bluuebunny/crossref_metadata_2025_split huggingface dataset:
β‐Hairpin prediction with quadratic discriminant analysis using diversity measure
Authors: Zou Dongsheng , He Zhongshi , He Jingyuan 
Published: March 2009

AbstractOn the basis of the features of protein sequential pattern, we used the method of increment of diversity combined with quadratic discriminant analysis (IDQD) to predict β‐hairpins motifs in protein sequences. Three rules are used to extract the raw β‐β motifs sequential patterns for fixed‐length. Amino acid basic compositions, dipeptide components, and amino acid composition distribution are combined to represent the compositional features. Eighteen feature variables on a sequential pattern to be predicted are defined in terms of ID. They are integrated in a single formal framework given by IDQD. The method is trained and tested on ArchDB40 dataset containing 3088 proteins. The overall accuracy of prediction and Matthew's correlation coefficient for the independent testing dataset are 81.7% and 0.60, respectively. In addition, a higher accuracy of 84.5% and Matthew's correlation coefficient of 0.68 for the independent testing dataset are obtained on a dataset previously used by Kumar et al. (Nucleic Acids Res 2005, 33, 154), which contains 2088 proteins. For a fair assessment of our method, the performance is also evaluated on all 63 proteins used in CASP6. The overall accuracy of prediction is 74.2% for the independent testing dataset. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Pseudo quasi‐3 designs and their applications to coding theory
Authors: Bracken Carl 
Published: March 2009

AbstractWe define a pseudo quasi‐3 design as a symmetric design with the property that the derived and residual designs with respect to at least one block are quasi‐symmetric. Quasi‐symmetric designs can be used to construct optimal self complementary codes. In this article we give a construction of an infinite family of pseudo quasi‐3 designs whose residual designs allow us to construct a family of codes with a new parameter set that meet the Grey Rankin bound. © 2009 Wiley Periodicals, Inc. J Combin Designs 17: 411–418, 2009
Commuting polarities and maximal partial ovoids of H(4,q2)
Authors: Cossidente Antonio , Siciliano Alessandro 
Published: March 2009

AbstractIn PG(4,q2), q odd, let Q(4,q2) be a non‐singular quadric commuting with a non‐singular Hermitian variety H(4,q2). Then these varieties intersect in the set of points covered by the extended generators of a non‐singular quadric Q0 in a Baer subgeometry Σ0 of PG(4,q2). It is proved that any maximal partial ovoid of H(4,q2) intersecting Q0 in an ovoid has size at least 2(q2+1). Further, given an ovoid O of Q0, we construct maximal partial ovoids of H(4,q2) of size q3+1 whose set of points lies on the hyperbolic lines 〈P,X〉 where P is a fixed point of O and X varies in O\{P}. © 2009 Wiley Periodicals, Inc. J Combin Designs 17: 307–313, 2009
Signaling molecules and pathways regulating the fate of spermatogonial stem cells
Authors: He Zuping , Kokkinaki Maria , Dym Martin 
Published: March 2009

AbstractSpermatogenesis is the process that involves the division and differentiation of spermatogonial stem cells (SSCs) into mature spermatozoa. SSCs are a subpopulation of type A spermatogonia resting on the basement membrane in the mammalian testis. Self‐renewal and differentiation of SSCs are the foundation of normal spermatogenesis, and thus a better understanding of molecular mechanisms and signaling pathways in the SSCs is of paramount importance for the regulation of spermatogenesis and may eventually lead to novel targets for male contraception as well as for gene therapy of male infertility and testicular cancer. Uncovering the molecular mechanisms is also of great interest to a better understanding of SSC aging and for developing novel therapeutic strategies for degenerative diseases in view of the recent work demonstrating the pluripotent potential of the SSC. Progress has recently been made in elucidating the signaling molecules and pathways that determine cell fate decisions of SSCs. In this review, we first address the morphological features, phenotypic characteristics, and the potential of SSCs, and then we focus on the recent advances in defining the key signaling molecules and crucial signaling pathways regulating self‐renewal and differentiation of SSCs. The association of aberrant expression of signaling molecules and cascades with abnormal spermatogenesis and testicular cancer are also discussed. Finally, we point out potential future directions to pursue in research on signaling pathways of SSCs. Microsc. Res. Tech., 2009. © 2009 Wiley‐Liss, Inc.
Transgene expression of transfected supercoiled plasmid DNA concatemers in mammalian cells
Authors: Maucksch Christof , Bohla Alexander , Hoffmann Florian , Schleef Martin , Aneja Manish Kumar , Elfinger Markus , Hartl Dominik , Rudolph Carsten 
Published: March 2009

