bluuebunny/crossref_metadata_2025 huggingface dataset:
Brief communication: Ancient nuclear DNA and kinship analysis: The case of a medieval burial in San Esteban Church in Cuellar (Segovia, Central Spain)
Authors: Gamba Cristina , Fernández Eva , Tirado Mirian , Pastor Francisco , Arroyo‐Pardo Eduardo
Published: December 2010

The aim of this work was to investigate a very common situation in the archaeological and anthropological context: the study of a burial site containing several individuals, probably related genetically, using ancient DNA techniques. We used available ancient DNA and forensic protocols to obtain reliable results on archaeological material. The results also enabled molecular sex determination to be compared with osteological data. Specifically, a modified ancient DNA extraction method combined with the amplification of nuclear markers with the AmpFlSTR®MiniFiler™ kit(Applied Biosystems) was used. Seven medieval individuals buried in four niches dated in the 15th Century at San Esteban Church in Cuellar (Segovia, Central Spain) were analyzed by the proposed method, and four of seven provided complete autosomal short tandem repeat (STRs) profiles. Kinship analyses comprising paternity and sibship relations were carried out with pedigree‐specific software used in forensic casework. A 99.98% paternity probability was established between two individuals, although lower percentages (68%) were obtained in other cases, and some hypothetical kinship relations were excluded. The overall results could eventually provide evidence for reconstructing the historical record. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.
Insectivory of savanna chimpanzees (Pan troglodytes verus) at Fongoli, Senegal
Authors: Bogart Stephanie L. , Pruetz Jill D.
Published: December 2010

Little is known about the behavior of chimpanzees living in savanna‐woodlands, although they are of particular interest to anthropologists for the insight they can provide regarding the ecological pressures affecting early hominins living in similar habitats. Fongoli, Senegal, is the first site where savanna chimpanzees have been habituated for observational data collection and is the hottest and driest site where such observation of chimpanzees occurs today. Previously, indirect evidence suggested these chimpanzees consumed termites throughout the year, an unusual occurrence for western and eastern chimpanzees. Although meat eating by chimpanzees continues to receive much attention, their use of invertebrate prey has received less emphasis in scenarios of hominin evolution. Here, we further examine the invertebrate diet of Fongoli chimpanzees using direct observational methods and accounting for potential environmental influences. Termite feeding positively correlated with high temperatures. Fongoli chimpanzees spend more time obtaining termites than any other chimpanzee population studied, and this extensive insectivory contributes to the list of distinctive behaviors they display relative to chimpanzees living in more forested habitats. We suggest that savanna chimpanzees at Fongoli differ significantly from chimpanzees elsewhere as a result of the selective pressures characterizing their harsh environment, and this contrast provides an example of a viable referential model for better understanding human evolution. Specifically, our results support the hypotheses that invertebrate prey may have figured more prominently into the diet of early hominins in similar habitats, especially given that invertebrates are an important source of protein and other essential nutrients in a highly seasonal environment. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.
Keys for Unlocking Photolabile Metal‐Containing Cages
Authors: Ciesienski Katie L. , Franz Katherine J.
Published: December 2010

Photolabile metal‐containing cages are metal complexes that undergo a change in coordination environment upon exposure to light of an appropriate wavelength. The light‐responsive functionality can either be a component of the encapsulating ligand or a property of the metal complex itself. The altered coordination properties of light‐responsive complexes can result in release of the coordinated metal ion into its surroundings, a differential reactivity of the metal center, or the liberation of a reactive molecule that had been passivated by binding to the metal center. These triggerable agents can be useful tools for manipulating the bioavailability of metals or their coordinating ligands in order to study biological pathways or for potential therapeutic purposes.
Protective Effect of Quercetin on Cadmium‐Induced Oxidative Toxicity on Germ Cells in Male Mice
Authors: Bu Tongliang , Mi Yuling , Zeng Weidong , Zhang Caiqiao
Published: December 2010

Cadmium is a toxic heavy metal that is widely distributed in the environment. As a critical process, oxidative toxicity mediates the morphological and functional damages in germ cells after cadmium exposure. In this study, the protective effect of quercetin on cadmium‐induced oxidative toxicity was investigated in mouse testicular germ cells. After oral administration of cadmium chloride at 4 mg/kg body weight for 2 weeks, damages in spermatozoa occurred in the early stage of spermatogenesis. Cadmium treatment significantly decreased the testicular antioxidant system, including decreases in the glutathione (GSH) level, superoxide dismutase (SOD), and GSH peroxidase (GSH‐Px) activities. Moreover, exposure to cadmium resulted in an increase of hydrogen peroxide production and lipid peroxidation in testes. In addition, cadmium provoked germ cell apoptosis by upregulating expression of the proapoptotic proteins Bax and caspase‐3 and downregulating expression of the antiapoptotic protein Bcl‐XL. However, combined administration of a common flavonoid quercetin at 75 mg/kg body weight significantly attenuated cadmium‐induced germ cell apoptosis by suppressing the hydrogen peroxide production and lipid peroxidation in testicular tissue. Simultaneous supplementation of quercetin markedly restored the decrease in GSH level and SOD and GSH‐Px activities elicited by cadmium treatment. Additionally, quercetin protected germ cells from cadmium‐induced apoptosis by downregulating the expression of Bax and caspase‐3 and upregulating Bcl‐XL expression. These results indicate that quercetin, due to its antioxidative and antiapoptotic characters, may manifest effective protective action against cadmium‐induced oxidative toxicity in mouse testicular germ cells. Anat Rec, 2011. © 2010 Wiley‐Liss, Inc.
A modern Bayesian look at the multi‐armed bandit
Authors: Scott Steven L.
Published: December 2010

