bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accumulation of monoterpenoid indole alkaloids in periwinkle seedlings (Catharanthus roseus) as a model for the study of plant–environment interactions
Authors: Lourdes Miranda‐Ham María de , Islas‐Flores Ignacio , Vázquez‐Flota and Felipe 
Published: May 2007

AbstractAlkaloids are part of the chemical arsenal designed to protect plants against an adverse environment. Therefore, their synthesis and accumulation are frequently induced in response to certain environmental conditions and are mediated by chemical signals, which are formed as the first responses to the external stimulus. A set of experiments using Catharanthus roseus seedlings is presented to illustrate this interaction. Using the well characterized induction of monoterpenoid indole alkaloid synthesis in response to methyl jasmonate, one chemical mediator; simple and reproducible experiments are proposed to demonstrate this type of plant–environment interaction to plant physiology or biochemistry B.Sc. students. After exposure to the inducer, seedlings are analyzed for alkaloid accumulation and for the increase of tryptophan decarboxylase (TDC) enzyme activity by means of thin layer chromatography, followed by UV spectrophotometry. Alkaloids should increase as a result of the exposure to the inducer, as well as TDC activity, which plays a critical role in channeling carbon skeletons from primary to secondary metabolism in this plant.
Exploring the feasibility of proactive reputations
Authors: Swamynathan Gayatri , Zhao Ben Y. , Almeroth Kevin C. 
Published: May 2007

AbstractReputation mechanisms help peers in a peer‐to‐peer system avoid unreliable or malicious peers. In application‐level networks, however, short peer lifetimes mean reputations are often generated from a small number of past transactions. These reputation values are less ‘reliable’, and more vulnerable to bad‐mouthing or collusion attacks. We address this issue by introducing proactive reputations, a first‐hand history of transactions initiated to augment incomplete or short‐term reputation values. We present several mechanisms to generate proactive reputations, along with a statistical similarity metric to measure their effectiveness. Copyright © 2007 John Wiley & Sons, Ltd.
TRIBLER: a social‐based peer‐to‐peer system
Authors: Pouwelse J. A. , Garbacki P. , Wang J. , Bakker A. , Yang J. , Iosup A. , Epema D. H. J. , Reinders M. , van Steen M. R. , Sips H. J. 
Published: May 2007

AbstractMost current peer‐to‐peer (P2P) file‐sharing systems treat their users as anonymous, unrelated entities, and completely disregard any social relationships between them. However, social phenomena such as friendship and the existence of communities of users with similar tastes or interests may well be exploited in such systems in order to increase their usability and performance. In this paper we present a novel social‐based P2P file‐sharing paradigm that exploits social phenomena by maintaining social networks and using these in content discovery, content recommendation, and downloading. Based on this paradigm's main concepts such as taste buddies and friends, we have designed and implemented the TRIBLER P2P file‐sharing system as a set of extensions to BitTorrent. We present and discuss the design of TRIBLER, and we show evidence that TRIBLER enables fast content discovery and recommendation at a low additional overhead, and a significant improvement in download performance. Copyright © 2007 John Wiley & Sons, Ltd.
Spatiotemporal expression of smooth muscle markers in developing zebrafish gut
Authors: Georgijevic Sonja , Subramanian Yazhini , Rollins Evvi‐Lynn , Starovic‐Subota Olivera , Tang Archie C.Y. , Childs Sarah J. 
Published: May 2007

AbstractSmooth muscle is important for the contractility and elasticity of visceral organs. The zebrafish is an excellent model for understanding embryonic development, yet due to a lack of appropriate markers, visceral smooth muscle development remains poorly characterized. Here, we develop markers and trace the development of gut and swim bladder smooth muscle in embryonic and juvenile fish. The first smooth muscle marker we detect in the vicinity of the gut is the myoblast marker nonmuscle myosin heavy chain‐b at 50 hours postfertilization (hpf), followed by the early smooth muscle markers SM22α‐b, and α‐smooth muscle actin at 56 and 60 hpf, respectively. Markers of more differentiated smooth muscle, smoothelin‐b and cpi‐17, appear by 3 days postfertilization (dpf). Tropomyosin, a relatively late marker, is first expressed at 4 dpf. We find that smooth muscle marker expression in the swim bladder follows the same sequence of marker expression as the gut, but markers have a temporal delay reflecting the later formation of swim bladder smooth muscle. Developmental Dynamics 236:1623–1632, 2007. © 2007 Wiley‐Liss, Inc.
Xenopus cDNA microarray identification of genes with endodermal organ expression
Authors: Changkyun Park Edmond , Hayata Tadayoshi , Cho Ken W.Y. , Han Jin‐Kwan 
Published: May 2007