AbstractBackgroundSupercoiled topology of transfected plasmid DNA (pDNA) is critical for transgene expression in mammalian cells. In the present study, we analysed transgene expression of transfected supercoiled pDNA concatemers.MethodsJurkat T cells were transfected with a supercoiled 4.7‐kb monomeric and, in parallel, a 9.4‐kb dimeric pEGFP plasmid concatemer using electroporation. The absolute amounts of pDNA delivered into the cytoplasm and the nucleus were quantified by quantitative real‐time polymerase chain reaction. Further, the number and mean fluorescent intensity (MFI) of enhanced green fluorescent protein (EGFP) expressing cells and the relative amounts of TOTO‐1 fluorescently‐labeled pDNA associated with the cell, located in the cytoplasm, and in the nucleus, were analysed by flow cytometry.ResultsFor both constructs, significantly higher amounts of pDNA were detected in the cytoplasm compared to the nucleus. Furthermore, from FACS analysis, we could infer the relative gene copy (Egene) and plasmid expression efficiency (Eplasmid) by determining the ratio of the EGFP MFI of the transfected cells to TOTO‐1 MFI per nucleus on the single cell level. Egene and Eplasmid were significantly 1.6‐and 3.5‐fold higher for EGFP‐dimer than for EGFP‐monomer, although the transfection rates considering the number of transfected cells were significantly lower for EGFP‐dimer than for EGFP‐monomer. Together with hydrodynamic plasmid diameter measurements, these observations suggest that concatemer arrangement increases relative gene expression efficiency, whereas plasmid size is important for cell and nucleus entry after electroporation.ConclusionsWe propose using preferably small supercoiled plasmid concatemers as the ideal plasmid vectors to maximize both transgene expression and the number of transfected target cells. Copyright © 2009 John Wiley & Sons, Ltd.
Baculovirus is an efficient vector for the transduction of the eye: comparison of baculovirus‐ and adenovirus‐mediated intravitreal vascular endothelial growth factor D gene transfer in the rabbit eye
Authors: Kinnunen Kati , Kalesnykas Giedrius , Mähönen Anssi J. , Laidinen Svetlana , Holma Liisa , Heikura Tommi , Airenne Kari , Uusitalo Hannu , Ylä‐Herttuala Seppo 
Published: March 2009

AbstractBackgroundThe present study aimed to determine the efficiency and safety of baculovirus‐mediated intravitreal gene transfer in rabbit eye and to compare its efficiency with adenovirus. We also studied how an intravitreal injection of vectors producing vascular endothelial growth factor D (VEGF‐D) impacts the vasculature of rabbit eye.MethodsBaculoviral (BacVEGF‐D) or adenoviral VEGF‐D (AdVEGF‐D) were administered intravitreally into the right eye at different doses (108, 109 and 1010 IU/ml) to 24 animals. Left eyes were injected with control viruses. To determine how long transgene expression lasted, we injected BacVEGF‐D or BacLacZ to the vitreous humour of 11 animals and followed them for 4 weeks. Vitreous samples were taken after sacrifice for enzyme‐linked immunosorbent assays and eyes were removed and fixed for histological analyses.ResultsBoth baculoviruses and adenoviruses caused efficient expression of VEGF‐D in the rabbit eyes. BacVEGF‐D caused a dose‐dependent vascular leakage and a moderate dilation of the capillaries. The highest effect was seen 6 days after gene transfer and was detectable for 2 weeks. Intravitreal injection of baculovirus caused expression of VEGF‐D in the inner retina, photorecetor cells and in retinal pigment epithelium cells, whereas adenovirus‐mediated VEGF‐D expression was detected in the nerve fiber layer and ganglion cell layer. Baculovirus caused a transient inflammation similar to adenoviruses.ConclusionsThe study suggests that baculoviruses are efficient vectors for ocular gene transfer, especially if deeper retinal layers need to be transduced. In addition, intravitreal VEGF‐D gene transfer caused blood–retina barrier breakdown but not neovessel formation in the rabbit eye. Copyright © 2009 John Wiley & Sons, Ltd.
Kinetic investigation on the reactions of p‐toluenesulfonyl chloride with p‐substituted benzoic acid(s) in the presence of triethylamine in aprotic solvents
Authors: Ananthalakshmi Subbiah , Nallu M. 
Published: March 2009