A multi‐armed bandit is an experiment with the goal of accumulating rewards from a payoff distribution with unknown parameters that are to be learned sequentially. This article describes a heuristic for managing multi‐armed bandits calledrandomized probability matching, which randomly allocates observations to arms according the Bayesian posterior probability that each arm is optimal. Advances in Bayesian computation have made randomized probability matching easy to apply to virtually any payoff distribution. This flexibility frees the experimenter to work with payoff distributions that correspond to certain classical experimental designs that have the potential to outperform methods that are ‘optimal’ in simpler contexts. I summarize the relationships between randomized probability matching and several related heuristics that have been used in the reinforcement learning literature. Copyright © 2010 John Wiley & Sons, Ltd.
Disposable Miniaturized Screen‐Printed pH and Reference Electrodes for Potentiometric Systems
Authors: Musa Arnaud Emmanuel , del Campo Francisco Javier , Abramova Natalia , Alonso‐Lomillo María Asunción , Domínguez‐Renedo Olga , Arcos‐Martínez María Julia , Brivio Monica , Snakenborg Detlef , Geschke Oliver , Kutter Jörg Peter
Published: December 2010

This work describes the development of a miniaturized potentiometric system comprising a miniaturized quasi‐reference electrode (QRE) coupled to a solid‐state ion‐selective electrode (ISE) for the monitoring of pH. We describe the optimization of materials and fabrication processes including screen‐printing (SP), electrode treatments (thermal and electrochemical) and the formulation and deposition of an ion‐selective membrane (ISM), to obtain a system compliant with biomedical specifications. We developed a potentiometric system composed of an Ag/AgCl QRE and a pH‐electrode (ISM deposited on a graphite electrode) that can be used continuously for a period of not less than 7 days in aqueous solutions. Curing the Ag/AgCl pastes during 20 minutes at 120 °C after printing allowed the QREs to display excellent potential stability, as demonstrated by an open‐circuit‐potential standard deviation of ±1.2 mV over a period of 7 days (n=3 samples). Promoting adhesion of the pH membrane over graphite electrodes improved the pH‐electrode performance. This was achieved through a combination of thermal treatment and electrochemical activation of the electrodes by cyclic voltammetry (CV). The final device integrated both the QRE and the pH‐electrode, and displayed an average pH sensitivity of −60.8±1.7 mV per pH unit, over a pH range of 7.00 to 7.63.
Theoretical models of separation selectivity for charged compounds in micellar electrokinetic chromatography
Authors: Puangpila Chanida , Petsom Amorn , Nhujak Thumnoon
Published: December 2010

Equations and theoretical models for MEKC separation selectivity (αMEKC) were established to explain a change in separation and electrophoretic mobility order of fully charged analytes, in which αMEKC is related to the dimensionless values of mobility selectivity in CZE (αCZE) and retention selectivity (αk) in MEKC, and where αCZE and αk are defined as the ratio of electrophoretic mobility in CZE and the ratio of retention factor (k) in MEKC for two charged analytes, respectively. Using four alkylparabens as test analytes, excellent agreement was found between the observed αMEKC and the proposed αMEKC models of test analytes in MEKC over a wide range of SDS concentrations and values of k. For example, in comparison with CZE separation of charged analytes, MEKC separation can enhance separation selectivity up to the maximum value when the selectivity ratio (ρ) is greater than 1.0 (ρ=αk/αCZE), while lower separation selectivity is obtained with ρ<1.0 (αCZE>αk>1).
Bundled capillary electrophoresis using microstructured fibres
Authors: Rogers Benjamin , Gibson Graham T. T. , Oleschuk Richard D.
Published: December 2010

Joule heating, arising from the electric current passing through the capillary, causes many undesired effects in CE that ultimately result in band broadening. The use of narrow‐bore capillaries helps to solve this problem as smaller cross‐sectional area results in decreased Joule heating and the rate of heat dissipation is increased by the larger surface‐to‐volume ratio. Issues arising from such small capillaries, such as poor detection sensitivity, low loading capacity and high flow‐induced backpressure (complicating capillary loading) can be avoided by using a bundle of small capillaries operating simultaneously that share buffer reservoirs. Microstructured fibres, originally designed as waveguides in the telecommunication industry, are essentially a bundle of parallel ∼5 μm id channels that extend the length of a fibre having otherwise similar dimensions to conventional CE capillaries. This work presents the use of microstructured fibres for CZE, taking advantage of their relatively high surface‐to‐volume ratio and the small individual size of each channel to effect highly efficient separations, particularly for dye‐labelled peptides.
5‐Aza‐2′‐deoxycytidine and interleukin‐1 cooperate to regulate matrix metalloproteinase‐3 gene expression
Authors: Couillard Julie , Estève Pierre‐Olivier , Pradhan Sriharsa , St‐Pierre Yves
Published: December 2010

