmong the 3 items of drugs prescribed per average encounter, 97% were dispensed from HFs, of which 67% were adequately labeled, 84% were on the national essential drug (ED) list, and 78% were prescribed by generic name. Seventy‐four percent of patients knew how to take the drugs they received, 47% of them received antibiotics (ABs), and 18% received injections. Forty‐seven percent of under‐five children with simple diarrhea received ABs, 77% received Oral Rehydration Salts (ORS) and 5% received anti‐diarrhea drugs, and 91% of such under‐five children with mid/moderate pneumonia received one of first line ABs, 15% received more than one ABs, and 41% of non‐pneumonia (flu) patients of any age received ABs.ConclusionThe use of drugs in Laos was not fully appropriate in terms of rationally prescribing and dispensing practices. Since prescriptions for AB, injections, non‐ED, and non‐generics are still high, information on drug use provided is insufficient. Therefore, continuous health education programs among both health staff and public are needed. Copyright © 2005 John Wiley & Sons, Ltd.
Cardiovascular risk of selective cyclooxygenase‐2 inhibitors and other non‐aspirin non‐steroidal anti‐inflammatory medications
Authors: Velentgas Priscilla , West William , Cannuscio Carolyn C. , Watson Douglas J. , Walker Alexander M. 
Published: January 2006

AbstractPurposeThe purpose of this study was to estimate rates of acute coronary syndrome (ACS), and sudden cardiac death in relation to use of rofecoxib, celecoxib, naproxen, diclofenac, and ibuprofen.MethodsWe conducted a retrospective cohort study among 424 584 health plan enrollees ages 40–64 who used non‐aspirin non‐steroidal anti‐inflammatory drugs (NANSAIDs) by prescription from 1999 to 2001. We used automated medical and pharmacy claims data to compute person‐time exposed to study drugs, and to identify hospitalizations for ACS. The primary endpoint was ACS, inclusive of myocardial infarction (MI), unstable angina, and sudden cardiac death as identified through claims data and confirmed through hospital medical records, or through the National Death Index.ResultsCompared with ibuprofen or diclofenac use, the relative risk (RR) of ACS during periods of current rofecoxib use was 1.35 (95%CI 1.09–1.68). For current use of celecoxib, the RR was 1.03 (95%CI 0.83–1.27). Risks in the first 30 days of rofecoxib and celecoxib use were modestly elevated. Rofecoxib use at the 25 mg/day (modal) dose was associated with an elevated risk of ACS (RR 1.54, 95%CI 1.15–2.04), while use at 26–50 mg/day (>modal) was not (RR 0.81, 95%CI 0.41–1.60). There were no increased risks with modal or greater than modal doses of celecoxib or naproxen compared with all doses of ibuprofen or diclofenac combined.ConclusionsThe incidence of ACS was 1.35 times greater during rofecoxib use than use of ibuprofen or diclofenac. No statistically significant elevation in risk was observed with celecoxib use. Naproxen use was not associated with risk of ACS. Copyright © 2005 John Wiley & Sons, Ltd.
Improvement of statistical potentials and threading score functions using information maximization
Authors: Solis Armando D. , Rackovsky S. 
Published: January 2006

AbstractWe show that statistical potentials and threading score functions, derived from finite data sets, are informatic functions, and that their performance depends on the manner in which data are classified and compressed. The choice of sequence and structural parameters affects estimates of the conditional probabilities P(C|S), the quantification of the effect of sequence S on conformation C, and determines the amount of information extracted from the data set, as measured by information gain. The mathematical link between information gain and mean conformational energy, established in this work using the local backbone potential as model, demonstrates that manipulation of descriptive parameters also alters the “energy” values assigned to native conformation and to decoy structures in the test pool, and consequently, the performance of such statistical potential functions in fold recognition exercises. We show that sequence and structural partitions that maximize information gain also minimize the mean energy of the ensemble of native conformations. Moreover, we establish an informatic basis for the placement of the native score within an energy spectrum given by the decoy pool in a threading exercise. We discover that, among all informatic quantities, information gain is the best predictor of threading success, even better than the standard Z‐score. Consequently, the choices of sequence and structural descriptors, extent of compression, and levels of discretization that maximize information gain must also produce the best potential functions. Strategies to optimize these parameters with respect to information extraction are therefore relevant to building better statistical potentials. Last, we demonstrate that the backbone torsion potential, defined by the trimer sequence, can be an effective tool in greatly reducing the set of possible conformations from a vast decoy pool. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Inferring protein interactions from experimental data by association probabilistic method
Authors: Chen Luonan , Wu Ling‐Yun , Wang Yong , Zhang Xiang‐Sun 
Published: January 2006