AbstractSecond‐order rate constants of the reactions of p‐toluenesulfonyl chloride with p‐substituted benzoic acids in the presence of triethylamine in acetonitrile/acetone under equimolar and pseudo‐first‐order conditions have been determined by the conductometric method using the Guggenheim principle at 25, 30, 35, and 40°C. The reactions follow second order with respect to the whole and first order with respect to each of the reactants. The order of reactivity of the substituents in benzoic acid is rationalized. Activation parameters are obtained by applying the usual methods. The Hammett plot has been found nonlinear, whereas the Bronsted plot shows good correlation. This may be explained on the basis of electronic effects of substituents on the reaction center. Kinetic data and the product analyses indicate that the reaction proceeds through direct nucleophilic attack on the sulfur center. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 303–308, 2009
Solution Self‐Assembly of Core‐Labeled Block Random‐Copolymers Prepared by Ring Opening Metathesis Polymerization
Authors: Sandholzer Martina , Slugovc Christian 
Published: March 2009

AbstractHerein, the synthesis of block random‐copolymers via ring opening metathesis polymerization (ROMP) is presented. A random‐copolymer of norbornene dimethyl ester with different xanthen‐functionalized norbornene derivatives was used as a hydrophobic block while, the hydrophilic part was built from an ethylene glycol‐substituted monomer. The self‐association of these block random‐copolymers in MeOH was strongly influenced by the ionization state of the dye molecules, as shown by a combination of UV–Vis absorption and dynamic light scattering measurements. Aggregate sizes were significantly smaller for samples with charged dye molecules in the core of the aggregate. These findings were attributed to ion pair formation of the charged dye molecules and the according counter ions, thus, inducing strongly attractive dipole–dipole interactions. The optical properties of the dyes under investigation, however, were preserved within the polymer aggregates.magnified image
New Perspective on Heat Deflection Temperature of Glassy Polycarbonate
Authors: Li Xiangyang , Mason James 
Published: March 2009

AbstractFor polycarbonate, the HDT values can vary over 20 °C. Many factors affect the test results. Among these, thermal dilatation and creep were discussed in detail. Quantitatively, the contribution from thermal dilatation to HDT values varies little with physical aging time, but the contribution from creep to HDT values changes greatly. When creep is insignificant, the HDT values can be calculated from an elastic beam deflection equation and are close to the Tg values. This paper qualitatively disputes the claims of the effect of residual stress on HDT values. It is argued that changes in residual stress level and HDT values with physical aging are symptoms of the structural relaxation, but no causal effect exists between these two symptoms. As a test method for amorphous polymers, Vicat or Tg can provide more reliable results than HDT.magnified image
Vesicles Formed by Oligostyrene‐block‐Oligoaniline‐block‐Oligostyrene Triblock Oligomer
Authors: Wang Hanfu , Han Yanchun 
Published: March 2009

AbstractNovel π‐conjugated coil–rod–coil triblock oligomers containing optoelectronic active oligoaniline segments were synthesized. The block oligomer can self‐assemble into diverse aggregating morphologies including spherical micelles and thin‐layer vesicles in THF, which is found associated with the removing of the protecting groups of oligoaniline segments. A possible mechanism was proposed to explain the self‐assembly behavior changes in which chain conformation variation of the aniline segments initiated from deprotection of the nitrogen atoms is pointed to be the key factor that dominates the transition process.magnified image
Comparison of Covalently and Noncovalently Functionalized Carbon Nanotubes in Epoxy
Authors: Liu Lei , Etika Krishna C. , Liao Kang‐Shyang , Hess Lance A. , Bergbreiter David E. , Grunlan Jaime C. 
Published: March 2009

AbstractCarbon nanotubes typically require the use of a dispersing or stabilizing agent to prevent significant aggregation during incorporation into a polymer matrix. These additives must be strongly associated, either covalently or physically, to achieve their purpose. In this study, multi‐walled carbon nanotubes (MWNTs) were dispersed into an epoxy matrix using polyethylenimine (PEI) as a dispersant that was either covalently attached to the nanotubes or physically mixed to result in only noncovalent interaction. Epoxy composites containing covalently modified MWNTs exhibited greater storage modulus and reduced electrical conductivity.magnified image
Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry
Authors: Dunn Jamie D. , Reid Gavin E. , Bruening Merlin L. 
Published: March 2009