Members of the matrix metalloproteinase (MMP) family of enzymes play a critical role in extracellular matrix remodeling in a number of normal and pathologic processes. Accordingly, activation of MMP gene expression is tightly regulated at the level of transcription by specific transcription factors, most notably following exposure to inflammatory cytokines. Recent studies with 5‐aza‐2′‐deoxycytidine (5‐aza‐dC), a specific DNA methylase inhibitor, also suggest that epigenetic processes contribute to the regulation of MMP expression. Although inflammation‐related aberrant patterns of DNA methylation have been described, a mechanistic link between inflammation and epigenetic alterations in the control of MMP expression remains unclear. Here, we provide evidence that increased MMP‐3 expression by 5‐aza‐dC is modulated by interleukin‐1 (IL‐1). More specifically, we found that stimulation with IL‐1, but not with IL‐6 or TNFα, significantly increased the hypomethylation status of the MMP‐3 promoter to a level similar to that found in dnmt1/dnmt3b‐deficient HCT116 (DKO) cells. Furthermore, we showed that increased MMP‐3 expression by 5‐aza‐dC was associated with increased expression and activity of specific transcription factors known to regulate MMP‐3 expression. In fact, treatment with 5‐aza‐dC was obligatory for some transcription factors to trigger an increase in MMP‐3 expression, such as Ap‐1. In contrast, CCAAT enhancer‐binding proteins and E‐twenty six were capable of inducing MMP‐3 alone. Overall, these findings provide a novel perspective of the collaborative role of 5‐aza‐dC and inflammatory cytokines with specific transcription factors that are normally involved in MMP‐3 expression.
Moving from assessment to institutional improvement
Authors: Blaich Charles F. , Wise Kathleen S.
Published: December 2010

This chapter describes strategies developed from the Wabash National Study of Liberal Arts Education to help institutions shift their focus from gathering assessment data to using it to improve student learning.
Effects of Progesterone, Testosterone, and Estrogen on Sexual Reproduction of the RotiferBrachionus calyciflorus
Authors: Yang Jiaxin , Snell Terry W.
Published: December 2010

It is known that some vertebrate reproductive hormones have effects on rotifer reproduction, but little is known about their effects in combination. This motivated us to examine the effects of waterborne progesterone (P), testosterone (T), and estradiol (E) on reproduction of the rotiferBrachionus calyciflorus, comparing exposures to single hormones and mixtures with a total concentration of 1000 μg/L. Asexual population growth (r) was high in all treatments, ranging from 1.28 to 1.43 d–1(P‐E), and from 0.99 to 1.22 d–1(P‐T). These results indicate that E, P, or T alone, or in combinations of P‐E and P‐T totaling 1000 µg/L, and the 3‐way combination P‐E‐T at 1200 µg/L do not reduce the asexual reproduction ofB. calyciflorus. However, significant effects were detected on sexual reproduction with exposure to these hormone concentrations. Exposure to P‐T and P‐E at 1000 μg/L decreased resting egg production significantly. Analysis of mating indicated that fertilization was 5.3 times higher in the control than in treatments where females were exposed to 500 µg/L each P‐T. A similar result was observed when both females and males were exposed to 500 µg/L each of P‐T. When males alone were treated with 500 µg/L each of P‐T, there was no significant difference in male fertility compared to the control. These results suggest thatB. calyciflorususes oxidized sterols similar to P and T to regulate sexual reproduction and waterborne exposure of females to these compounds interferes with fertilization and resting egg production. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Inorganic coatings for cardiovascular stents: In vitro and in vivo studies
Authors: Mikhalovska Lyuba , Chorna Nataliya , Lazarenko Oleg , Haworth Peter , Sudre Arnaud , Mikhalovsky Sergey
Published: December 2010

The in‐vitro and in‐vivo biocompatibility of two oxides (TiO and ZrO) and diamond‐like carbon (D) coated stents has been assessed and compared with uncoated stainless steel (St) stents. In vitro studies demonstrated that both fibrinogen adsorption and platelet adhesion were significantly higher on D coating compared to those on oxide coatings and uncoated stainless steel. In addition TiO and ZrO coatings showed evidence of a minor inflammatory response and more complete endothelialization of the aorta than that seen around D coated and uncoated St stents. The resulting neointimal growth in the aorta with TiO, ZrO, and D coated and uncoated St stents, measured 8 weeks after stenting (the ratio of the neointima in the stented artery to the non‐stented artery) was 1.03 + 0.28, 0.85 + 0.36, 1.78 + 1.26, and 1.15 + 0.56, accordingly. From the data obtained it could be concluded that the increased neointima measured around D‐coated stents, may be due to both, the inferior haemocompatibility of the diamond‐like carbon coating and mechanical instability of D coating observed in an in vivo environment. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
Anti‐DNA antibody modified coronary stent for plasmid gene delivery: results obtained from a porcine coronary stent model
Authors: Zhang Lin‐Hua , Luo Tong , Zhang Chao , Luo Peng , Jin Xu , Song Cun‐Xian , Gao Run‐Lin
Published: December 2010

Background

Previous work in our laboratory has demonstrated that the anti‐DNA antibody‐immobilized stent results in highly site‐specific gene delivery in a rabbit carotid model. As a result of the similarity in the anatomy and physiology of the pig and human cardiovascular systems, the porcine coronary stent model was used in the present study to evaluate the site‐specificity, efficiency and long‐term therapeutic effect of this gene delivery system in pig coronary arteries.