AbstractThe endoderm is classically defined as the innermost layer of three Metazoan germ layers. During organogenesis, the endoderm gives rise to the digestive and respiratory tracts as well as associated organs such as the liver, pancreas, and lung. At present, however, how the endoderm forms the variety of cell types of digestive and respiratory tracts as well as the budding organs is not well understood. In order to investigate the molecular basis and mechanism of organogenesis and to identify the endodermal organ‐related marker genes, we carried out microarray analysis using Xenopus cDNA chips. To achieve this goal, we isolated the Xenopus gut endoderm from three different stages of Xenopus organogenesis, and separated each stage of gut endoderm into anterior and posterior regions. Competitive hybridization of cDNA between the anterior and posterior endoderm regions, to screen genes that specifically expressed in the major organs, revealed 915 candidates. We then selected 104 clones for in situ hybridization analysis. Here, we report the identification and expression patterns of the 104 Xenopus endodermal genes, which would serve as useful markers for studying endodermal organ development. Developmental Dynamics 236:1633–1649, 2007. © 2007 Wiley‐Liss, Inc.
Self‐efficacy as a moderator of negative and positive self‐fulfilling prophecy effects: mothers' beliefs and children's alcohol use
Authors: Willard Jennifer , Madon Stephanie , Guyll Max , Spoth Richard , Jussim Lee 
Published: May 2007

AbstractThis research examined two issues relevant to self‐fulfilling prophecies. First, it examined whether children's risk for alcohol use, as indicated by their self‐efficacy to refuse alcohol from peers, moderated their susceptibility to negative and positive self‐fulfilling prophecy effects created by their mothers. Second, it explored behavioral mediators that could be involved in the self‐fulfilling process between mothers and children. Longitudinal data from 540 mother–child dyads indicated that (1) low self‐efficacy children were more susceptible to their mothers' positive than negative self‐fulfilling effects, whereas high self‐efficacy children's susceptibility did not vary, (2) mothers' global parenting and children's perception of their friends' alcohol use partially mediated mothers' self‐fulfilling effects, and (3) these mediators contributed to low self‐efficacy children's greater susceptibility to positive self‐fulfilling prophecy effects. The power of self‐fulfilling prophecies, their link to social problems, and the potential for mothers' favorable beliefs to have a protective influence on adolescent alcohol use are discussed. Copyright © 2007 John Wiley & Sons, Ltd.
Measurement uncertainty analysis for calorimetry apparatuses
Authors: Zhao Lei , Dembsey Nicholas A. 
Published: May 2007

AbstractThe absence of a standardized uncertainty analysis methodology for fire calorimetry apparatuses makes significant comparison of test results between fire laboratories difficult. From a testing (pass/fail) perspective, the lack of a common means to estimate the uncertainty is problematic. From a material development viewpoint, the ability to differentiate versions of material systems is uncertain which potentially results in economic penalties for the developer. Probability and statistics methodologies recommended by International Organization for Standardization and National Institute of Standards and Technology were applied to begin developing a standardized measurement uncertainty method for fire calorimetry apparatuses. The method was applied to each component instrument (intrinsic and calibration uncertainty only) and each related physics quantity measured indirectly. Results were reported at the 95% confidence level. The results were compared with various reference cases as well as those from a Monte Carlo Simulation technique modelling the experiments. The consistency verified our measurement uncertainty method. The results for heat release rate and average heat of combustion provide the user of Cone Calorimeter data with the
ability to estimate potential experimental error inherent in the operation of the Cone. This information can be used to make informed decisions related to the matters cited above. Copyright © 2007 John Wiley & Sons, Ltd.
Vorticity–strain residual‐based turbulence modelling of the Taylor–Green vortex
Authors: Bensow R. E. , Larson M. G. , Vesterlund P. 
Published: May 2007