AbstractMass spectrometry is the tool of choice to investigate protein phosphorylation, which plays a vital role in cell regulation and diseases such as cancer. However, low abundances of phosphopeptides and low degrees of phosphorylation typically necessitate isolation and concentration of phosphopeptides prior to MS analysis. This review discusses the enrichment of phosphopeptides with immobilized metal affinity chromatography, reversible covalent binding, and metal oxide affinity chromatography. Capture of phosphopeptides on TiO2 seems especially promising in terms of selectivity and recovery, but the success of all methods depends on careful selection of binding, washing, and elution solutions. Enrichment techniques are complementary, such that a combination of methods greatly enhances the number of phosphopeptides isolated from complex samples. Development of a standard series of phosphopeptides in a highly complex mixture of digested proteins would greatly aid the comparison of different enrichment methods. Phosphopeptide binding to magnetic beads and on‐plate isolation prior to MALDI‐MS are emerging as convenient methods for purification of small (µL) samples. On‐plate enrichment can yield >70% recoveries of phosphopeptides in mixtures of a few digested proteins and can avoid sample‐handling steps, but this technique is likely limited to relatively simple samples such as immunoprecipitates. With recent advances in enrichment techniques in hand, MS analysis should provide important insights into phosphorylation pathways. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:29–54, 2010
Effect of ultraviolet B radiation on activator protein 1 constituent proteins and modulation by dietary energy restriction in SKH‐1 mouse skin
Authors: Hopper Brian D. , Przybyszewski Joseph , Chen Haw‐Wen , Hammer Kimberly D.P. , Birt Diane F. 
Published: March 2009

AbstractThe study examined the timing of modulation of activator protein 1(AP‐1):DNA binding and production of AP‐1 constituent proteins by ultraviolet B (UVB) radiation and effect of dietary energy restriction [DER, 40% calorie reduction from fat and carbohydrate compared to control ad libitum (AL) diet] in SKH‐1 mouse epidermis. AP‐1:DNA binding by electromobility shift assay (EMSA) was increased in a biphasic manner after treatment with a tumor‐promoting suberythemal dose (750 mJ/cm2) of UVB light (311–313 nm) with peaks at 3 and 18 h postirradiation. DER overall reduced AP‐1:DNA binding in mock‐treated and UVB‐treated skin at 3 and 18 h after UVB treatment. The timing of modulation of production of AP‐1 constituent proteins by Western blot analysis was examined at 0 h (mock treatment), 3, 9, 18, and 24 h. We found that c‐jun (9 h), jun‐B (9 and 18 h), phosphorylated c‐jun (3 h), and fra‐1 (18 h) protein levels were increased after UVB treatment compared to mock controls. In a follow‐up diet experiment, animals were placed on DER or AL diet for 10–12 wk and treated with UVB as before. DER was found to completely block the UVB‐induced increase in phosphorylated c‐jun protein levels and decrease in fra‐2 protein levels at 18 h. In addition, DER enhanced UVB‐induced increase in jun B levels and lowered basal levels of c‐fos seen 18 h after UVB. These data suggest that DER may be able to assist in the prevention of UVB‐induced skin carcinogenesis by modulating AP‐1:DNA binding and AP‐1 constituent protein levels. © 2009 Wiley‐Liss, Inc.
Molecular effects of soy phytoalexin glyceollins in human prostate cancer cells LNCaP
Authors: Payton‐Stewart Florastina , Schoene Norberta W. , Kim Young S. , Burow Matthew E. , Cleveland Thomas E. , Boue Stephen M. , Wang Thomas T. Y. 
Published: March 2009

AbstractGlyceollins are soy‐derived phytoalexins that have been proposed to be candidate cancer preventive compounds. The effect of the glyceollins on prostate cancer is unknown. The present study examined the molecular effects of soy phytoalexin, glyceollins, on human prostate cancer cell LNCaP to further elucidate its potential effects on prostate cancer prevention. We found that the glyceollins inhibited LNCaP cell growth similar to that of the soy isoflavone genistein. The growth inhibitory effects of the glyceollins appeared to be due to an inhibition of G1/S progression and correlated with an up‐regulation of cyclin‐dependent kinase inhibitor 1 A and B mRNA and protein levels. By contrast, genistein only up‐regulates cyclin‐dependent kinase inhibitor 1A. In addition, glyceollin treatments led to down‐regulated mRNA levels for androgen responsive genes. In contrast to genistein, this effect of glyceollins on androgen responsive genes appeared to be mediated through modulation of an estrogen‐ but not androgen‐mediated pathway. Hence, the glyceollins exerted multiple effects on LNCaP cells that may be considered cancer preventive and the mechanisms of action appeared to be different from other soy‐derived phytochemicals. © 2009 Wiley‐Liss, Inc.
An exponentially fitted method for solving Burgers' equation
Authors: Öziş Turgut , Erdoğkan Utku 
Published: March 2009