Methods

A reporter plasmid pEGFP (pEGFP‐C1) was tethered on the antibody‐immobilized stents and assessed for site‐specificity and efficiency in a pig coronary stent model. Inducible nitric oxide synthase (NOS) cDNA (pcDNA3.1‐iNOS) was tethered on the stent as a therapeutic gene to evaluate the site‐specificity and long‐term therapeutic effect of this novel gene delivery system for the inhibition of restenosis after coronary stenting for 28 days.

Results

Both the pEGFP‐C1 and pcDNA3.1‐iNOS tethered stents achieved site‐specific gene transfection without distal spreading in the porcine coronary model. The overall GFP transfection efficiency was 2.6 ± 0.9% of the total cells, whereas the neointimal transfection was more than 6%. Histology and morphology studies showed no significant artery stenosis and intimal proliferation for 28 days after coronary stenting using pcDNA3.1‐iNOS tethered stents.

Conclusions

For the first time, we report the successful use of anti‐DNA antibody‐immobilized stent as plasmid gene delivery system that possess high efficiency and site‐specificity in a porcine coronary stent model. The novel system showed long‐term therapeutic effects on the inhibition of restenosis when pcDNA3.1‐iNOS was tethered on the stent. Copyright © 2010 John Wiley & Sons, Ltd.
Tritium labelling of pharmaceuticals by metal‐catalysed exchange methods
Authors: Hesk D. , Lavey C. F. , McNamara P.
Published: December 2010

Metal‐catalysed exchange with tritiated water and tritium gas has been extensively used to prepare a wide range of tritium‐labelled compounds in support of pharmaceutical research. Examples of the utility of both heterogeneous and homogeneous metal catalysts to label a very broad range of structures will be discussed in this review. Copyright © 2010 John Wiley & Sons, Ltd.
The use of metal‐catalysed hydrogen isotope exchange in the contract supply of tritiated compounds
Authors: Chappelle Michael R. , Hawes Calvin R.
Published: December 2010

The metal‐catalysed tritium exchange labelling methods available to a contract labelling facility, and the principles that dictate the selection of the most appropriate method are described. Copyright © 2010 John Wiley & Sons, Ltd.
Novel isolation of phytochemical compositions by phase transition extraction with acetonitrile
Authors: Liu Guozhu , Yang Huawu , Zhang Mingshan , Li Shengjun , Chen Bo , Yao Shouzhuo
Published: December 2010

Based on the phenomenon that hydrophilic acetonitrile can be separated from water by adding a hydrophobic solvent, a phase transition extraction (PTE) method for isolation of phytochemical compositions was developed. The isolation efficiency of the proposed method was assessed in complete grouping of the constituents in three important traditional Chinese medicine plants. Further study of the PTE for Scutellaria bacalensis Georgi found that the constituents in the organic phase are all flavonoid aglycones while the ones in the aqueous phase are all flavonoid glycosides, revealing the property of high structure selectivity for the proposed PTE process. The effect of using different modifiers on the isolation efficiency was investigated. The results obtained by using non‐oxygenated hydrophobic solvents are perfect while those by inorganic salts are acceptable, but those by oxygenated hydrophobic solvents are bad. Subsequent GC analysis revealed that the solvent composition difference between the two separated phases among PTE processes using different types of modifier is responsible for the different isolation results obtained. Finally, the proposed method was proved to be insensitive to both the acetonitrile concentration and the added amount of modifier.
Transparent and Conductive Graphene Oxide/Poly(ethylene glycol) diacrylate Coatings Obtained by Photopolymerization
Authors: Sangermano Marco , Marchi Sophie , Valentini Luca , Bon Silvia Bittolo , Fabbri Paola
Published: December 2010

Water‐dispersed graphene oxide sheets were used to prepare graphene/poly(ethylene glycol) diacrylate resin composites by photopolymerization. It was found that graphene sheets undergo excellent morphological distribution within the resin system, giving rise to transparent composites with unaltered thermal properties with respect to the neat resin, that are electrically conductive at loading ratios as low as 0.02 wt.‐% of graphene oxide. The proposed strategy based on photopolymerization provides an easy, energy‐saving and environmental friendly technique that can find a wide application in coating technology, mainly for electromagnetic shielding and antistatic coatings.

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Mass spectrometry‐based proteomics approaches applied in cataract research
Authors: Kyselova Z.
Published: December 2010

Cataract, the opacification of the eye lens, is the leading cause of blindness worldwide—it accounts for approximately 42% of all cases. The lens fibers have the highest protein content within the body, more than 35% of their wet weight. Given the eye lens pure composition of highly abundant structural proteins crystallins (up to 90%), it seems to be an ideal proteomic entity to study and might be also hypothesized to model the other protein conformational diseases. Crystallins are extremely long‐lived, and there is virtually no protein turnover. This provides great opportunities for post‐translational modifications (PTM) to occur and to predispose lens to the cataract formation. Despite recent progress in proteomics, the human lens proteome remains largely unknown. Mass spectrometry hold great promise to determine which crystallin modifications lead to a cataract. Quantitative analysis of PTMs at the peptide level with proteomics is a powerful bioanalytical tool for lens‐tissue samples, and provides more comprehensive results. New mass spectrometry‐based approaches that are being applied to lens research will be highlighted. Finally, the future directions of proteomics cataract research will be outlined. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:1173–1184, 2011
Numerical modeling of hot tearing formation in metal casting and its validations
Authors: Zhu J. Z. , Guo J. , Samonds M. T.
Published: December 2010