AbstractThis paper describes turbulence properties for a residual‐based turbulence model using fine‐scale approximations of strain and vorticity, emanating from a split of the non‐linear term in the Navier–Stokes equations. We will discuss the modelling of the fine‐scale terms and their impact in the light of simulation results of turbulent transition of the Taylor–Green vortex. Copyright © 2007 John Wiley & Sons, Ltd.
An explicit formulation for the evolution of nonlinear surface waves interacting with a submerged body
Authors: Kent Christopher P. , Choi Wooyoung 
Published: May 2007

AbstractAn explicit formulation to study nonlinear waves interacting with a submerged body in an ideal fluid of infinite depth is presented. The formulation allows one to decompose the nonlinear wave–body interaction problem into body and free‐surface problems. After the decomposition, the body problem satisfies a modified body boundary condition in an unbounded fluid domain, while the free‐surface problem satisfies modified nonlinear free‐surface boundary conditions. It is then shown that the nonlinear free‐surface problem can be further reduced to a closed system of two nonlinear evolution equations expanded in infinite series for the free‐surface elevation and the velocity potential at the free surface. For numerical experiments, the body problem is solved using a distribution of singularities along the body surface and the system of evolution equations, truncated at third order in wave steepness, is then solved using a pseudo‐spectral method based on the fast Fourier transform. A circular cylinder translating steadily near the free surface is considered and it is found that our numerical solutions show excellent agreement with the fully nonlinear solution using a boundary integral method. We further validate our solutions for a submerged circular cylinder oscillating vertically or fixed under incoming nonlinear waves with other analytical and numerical results. Copyright © 2007 John Wiley & Sons, Ltd.
Numerical aspects of improvement of the unsteady pipe flow equations
Authors: Szymkiewicz Romuald , Mitosek Marek 
Published: May 2007

AbstractThe paper presents an analysis of some recently proposed improvements of the water hammer equations, which concern the friction term in the momentum equation. A comparison of the experimental data and numerical results shows that the required damping and smoothing of the pressure wave cannot be obtained by modification of the friction factor only.In order to evaluate the significance of the introduced improvements into the momentum equation, the accuracy of the numerical solution has been analysed using the modified equation approach. The analysis shows why the physical dissipation process observed in the water hammer phenomenon cannot be reproduced with the commonly used source term in Darcy–Weisbach form, representing friction force in the momentum equation. Therefore, regardless of the proposed form of the friction factor for unsteady flow, the model of water hammer improved in such a way keeps its hyperbolic character. Consequently, it cannot ensure the expected effects of damping and smoothing of the calculation head oscillations. Copyright © 2007 John Wiley & Sons, Ltd.
A stabilized mixed finite element method for Darcy–Stokes flow
Authors: Masud Arif 
Published: May 2007

AbstractThis paper presents a new stabilized finite element method for the Darcy–Stokes equations also known as the Brinkman model of lubrication theory. These equations also govern the flow of incompressible viscous fluids through permeable media. The proposed method arises from a decomposition of the velocity field into coarse/resolved scales and fine/unresolved scales. Modelling of the unresolved scales corrects the lack of stability of the standard Galerkin formulation for the Darcy–Stokes equations. A significant feature of the present method is that the structure of the stabilization tensor τ appears naturally via the solution of the fine‐scale problem. The issue of arbitrary combinations of pressure–velocity interpolation functions is addressed, and equal‐order combinations of C° interpolations are shown to be stable and convergent. Copyright © 2007 John Wiley & Sons, Ltd.
A 3D adaptive mesh moving scheme
Authors: Kanchi Harish , Masud Arif 
Published: May 2007

AbstractThis paper presents an adaptive mesh moving technique for three‐dimensional (3D) fluid flow problems that involve moving fluid boundaries and fluid–solid interfaces. Such mesh moving techniques are an essential ingredient of fluid–structure interaction methods that typically employ arbitrary Lagrangian–Eulerian (ALE) frameworks. In the ALE frame, the velocity field representing motion of the underlying continuum is integrated in the fluid flow equations. In the discretized setting, the velocity field of the underlying continuum gives rise to the mesh displacement field that needs to be solved for in addition to the flow equations and the structural equations. Emphasis in the present work is on the motion and deformation of 3D grids that are composed of linear tetrahedral and hexahedral elements in structured and unstructured configurations. The proposed method can easily be extended to higher‐order elements in 3D. A variety of moving mesh problems from different fields of engineering are presented that show the range of applicability of the proposed method and the class of problems that can be addressed with it. Copyright © 2007 John Wiley & Sons, Ltd.
The adjoint weighted equation for steady advection in a compressible fluid
Authors: Oberai Assad A. , Barbone Paul E. , Harari Isaac 
Published: May 2007