AbstractTo elucidate protein interaction networks is one of the major goals of functional genomics for whole organisms. So far, various computational methods have been proposed for inference of protein–protein interactions. Based on the association method by Sprinzak et al., we propose an association probabilistic method in this short communication to infer protein interactions directly from the experimental data, which outperformed other existing methods in terms of both accuracy and efficiency despite its simple form. Specifically, we show that the association probabilistic method achieves the highest accuracy among the existing approaches for the measures of root‐mean‐square error and the Pearson correlation coefficient, and also runs much faster than the LP‐based method, by experimental dataset in Yeast. Software is available from the authors upon request. Proteins 2006. © 2006 Wiley‐Liss, Inc.
PSI‐DOCK: Towards highly efficient and accurate flexible ligand docking
Authors: Pei Jianfeng , Wang Qi , Liu Zhenming , Li Qingliang , Yang Kun , Lai Luhua 
Published: January 2006

AbstractWe have developed a new docking method, Pose‐Sensitive Inclined (PSI)‐DOCK, for flexible ligand docking. An improved SCORE function has been developed and used in PSI‐DOCK for binding free energy evaluation. The improved SCORE function was able to reproduce the absolute binding free energies of a training set of 200 protein–ligand complexes with a correlation coefficient of 0.788 and a standard error of 8.13 kJ/mol. For ligand binding pose exploration, a unique searching strategy was designed in PSI‐DOCK. In the first step, a tabu‐enhanced genetic algorithm with a rapid shape‐complementary scoring function is used to roughly explore and store potential binding poses of the ligand. Then, these predicted binding poses are optimized and compete against each other by using a genetic algorithm with the accurate SCORE function to determine the binding pose with the lowest docking energy. The PSI‐DOCK 1.0 program is highly efficient in identifying the experimental binding pose. For a test dataset of 194 complexes, PSI‐DOCK 1.0 achieved a 67% success rate (RMSD <2.0 Å) for only one run and a 74% success rate for 10 runs. PSI‐DOCK can also predict the docking binding free energy with high accuracy. For a test set of 64 complexes, the correlation between the experimentally observed binding free energies and the docking binding free energies for 64 complexes is r = 0.777 with a standard deviation of 7.96 kJ/mol. Moreover, compared with other docking methods, PSI‐DOCK 1.0 is extremely easy to use and requires minimum docking preparations. There is no requirement for the users to add hydrogen atoms to proteins because all protein hydrogen atoms and the flexibility of the terminal protein atoms are intrinsically taken into account in PSI‐DOCK. There is also no requirement for the users to calculate partial atomic charges because PSI‐DOCK does not calculate an electrostatic energy term. These features are not only convenient for the users but also help to avoid the influence of different preparation methods. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Three‐dimensional model of the human aromatase enzyme and density functional parameterization of the iron‐containing protoporphyrin IX for a molecular dynamics study of heme‐cysteinato cytochromes
Authors: Favia Angelo Danilo , Cavalli Andrea , Masetti Matteo , Carotti Angelo , Recanatini Maurizio 
Published: January 2006