Hot tearing is one of the most serious defects for a metal casting. The nucleation and propagation of the hot tearing can result in permanent defects in the casting, which may cause the final cast product to be unusable. It is believed that the imposed strains and stresses on the solid framework in the mushy zone by the solidification shrinkage and thermal contraction create the conditions for hot tearing. It has been very well documented that the composition of the alloy and the mechanical properties of the metals in the semi‐solid state play critical roles in the formation of hot tears. To predict the susceptibility of hot tearing in a casting, a hot tearing indictor is proposed which is based on Gurson's constitutive model and uses the thermophysical and thermomechanical properties obtained from a thermodynamic calculation in the final stage of solidification. The numerical implementation of the hot tearing indicator is described in detail and the numerical modeling of the hot tearing formation is validated by experiments. Copyright © 2010 John Wiley & Sons, Ltd.
Conforming local meshfree method
Authors: Tian Rong , To Albert C. , Liu Wing Kam
Published: December 2010

This work is motivated by the current numerical limitation in multiscale simulation of ductile fracture processes at scale down to the microstructure size and aims to overcome the difficulties in 3D complicated mesh generation and locally extremely large strain analysis (local mesh distortion). The proposed ‘conforming local meshfree approximation’ directly and exactly satisfies displacement compatibility on a non‐conforming assembly mesh. Local meshfree nodes, which can be freely placed and move on a finite element mesh, describe local large deformation. The improved accuracy on non‐conforming mesh, the exactness in geometry representation on a structured mesh, and the good tolerance to mesh distortion are demonstrated by numerical examples. Copyright © 2010 John Wiley & Sons, Ltd.
A new shell formulation using complete 3D constitutive laws
Authors: Sansalone M. , Sabourin F. , Brunet M.
Published: December 2010

This paper should not be only regarded as a presentation of new shell elements but rather as a methodology which can be applied to most classical shell elements and has two aims: Achieving the same results in bending cases while breaking from plane stress state hypothesis and adding a normal stress component for process simulations such as hydro‐forming, hemming, sheet metal forming with bottoming, flanging, incremental forming and so on. Owing to the non‐linear applications quoted before, only shell elements with one integration point on the mid‐plane are selected: Triangles that are naturally constant strain elements and reduced integration quadrilaterals. The method mainly consists of adding a central node at the center (of gravity for a triangle) with two degrees of freedom: Two translations normal to the mid‐surface for which one corresponds to the bottom surface (‘lower skin’ of the shell) and the other to the top surface (‘upper skin’ of the shell). Then a full 3D constitutive strain–stress behavior can be used. For triangles in bending state—either based on Kirchhoff's or on Mindlin's assumptions—, it is shown that the results are exactly the same as those given by the initial formulation of these elements using a plane stress hypothesis. For quadrilaterals, the results are slightly different but many numerical examples—including non‐linear computations—prove that those differences are not significant. Copyright © 2010 John Wiley & Sons, Ltd.
Preparation of cycloolefin copolymers of a bulky tricyclopentadiene
Authors: Park Hyeong Cheol , Kim Ahreum , Lee Bun Yeoul
Published: December 2010

Copolymerizations of ethylene and tricyclopentadiene (TCPD) are realized without formation of a gel with a high activity (3–18 × 106 g/molZr·h) using a catalytic system of [Ph2C(Flu)(Cp)]ZrCl2/MMAO. The monomer reactivity ratios, rethylene and rTCPD, determined through the Fineman‐Ross plot, are 6.4 and 0.044, respectively, indicating that TCPD insertion is unfavorable, negligibly allowing the successive TCPD insertions. A significant higher glass transition temperature (Tg) is attained than those observed for other reported cycloolefin copolymers at the same cycloolefin content. A Tg as high as 214 °C is attainable at 41 mol % TCPD content. The remaining double bond can be hydrogenated to saturated hydrocarbon or converted to an epoxide group. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Characterizing diffusion dynamics of a membrane protein associated with nanolipoproteins using fluorescence correlation spectroscopy
Authors: Gao Tingjuan , Blanchette Craig D. , He Wei , Bourguet Feliza , Ly Sonny , Katzen Federico , Kudlicki Wieslaw A. , Henderson Paul T. , Laurence Ted A. , Huser Thomas , Coleman Matthew A.
Published: December 2010

Nanolipoprotein particles (NLPs) represent a unique nanometer‐sized scaffold for supporting membrane proteins (MP). Characterization of their dynamic shape and association with MP in solution remains a challenge. Here, we present a rapid method of analysis by fluorescence correlation spectroscopy (FCS) to characterize bacteriorhodopsin (bR), a membrane protein capable of forming a NLP complex. By selectively labeling individual components of NLPs during cell‐free synthesis, FCS enabled us to measure specific NLP diffusion times and infer size information for different NLP species. The resulting bR‐loaded NLPs were shown to be dynamically discoidal in solution with a mean diameter of 7.8 nm. The insertion rate of bR in the complex was ∼55% based on a fit model incorporating two separate diffusion properties to best approximate the FCS data. More importantly, based on these data, we infer that membrane protein associated NLPs are thermodynamically constrained as discs in solution, while empty NLPs appear to be less constrained and dynamically spherical.
Synergistic and antagonistic interactions of terpenes againstMeloidogyne incognitaand the nematicidal activity of essential oils from seven plants indigenous to Greece
Authors: Ntalli Nikoletta G , Ferrari Federico , Giannakou Ioannis , Menkissoglu‐Spiroudi Urania
Published: December 2010