AbstractIn this paper, an exponentially fitted method is used to numerically solve the one‐dimensional Burgers' equation. The performance of the method is tested on the model involving moderately large Reynolds numbers. The obtained numerical results show that the method is efficient, stable and reliable for solving Burgers' equation accurately even involving high Reynolds numbers for which the exact solution fails. Copyright © 2009 John Wiley & Sons, Ltd.
Thermodynamically consistent time‐stepping algorithms for non‐linear thermomechanical systems
Authors: Romero Ignacio 
Published: March 2009

AbstractWe present the basic theory for developing novel monolithic and staggered time‐stepping algorithms for general non‐linear, coupled, thermomechanical problems. The proposed methods are thermodynamically consistent in the sense that their solutions rigorously comply with the two laws of thermodynamics: for isolated systems they preserve the total energy and the entropy never decreases. Furthermore, if the governing equations of the problem have symmetries, the proposed integrators preserve them too. The formulation of such methods is based on two ideas: expressing the evolution equation in the so‐called General Equations for Non‐Equilibrium Reversible Irreversible Coupling format and enforcing from their inception certain directionality and degeneracy conditions on the discrete vector fields. The new methods can be considered as an extension of the energy–momentum integration algorithms to coupled thermomechanical problems, to which they reduce in the purely Hamiltonian case. In the article, the new ideas are applied to a simple coupled problem: a double thermoelastic pendulum with symmetry. Numerical simulations verify the qualitative features of the proposed methods and illustrate their excellent numerical stability, which stems precisely from their ability to preserve the structure of the evolution equations they discretize. Copyright © 2009 John Wiley & Sons, Ltd.
Electrical properties of isolated poly(3,4‐ethylenedioxythiophene) nanowires prepared by template synthesis
Authors: Long Y. Z. , Duvail J. L. , Chen Z. J. , Jin A. Z. , Gu C. Z. 
Published: March 2009

AbstractElectrical conductivity, current–voltage (I–V) characteristics, and low‐temperature magnetoresistance of template‐synthesized poly(3,4‐ethylenedioxythiophene) (PEDOT) nanowires are reported. The room‐temperature conductivity of the semiconducting nanowire with a diameter of 82 nm is about 80 S/cm. It is found that with lowering temperature, the I–V curves show a transition from linear to nonlinear around 50 K and a clear Coulomb‐gap‐like structure appears on the differential conductance (dI/dV) curves possibly due to enhanced electron–electron interaction. The resistance below 70 K is dependent on the applied bias voltage used in the resistance measurements due to the nonlinear I–V characteristics. The magnetoresistance below 10 K is positive and increases with lowering temperature due to the wavefunction shrinkage effect on hopping conduction. Copyright © 2009 John Wiley & Sons, Ltd.
Maximally safe resection followed by hypofractionated re‐irradiation for locally recurrent ependymoma in children
Authors: Liu Arthur K. , Foreman Nicholas K. , Gaspar Laurie E. , Trinidad Elizabeth , Handler Michael H. 
Published: March 2009

AbstractBackgroundTreatment failure in children with ependymoma is relatively common, with the majority of events consisting of local failure. Salvage therapy for these children historically had poor results, with repeated local recurrences. To improve these outcomes, we began to offer hypofractionated re‐irradiation after resection at first local recurrence. To minimize the duration of therapy, we chose a hypofractionated regimen that has been shown to be well tolerated in adult patients.ProcedureWe performed a review of the experience at the Children's Hospital in Denver and at the Department of Radiation Oncology at the University of Colorado Denver from 1995 to 2008 with hypofractionated re‐irradiation after maximally safe resection in children with locally recurrent ependymoma.ResultsSix children with locally recurrent ependymoma were seen in that time period. After maximally safe resection, all six received hypofractionated radiation therapy of 24–30 Gy delivered in three fractions. With a median follow‐up of 28 months from the time of re‐irradiation, all six children are alive with no evidence of disease. Three children had evidence of radiation necrosis, either clinically or based on imaging, but none required significant intervention.ConclusionsHypofractionated re‐irradiation after resection for locally recurrent ependymoma is well tolerated. This approach also appears to provide good local control. Additional follow‐up is required to determine the efficacy and potential late effects of hypofractionated re‐irradiation in this patient population. Pediatr Blood Cancer 2009;52:804–807. © 2009 Wiley‐Liss, Inc.