AbstractMammalian cytochromes P450 (CYP) are enzymes of great biological and pharmaco‐toxicological relevance. Due to their membrane‐bound nature, the structural characterization of these proteins is extremely difficult, and therefore computational techniques, such as comparative modeling, may help obtaining reliable structures of members of this family. An important feature of CYP is the presence of an iron‐containing porphyrin group at the enzyme active site. This calls for quantum chemical calculations to derive charges and parameters suitable for classical force field‐based investigations of this proteins family. In this report, we first carried out density functional theory (DFT) computations to derive suitable charges for the Fe2+‐containing heme group of P450 enzymes. Then, by means of the homology modeling technique, and taking advantage of the recently published crystal structure of the human CYP2C9, we built a new model of the human aromatase (CYP19) enzyme. Furthermore, to study the thermal stability of the new model as well as to test the suitability of the new DFT‐based heme parameters, molecular dynamics (MD) simulations were carried out on both CYP2C9 and CYP19. Finally, the last few ns of aromatase MD trajectories were investigated following the essential dynamics protocol that allowed the detection of some correlated motions among some protein domains. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Energetics of the native and non‐native states of the glycophorin transmembrane helix dimer
Authors: Mottamal Madhusoodanan , Zhang Jinming , Lazaridis Themis 
Published: January 2006

AbstractUsing an implicit membrane model (IMM1), we examine whether the structure of the transmembrane domain of Glycophorin A (GpA) could be predicted based on energetic considerations alone. The energetics of native GpA shows that van der Waals interactions make the largest contribution to stability. Although specific electrostatic interactions are stabilizing, the overall electrostatic contribution is close to zero. The GXXXG motif contributes significantly to stability, but residues outside this motif contribute almost twice as much. To generate non‐native states a global conformational search was done on two segments of GpA: an 18‐residue peptide (GpA74‐91) that is embedded in the membrane and a 29‐residue peptide (GpA70–98) that has additional polar residues flanking the transmembrane region. Simulated annealing was done on a large number of conformations generated from parallel, antiparallel, left‐ and right‐handed starting structures by rotating each helix at 20° intervals around its helical axis. Several crossing points along the helix dimer were considered. For 18‐residue parallel topology, an ensemble of native‐like structures was found at the lowest effective energy region; the effective energy is lowest for a right‐handed structure with an RMSD of 1.0 Å from the solid‐state NMR structure with correct orientation of the helices. For the 29‐residue peptide, the effective energies of several left‐handed structures were lower than that of the native, right‐handed structure. This could be due to deficiencies in modeling the interactions between charged sidechains and/or omission of the sidechain entropy contribution to the free energy. For 18‐residue antiparallel topology, both IMM1 and a Generalized Born model give effective energies that are lower than that of the native structure. In contrast, the Poisson‐Boltzmann solvation model gives lower effective energy for the parallel topology, largely because the electrostatic solvation energy is more favorable for the parallel structure. IMM1 seems to underestimate the solvation free energy advantage when the CO and NH dipoles just outside the membrane are parallel. This highlights the importance of electrostatic interactions even when these are not obvious by looking at the structures. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Structural and magnetic characterization of MgxNi1−xSm0.02Fe1.98O4 ferrites
Authors: Al‐Haj Mansour 
Published: January 2006

AbstractThe Mgx Ni1−x Sm0.02Fe1.98O4 ferrites were prepared by the solid‐state reaction method and were characterized by X‐ray diffraction and magnetization measurements. A single spinel phase was obtained in all prepared samples. It was found that the lattice parameter increases and the X‐ray density decreases as the Ni2+ ions on the octahedral sites are replaced by the Mg2+ ions. The coercivity measurements indicated a decrease of internal strains in samples for x > 0.5. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microstructure–magnetic properties relationships in nanocrystalline Nd–Fe–Co–Ge–B annealed ribbons
Authors: Gholamipour R. , Beitollahi A. , Marghusian V. K. , Ohkubo T. , Hono K. , Andreev S. V. , Bogatkin A. N. , Duragin S. S. , Kozolov A. N. , Kudervatykh N. V. 
Published: January 2006