BACKGROUND:Biorational means for phytonematode control were studied within the context of an increasingly ecofriendly pest management global approach. The nematicidal activity and the chemical composition of essential oils (EOs) isolated from seven plants grown in Greece and ten selected compounds extracted from them against second‐stage juveniles (J2) ofMeloidogyne incognita(Kof. & White) Chitwood were evaluated using juvenile paralysis experiments. Additionally, synergistic and antagonistic interactions between nematicidal terpenes were studied using an effect addition model, with the comparison made at one concentration level.

RESULTS:The 96 h EC50values ofFoeniculum vulgareMill.,Pimpinella anisumL.,Eucalyptus meliodoraA Cunn ex Schauer andPistacia terebinthusL. were 231, 269, 807 and 1116 µg mL−1, respectively, in an immersion bioassay. Benzaldehyde (9 µg mL−1) was the most toxic compound, followed by γ‐eudesmol (50 µg mL−1) and estragole (180 µg mL−1), based on 96 h EC50values. The most potent terpene pairs between which synergistic actions were found, in decreasing order, were:trans‐anethole/geraniol,trans‐anethole/eugenol, carvacrol/eugenol and geraniol/carvacrol.

CONCLUSION:This is the first report on the activity ofF. vulgare, P. anisum, E. meliodoraandP. terebinthus, and additionally on synergistic/antagonistic nematicidal terpene interactions, againstM. incognita, providing alternative methods for nematode control. Copyright © 2010 Society of Chemical Industry
Isolated silicon waveguides via porous silicon formation by targeted fluorine doping
Authors: Winans Joshua D. , Lee Jonathan Y. , Veeramachaneni Bharat , Hu Shaoting , Kawamura Daiji , Witt Kevin , Hirschman Karl D. , Fauchet Philippe M.
Published: December 2010

In this work, a combination of fluorine and boron ion implantation is used to create regions of higher and lower effective hole concentrations. Porous silicon formation is selective to the areas of higher hole concentration and this selectivity leads to isolated silicon regions surrounded by porous silicon. The effect of varying the annealing conditions on the final depth of the isolated crystalline silicon is also explored. The resulting porous silicon is oxidized to create an isolated region of crystalline silicon capable of functioning as an optical waveguide near 1550 nm.

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The cross section of a typical waveguide created with this process and an overlay of the TE fundamentalE‐field mode profile for 1550 nm wavelength light source.
Effect of wet‐chemical substrate pretreatment on electronic interface properties and recombination losses of a ‐Si:H/c ‐Si and a ‐SiNx:H/c ‐Si hetero‐interfaces
Authors: Angermann Heike , Wünsch Frank , Kunst Marinus , Laades Abdelazize , Stürzebecher Uta , Conrad Erhard , Korte Lars , Schmidt Manfred
Published: December 2010

Surface charge, surface state density and interface recombination behavior on polished float zone (FZ) solar cell substrates were investigated after various wet‐chemical pre‐cleaning procedures and deposition of amorphous silicon (a‐Si:H) or silicon nitride (a‐SiNx:H). Applying surface photo voltage (SPV), microwave detected photo conductance decay (µW‐PCD) and transient microwave conduction (TRMC) measurements, electronic interface properties were monitored repeatedly during the preparation processes. As shown for an inverted a‐Si:H/c‐Si hetero‐junction structure, with front side passivation by a‐SiNx:H and a p‐type a‐Si:H emitter on the rear side, the effect of optimised wet‐chemical pre‐treatment can be preserved during the subsequent soft plasma enhanced chemical vapour deposition of a‐Si:H or a‐SiNx:H. This leads to hetero‐interfaces with low interface recombination velocities. These results were compared to previously reported findings, obtained on textured Czochralski (CZ) single crystalline substrates. a‐SiNx:H is known to result in a field effect passivation. Nevertheless a strong influence of wet‐chemical treatments on surface charge and recombination losses was observed on both flat and textured a‐SiNx:H/c‐Si interfaces. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Morphology of contact printed colloidal quantum dots in organic semiconductor films: Implications for QD‐LEDs
Authors: Aidala Katherine E. , Panzer Matthew J. , Anikeeva Polina O. , Halpert Jonathan E. , Bawendi Moungi G. , Bulović Vladimir
Published: December 2010

Quantum dot light emitting devices (QD‐LEDs) con‐sist of a monolayer of QDs sandwiched between a hole transporting layer (HTL) and electron transporting layer (ETL) of organic materials. These hybrid devices emit with the narrow bandwidth characteristic of the QDs. The precise position of the QD layer, relative to the interface between the ETL and HTL, can affect the quantum efficiency of the device on the scale of 10 nm or less.