AbstractAn alternative variational framework suitable for pure advection is obtained by discarding the Galerkin part of stabilized methods. The resulting scheme is similar to the least‐squares approach, but with the adjoint operator in the weighting slot. This formulation is not restricted to solenoidal (i.e. divergence free) velocities. Initial numerical results for such problems show that the method is promising. Copyright © 2007 John Wiley & Sons, Ltd.
Characterizing hydrodynamics on boreal landscapes using archived synthetic aperture radar imagery
Authors: Sass G. Z. , Creed I. F. 
Published: May 2007

AbstractCharacterizing the spatial and temporal variation in surface hydrological dynamics of large boreal landscapes is vital, since these patterns define the occurrence of key areas of land‐to‐lake and land‐to‐atmosphere hydrological and biogeochemical linkages that are critical in the movement of matter and energy at local to global scales. However, monitoring surface hydrological dynamics over large geographic extents and over long periods of time is a challenge for hydrologists, as traditional point measurements are not practical. In this study we used European Remote Sensing satellite radar imagery to monitor the variation in surface hydrological patterns over a 12‐year period and to assess the change in the organization of saturated and inundated areas of the landscape. Using the regional Utikuma River drainage basin (2900 km2) as the test area, the analyses of patterns of wetlands indicated that, during dry climatic conditions, wetland sizes were small and disconnected from each other and receiving bodies of water. As climatic conditions changed from dry to mesic, wetland numbers increased but were still disconnected. Very wet climatic conditions were required before the disconnected wetlands coalesced and connected to lakes. During these wet conditions, the response of the lake level at Utikuma Lake was observed to be much higher than under drier conditions. Analyses of individual wetland maps and integrated wetland probability maps have the potential to inform future biogeochemical and ecological investigations and forest management on the Boreal Plain. Copyright © 2007 John Wiley & Sons, Ltd.
Loss of α6 integrins in keratinocytes leads to an increase in TGFβ and AP1 signaling and in expression of differentiation genes
Authors: Rodius Sophie , Indra Gitali , Thibault Christelle , Pfister Véronique , Georges‐Labouesse Elisabeth 
Published: May 2007

AbstractMice lacking the α6 integrin chain die at birth with severe skin blistering. To further study the function of α6 integrin in skin, we generated conditionally immortalized cell lines from the epidermis of wild‐type and α6 deficient mouse embryos. Mutant cells presented a decreased adhesion on laminin 5, the major component of the basement membrane in the skin, and on laminins 10/11 and 2. A DNA array analysis revealed alterations in the expression of extracellular matrix (ECM) components including laminin 5, cytoskeletal elements, but also membrane receptors like the hemidesmosomal components integrin β4 and collagen XVII, or growth factors and signaling molecules of the TGFβ, EGF, and Wnt pathways. Finally, an increase of several epidermal differentiation markers was observed in cells and tissue at the protein level. Further examination of the mutant tissue revealed alterations in the filaggrin signal. These differences may be linked to an upregulation of the TGFβ and the Jun/Fos pathways in mutant keratinocytes. These results are in favor of a role for integrin α6β4 in the maintenance of basal keratinocyte properties and epidermal homeostasis. J. Cell. Physiol. 212: 439–449, 2007. © 2007 Wiley‐Liss, Inc.
GADD45A is a mediator of CD437 induced apoptosis in ovarian carcinoma cells
Authors: Jiang Tianying , Soprano Dianne Robert , Soprano Kenneth J. 
Published: May 2007