AbstractIn this work, the effects of Ge addition on the microstructure and magnetic properties of some rapidly quenched Nd13.5Fe(74.9–z )Co5.5Gez B6 alloys with z = 0.0, 0.18, 0.36, 0.54, 0.72 and 0.9 prepared by a rapid solidification method were studied. For the first time, detailed microstructural study of nanometer size grain boundaries enriched with very small amount of Ge as well as Nd was carried out using 3 Dimensional Atom Probe (3DAP) technique. The magnitudes of B r and (BH )max were seen to increase for the samples substituted with up to 0.36 at% Ge in spite of the fact that Ge is a non‐magnetic atom. This was related to the observed change of Co concenteration in matrix phase. However, the magnetic properties deteriorated for the samples with Ge addition beyond 0.36 at%. The observed magnetic properties are discussed in relation with the observed microstructural changes monitored by 3DAP and TEM techniques. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron transport anisotropies in pseudomorphic InGaAs channel materials and their structural origin
Authors: Wilson J. A. , MacKenzie M. , MacFadzean S. , McMullen T. , Hamill S. , Stopford P. , Holland M. C. , Stanley C. R. , Long A. R. 
Published: January 2006

AbstractMeasurements of the electron transport properties in Inx Ga1−x As (x = 0.2 and x = 0.3) channel heterostructures have consistently shown the transport mobility to be higher in the [01&1macr;] direction compared to [011] on a (100) wafer. Low temperature (1.6 K) measurements of these materials show that the mobility difference can be as large as 30% whilst the differences in carrier concentrations for the two directions are negligible in comparison. The mobility anisotropy decreases to below 5% at room temperature as the effects of phonon scattering, which is isotropic, begin to dominate. The anisotropy in the quantum mobility is much less pronounced than that in the transport mobility. This suggests that the low mobility in the [011] direction is primarily a result of large angle scattering. Transmission electron microscopy (TEM) analysis was performed on cross‐sections of material in the two directions. Thickness ﬂuctuations in the channel were observed whilst traversing the channel of a (01&1macr;) section in the [011] direction where as none were observed in (011) sections along the [01&1macr;] direction. The length scale of the ﬂuctuations was variable but typically around 50–100 nm. Transport simulations reveal that a 1‐dimensional potential modulation with a wavelength similar to that of the fluctuations produces a mobility anisotropy with the observed sign. Therefore it is likely that the thickness variations, possibly combined with synchronous fluctuations in the indium concentration along the [011] direction, are responsible for the reduced mobility in [011] transport. Although to the best of our knowledge these thickness fluctuations are reported here for the first time, similar growth anisotropies are well known for Inx Ga1−x As layers deposited on InP. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reactive magnetron sputtering of highly (001)‐textured WS2−x films: Influence of Ne+, Ar+ and Xe+ ion bombardment on the film growth
Authors: Ellmer K. , Seeger S. , Sieber I. , Bohne W. , Röhrich J. , Strub E. , Mientus R. 
Published: January 2006

AbstractLayer‐type van der Waals semiconductor WS2−x films were grown by radio frequency reactive magnetron sputtering from a metallic tungsten target onto oxidized silicon substrates. The sputtering atmosphere consisted of 75% hydrogen sulfide and 25% neon, argon or xenon. The substrate voltage and hence the energy of the ions bombarding the growing film, was varied from about 20 V (floating potential) to −80 V. By in situ energy‐dispersive X‐ray diffraction the growth of the films was monitored and by elastic recoil detection analysis the film composition was measured. It was found that with xenon in the sputtering atmosphere a substrate voltage of −20 V is sufficient to suppress the crystalline film growth, while for argon as the sputtering rare gas this occurs only at −80 V. The disturbed film growth is accompanied by a sulfur loss of the growing WS2−x films down to x = 1.1 for sputtering in Ar + H2S at a substrate potential of −60 V. The results are tentatively explained by the different momentum transfers to sulfur atoms, which is highest for argon ions. It has also to be taken into account that the low‐energy xenon bombardment is a many‐body cascade process with a much higher local energy density compared to argon and neon bombardment and leading to a higher defect density and a supression of the crystalline growth. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)