Motivated by this observation, the exact nature of the morphology of contact printed and self‐assembled QDs on typical organic materials is investigated. The QDs are substantially pressed into the organic material, to a somewhat greater extent when contact printed compared to self‐assembled structures. Measured device characteristics from samples made with the two methods are consistent with these observations (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
6 MHz BAW resonators fabricated using new piezoelectric crystals PrCa4O(BO3)3and NdCa4O(BO3)3
Authors: Yu Fapeng , Zhang Shujun , Zhao Xian , Yuan Duorong , Wang Qing‐ming , Shrout Thomas R.
Published: December 2010

Thickness shear mode Bulk Acoustic Wave (BAW) resonators with frequency of 6 MHz, were fabricated using monoclinic piezoelectric crystals PrCa4O(BO3)3(PrCOB) and NdCa4O(BO3)3(NdCOB). Zero temperature coefficient of frequency (TCF) characteristics were achieved over the temperature range of –140 °C to 200 °C for (YXt)–1.5° cut PrCOB and (YXt)15° cut NdCOB, with the turnover temperature at 20 °C. The electromechanical coupling factork26and the piezoelectric coefficientd26were determined to be 30.2% and 15.8 pC/N for PrCOB, 29.0% and 15.1 pC/N for NdCOB resonators, respectively. The temperature independent frequency behavior, large coupling factor, high piezoelectric coefficient, together with noticeable mechanical quality factors (Q> 2,500), make PrCOB and NdCOB crystals good candidates for sensing applications with expanded temperature usage range. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Flavonoids inhibit angiogenic cytokine production by human glioma cells
Authors: Freitas Sandra , Costa Silvia , Azevedo Camila , Carvalho Gerson , Freire Songeli , Barbosa Pedro , Velozo Eudes , Schaer Robert , Tardy Marcienne , Meyer Roberto , Nascimento Ivana
Published: December 2010

VEGF and TGF‐β1 are cytokines that stimulate tissue invasion and angiogenesis. These factors are considered as molecular targets for the therapy of glioblastoma. Bevacizumab, a recombinant humanized monoclonal antibody developed against VEGF, inhibits endothelial cell proliferation and vessel formation. Flavonoids obtained from Dimorphandra mollis and Croton betulaster have been described as proliferation inhibitors of a human glioblastoma derived cell line. VEGF and TGF‐β1 levels were dosed by ELISA in a GL‐15 cell line treated with bevacizumab and also with the flavonoids rutin, 5‐hydroxy‐7,4′‐dimethoxyflavone, casticin, apigenin and penduletin. Rutin reduced the VEGF and TGF‐β1 levels after 24 h but not after 72 h. The other flavonoids significantly reduced TGF‐β1 production. Bevacizumab reduced only the VEGF levels in the supernatant from GL‐15 cultures. These results suggest that the flavonoids studied, and commonly used in popular medicine, present an interesting subject of study due to their potential effect as angiogenic factor inhibitors. Copyright © 2010 John Wiley & Sons, Ltd.
Generalized pairwise comparisons of prioritized outcomes in the two‐sample problem
Authors: Buyse Marc
Published: December 2010

This paper extends the idea behind the U‐statistic of the Wilcoxon–Mann–Whitney test to perform generalized pairwise comparisons between two groups of observations. The observations are outcomes captured by a single variable, possibly repeatedly measured, or by several variables of any type (e.g. discrete, continuous, time to event). When several outcomes are considered, they must be prioritized. We show that generalized pairwise comparisons extend well‐known non‐parametric tests, and illustrate their interest using data from two randomized clinical trials. We also show that they lead to a general measure of the difference between the groups called the ‘proportion in favor of treatment’, denoted Δ, which is related to traditional measures of treatment effect for a single variable. Copyright © 2010 John Wiley & Sons, Ltd.
Estimating the distribution of the window period for recent HIV infections: A comparison of statistical methods
Authors: Sweeting Michael J. , De Angelis Daniela , Parry John , Suligoi Barbara
Published: December 2010

In the past few years a number of antibody biomarkers have been developed to distinguish between recent and established Human Immunodeficiency Virus (HIV) infection. Typically, a specific threshold/cut‐off of the biomarker is chosen, values below which are indicative ofrecent infections. Such biomarkers have attracted considerable interest as the basis for incidence estimation using a cross‐sectional sample. An estimate of HIV incidence can be obtained from the prevalence ofrecent infection, as measured in the sample, and knowledge of the time spent in therecent infectionstate, known as the window period. However, such calculations are based on a number of assumptions concerning the distribution of the window period. We compare two statistical methods for estimating the mean and distribution of a window period using data on repeated measurements of an antibody biomarker from a cohort of HIV seroconverters. The methods account for the interval‐censored nature of both the date of seroconversion and the date of crossing a specific threshold. We illustrate the methods using repeated measurements of the Avidity Index (AI) and make recommendations about the choice of threshold for this biomarker so that the resulting window period satisfies the assumptions for incidence estimation. Copyright © 2010 John Wiley & Sons, Ltd.
The analysis of cross‐over trials with baseline measurements
Authors: Metcalfe Chris
Published: December 2010