AbstractOvarian cancer is one of the leading causes of cancer death in women. A number of studies have suggested that synthetic retinoids may play an important role as an ovarian cancer chemotherapeutic agent. The synthetic retinoid CD 437 induces apoptosis in ovarian tumor cells by a mechanism that is not completely understood. In this study we demonstrate that CD437 treatment leads to an increase in GADD45A and GADD45B mRNA expression in CA‐OV3 cells but not in CA‐CD437R cells, a cell line which is resistant to CD437. This induction is specific to CD437 since no change in expression of either GADD45A or GADD45B was observed with either all‐trans‐RA or 4‐HPR treatment. Western blot analysis demonstrated that the induction of GADD45A mRNA in the CA‐OV3 cell line by CD437 was accompanied by an increase in GADD45A protein. Upregulation of GADD45A by CD437 is regulated at least in part at the post‐transcriptional level. In contrast, CD437 regulates GADD45B expression by different mechanisms. The importance of GADD45A induction in mediating apoptosis was demonstrated in CA‐OV3 cells overexpressing GADD45A antisense RNA (GADD45A‐AS cells). Our results suggest that induction of GADD45A expression might play a role in mediating the apoptotic response of ovarian cancer cells to the synthetic retinoid CD437. J. Cell. Physiol. 212:771–779, 2007. © 2007 Wiley‐Liss, Inc.
Sperm surface arylsulfatase A can disperse the cumulus matrix of cumulus oocyte complexes
Authors: Wu Alexander , Anupriwan Araya , Iamsaard Sitthichai , Chakrabandhu Krittalak , Santos Daniela Costa , Rupar Tony , Tsang Benjamin K. , Carmona Euridice , Tanphaichitr Nongnuj 
Published: May 2007

AbstractCumulus cell layers of expanded cumulus oocyte complexes (COCs) are interlinked with networks of hyaluronic acid, chondroitin sulfate B proteoglycans and link proteins, and they can be dispersed by sperm surface hyaluronidases. In this report, we showed that arylsulfatase A (AS‐A), existing on the sperm head surface, also had this dispersion action. Purified AS‐A free of protease, hyaluronidase and chondroitinase activities could disperse the cumulus matrix of expanded COCs. However, this COC dispersion action was not associated with AS‐A desulfation activity, assayed by using p‐nitrocatecholsulfate (artificial substrate). COCs incubated for 1 h with sperm pretreated with anti‐AS‐A IgG in the presence of apigenin (a hyaluronidase inhibitor) did not exhibit matrix dispersion, whereas several cumulus layers were already dispersed in COCs incubated with sperm pretreated with preimmune IgG. Furthermore, sperm from AS‐A null mice showed a significant delay in COC dispersion, compared with wild‐type sperm. Within 1 h of sperm‐COC co‐incubation, the size of COCs incubated with AS‐A null sperm was 65% of the original dimension, whereas that of COCs inseminated with wild‐type sperm was only 17%. A further delay in COC dispersion by AS‐A(−/−) mouse sperm was observed when apigenin was present in the co‐incubation. We also showed for the first time that AS‐A had a specific affinity for chondroitin sulfate B, a component of cumulus matrix proteoglycan networks; this might provide a mechanism of cumulus matrix destabilization induced by sperm surface AS‐A. J. Cell. Physiol. 213: 201–211, 2007. © 2007 Wiley‐Liss, Inc.
Inhibition of HIV‐1 multiplication by a modified U7 snRNA inducing Tat and Rev exon skipping
Authors: Asparuhova Maria B. , Marti Gabriela , Liu Songkai , Serhan Fatima , Trono Didier , Schümperli Daniel 
Published: May 2007

AbstractThe HIV‐1 regulatory proteins Tat and Rev are encoded by multiply spliced mRNAs that differ by the use of alternative 3' splice sites at the beginning of the internal exon. If these internal exons are skipped, the expression of these genes, and hence HIV‐1 multiplication, should be inhibited. We have previously developed a strategy, based on antisense derivatives of U7 small nuclear RNA, that allows us to induce the skipping of an internal exon in virtually any gene. Here, we have successfully applied this approach to induce a partial skipping of the Tat, Rev (and Nef) internal exons. Three functional U7 constructs were subcloned into a lentiviral vector. Two of them strongly reduced the efficiency of lentiviral particle production compared to vectors carrying either no U7 insert or unrelated U7 cassettes. This defect could be partly or fully compensated by coexpressing Rev from an unspliced mRNA in the producing cell line. Upon stable transduction into CEM‐SS or CEM T‐lymphocytes, the most efficient of these constructs inhibits HIV‐1 multiplication. Although the inhibition is not complete, it is more efficient in combination with another mechanism inhibiting HIV multiplication. Therefore, this new approach targeting HIV‐1 regulatory genes at the level of pre‐mRNA splicing, in combination with other antiviral strategies, may be a useful new tool in the fight against HIV/AIDS. Copyright © 2007 John Wiley & Sons, Ltd.