The statistical power of cross‐over trials can be increased by taking ‘baseline’ measurements of the outcome variable at the start of each treatment period. Analysis of covariance (ANCOVA), rather than analysis of change scores, takes best advantage of this. However, ANCOVA can give biased treatment effect estimates in observational studies with true baseline imbalance. While in truth balanced, chance baseline imbalance is possible in individual randomized cross‐over studies due to their typically small sample size. Although such chance imbalance does not cause biased estimation on average over repeated trials, this simulation study will aim to confirm the appropriateness of ANCOVA when faced with the analysis of data from an individual trial in which chance baseline imbalance is clearly apparent. Randomized cross‐over trials were simulated, varying in sample size and the pattern and strength of correlation between repeated measures. Estimates from ANCOVA, change scores, and post‐treatment difference were unbiased on average across each set of simulated data sets. ANCOVA and change scores could use baseline information to improve precision, but change scores could also reduce precision if baseline measures were uninformative. Change scores only were correlated with chance within‐subject baseline imbalance. All three estimators could be correlated with chance between‐subjects imbalance in the first period baseline measurements, the strongest associations being with the post‐treatment difference. Consistent results were obtained from a real data example. In conclusion, ANCOVA took best advantage of baseline measures to improve precision, and avoided bias in the widest set of circumstances with chance imbalance in those baseline measures. Copyright © 2010 John Wiley & Sons, Ltd.
Time‐dependent ROC analysis for a three‐class prognostic with application to kidney transplantation
Authors: Foucher Y. , Giral M. , Soulillou J. P. , Daures J. P.
Published: December 2010

The medical decision‐making community has an extensive literature on the use of receiver operating characteristic (ROC) graphs for diagnostic testing. Heagertybiet al. have recently developed this ROC curve theory within the context of survival data (Biometrics 2000; 56:337–344). The time‐dependent ROC method allows evaluating the accuracy of a marker to predict a time‐dependent failure, whereas the classic methodology focuses on diagnosis. One limitation to this approach, however, is to analyse a single failure. In many medical situations, a marker can be useful to predict different competitive failures. For example in kidney transplantation, the terminal evolution can be a return to dialysis or the death of the patient. With this application in mind, our paper proposes an extension of the time‐dependent ROC method for analysing the accuracy of a marker to predict two competitive events. Copyright © 2010 John Wiley & Sons, Ltd.
Composition and starch digestibility of whole grain bars containing maize or unripe banana flours
Authors: Utrilla‐Coello Rubí G. , Agama‐Acevedo Edith , Osorio‐Díaz Perla , Tovar Juscelino , Bello‐Pérez Luis A.
Published: December 2010

The development of functional foods with low glycemic index and high levels of RS are of importance in the fight against the rapidly increasing rates of obesity and chronic diseases in modern societies. In this work, three cereal bars containing white maize, blue maize, or unripe banana flours were prepared. The proximal composition, in vitro starch digestibility and product acceptability were evaluated. The bar prepared with blue maize exhibited the highest level of protein and fat, and that containing white maize the highest dietary fiber and indigestible fraction contents. However, the product prepared with unripe banana flour showed the highest total and rapidly digestible starch levels, while that added with blue maize exhibited greater slowly digestible starch values. No difference in RS content was detected among the three bars. The starch hydrolysis indices and predicted glycemic indices of the three preparations were low (40–54% and 42–54%, respectively). Similar acceptation scores were recorded for the three experimental bars. Cereal bars with variable starch digestibility features and good acceptation by consumers may be prepared following the proper choice of functional ingredients.
Soil‐structure interaction effects on the fundamental periods of the shear‐wall dominant buildings
Authors: Balkaya Can , Yuksel S. Bahadir , Derinoz Okan
Published: December 2010

Shear‐wall dominant reinforced concrete buildings constructed with tunnel‐form technique are prevalently constructed in regions with high seismicity due to their ease of construction and inherent resistance to lateral forces. However, the current seismic codes and the design provisions constitute inadequate guidelines for the earthquake‐resistance design of these buildings. In particular, the prediction of their fundamental periods via current empirical expressions yields not only erroneous results, but also ignores soil‐structure interaction (SSI) effects. For the objective of understanding their dynamic characteristics, a series of eigen analyses is conducted with and without considering SSI effects. The soil effects on foundations are represented by linear translational and rotational winkler springs, and rigidities of the springs are computed from the foundation size and the uniform soil compressibility. An ensemble of 140 different shear‐wall dominant buildings with varying heights is simulated in three‐dimensions considering four different soil conditions. It is proven that the vibration periods and the mode shapes of the shear‐wall dominant buildings may change depending on the different soil conditions. Based on the results of the three dimensional finite element analyses, a set of new empirical equations was proposed to predict the fundamental periods of the shear‐wall dominant buildings accounting the SSI effects. Copyright © 2010 John Wiley & Sons, Ltd.
Simulation of cellular biochemical system kinetics
Authors: Beard Daniel A.
Published: December 2010

The goal of realistically and reliably simulating the biochemical processes underlying cellular function is achievable through a systematic approach that makes use of the broadest possible amount of in vitro and in vivo data, and is consistent with all applicable physical chemical theories. Progress will be facilitated by establishing: (1) a concrete self‐consistent theoretical foundation for systems simulation; (2) extensive and accurate databases of thermodynamic properties of biochemical reactions; (3) parameterized and validated models of enzyme and transporter catalytic mechanisms that are consistent with physical chemical theoretical foundation; and (4) software tools for integrating all these concepts, data, and models into a cohesive representation of cellular biochemical systems. Ongoing initiatives are laying the groundwork for the broad‐based community cooperation that will be necessary to pursue these elements of a strategic infrastructure for systems simulation on a large scale. WIREs Syst Biol Med 2011 3 136–146 DOI: 10.1002/wsbm.116

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Models of Systems Properties and Processes > Cellular Models