bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Dickkopf‐1 (huDKK1) protein: Characterization of glycosylation and determination of disulfide linkages in the two cysteine‐rich domains
Authors: Haniu Mitsuru , Horan Tom , Spahr Chris , Hui John , Fan Wei , Chen Ching , Richards William G. , Lu Hsieng S. 
Published: July 2011

AbstractHuman Dickkopf‐1 (huDKK1), an inhibitor of the canonical Wnt‐signaling pathway that has been implicated in bone metabolism and other diseases, was expressed in engineered Chinese hamster ovary cells and purified. HuDKK1 is biologically active in a TCF/lef‐luciferase reporter gene assay and is able to bind LRP6 coreceptor. In SDS‐PAGE, huDKK1 exhibits molecular weights of 27–28 K and 30 K at ∼ 1:9 ratio. By MALDI‐MS analysis, the observed molecular weights of 27.4K and 29.5K indicate that the low molecular weight form may contain O‐linked glycans while the high molecular weight form contains both N‐ and O‐linked glycans. LC‐MS/MS peptide mapping indicates that ∼ 92% of huDKK1 is glycosylated at Asn225 with three N‐linked glycans composed of two biantennary forms with 1 and 2 sialic acid (23% and 60%, respectively), and one triantennary structure with 2 sialic acids (9%). HuDKK1 contains two O‐linked glycans, GalNAc (sialic acid)‐Gal‐sialic acid (65%) and GalNAc‐Gal[sialic acid] (30%), attached at Ser30 as confirmed by β‐elimination and targeted LC‐MS/MS. The 10 intramolecular disulfide bonds at the N‐ and C‐terminal cysteine‐rich domains were elucidated by analyses including multiple proteolytic digestions, isolation and characterization of disulfide‐containing peptides, and secondary digestion and characterization of selected disulfide‐containing peptides. The five disulfide bonds within the huDKK1 N‐terminal domain are unique to the DKK family proteins; there are no exact matches in disulfide positioning when compared to other known disulfide clusters. The five disulfide bonds assigned in the C‐terminal domain show the expected homology with those found in colipase and other reported disulfide clusters.
Activation of the human nuclear xenobiotic receptor PXR by the reverse transcriptase‐targeted anti‐HIV drug PNU‐142721
Authors: Cheng Yuan , Redinbo Matthew R. 
Published: July 2011

AbstractThe human pregnane X receptor (PXR) is a member of the nuclear receptor superfamily of ligand‐regulated transcription factors. PXR responds to a structurally diverse variety of endogenous and xenobiotic compounds, and coordinates the expression of genes central to the metabolism and excretion of potentially harmful chemicals, including human therapeutics. The reverse transcriptase inhibitor PNU‐142721 has been designed to treat human immunodeficiency virus (HIV) infection. Although this compound has anti‐HIV activity, it was established using cell‐based assays that PNU‐142721 is an efficacious PXR agonist. We present here the 2.8 Å resolution crystal structure of the human PXR ligand‐binding domain in complex with PNU‐142721. PXR employs one hydrogen bond and fourteen van der Waals contacts to interact with the ligand, but allows two loops adjacent to the ligand‐binding pocket to remain disordered in the structure. These observations highlight the role structural flexibility plays in PXR's promiscuous responses to xenobiotics. The crystal structure also explains why PNU‐173575, a thiomethyl metabolite of PNU‐142721, exhibits enhanced PXR activation relative to the unmodified compound and why PNU‐142721 can also activate rat PXR. Taken together, the results presented here elucidate the structural basis for PXR activation by PNU‐142721 and related chemicals.
GFP‐based evaluation system of recombinant expression through the secretory pathway in insect cells and its application to the extracellular domains of class C GPCRs
Authors: Ashikawa Yuji , Ihara Makoto , Matsuura Noriko , Fukunaga Yuko , Kusakabe Yuko , Yamashita Atsuko 
Published: July 2011

AbstractApplications of the GFP‐fusion technique have greatly facilitated evaluations of the amounts and qualities of sample proteins used for structural analyses. In this study, we applied the GFP‐based sample evaluation to secreted protein expression by insect cells. We verified that a GFP variant, GFPuv, retains proper folding and monodispersity within all expression spaces in Sf9 cells, such as the cytosol, organelles, and even the extracellular space after secretion, and thus can serve as a proper folding reporter for recombinant proteins. We then applied the GFPuv‐based system to the extracellular domains of class C G‐protein coupled receptors (GPCRs) and examined their localization, folding, and oligomerization upon insect cell expression. The extracellular domain of metabotropic glutamate receptor 1 (mGluR1) exhibited good secreted expression by Sf9 cells, and the secreted proteins formed dimer with a monodisperse hydrodynamic state favorable for crystallization, consistent with the results from previous successful structural analyses. In contrast, the extracellular domains of sweet/umami taste receptors (T1R) almost completely remained in the cell. Notably, the T1R and mGluR1 subfractions that remained in the cellular space showed polydisperse hydrodynamic states with large aggregated fractions, without forming dimers. These results indicated that the proper folding and oligomerization of the extracellular domains of the class C GPCR are achieved through the secretory pathway.
The Friedrichs model and its use in resonance phenomena
Authors: Gadella M. , Pronko G.P. 
Published: July 2011

AbstractWe present here a relation of different types of Friedrichs models and their use in the description and comprehension of resonance phenomena. We first discuss the basic Friedrichs model and obtain its resonance in the case that this is simple or doubly degenerated. Next, we discuss the model with N levels and show how the probability amplitude has an oscillatory behavior. Two generalizations of the Friedrichs model are suitable to introduce resonance behavior in quantum field theory. We also discuss a discrete version of the Friedrichs model and also a resonant interaction between two systems both with continuous spectrum. In an appendix, we review the mathematics of rigged Hilbert spaces.
Combined Impact of Ultraviolet and Chemical Fluids on High‐density Polyethylene Packaging Material
Authors: Geburtig Anja , Goedecke Thomas , Wachtendorf Volker 
Published: July 2011

To investigate the ageing behaviour of filled plastic containers outdoors, square cuts of the wall of two high‐density polyethylene (HDPE) types were exposed to ultraviolet (UV) radiation at their front side and to specific liquid chemicals (de‐ionized water, surfactant or White Spirit) at their back. The UV radiant exposure at the front side was 80 MJ/m².To compare the actions of the different exposures, separate dark backside fluid exposures were performed, in parallel. Besides, UV weathering was carried out until a UV radiant exposure of 325 MJ/m², being roughly comparable to outdoor exposure of one year in Northern Australia.An unpigmented HDPE included in the investigation gave no sufficient protection for the White Spirit. In addition, it showed clear degradation after several of these exposures. In combination with the White Spirit, an increase of carbonyl bonds was measured, presumably assignable to degradation products of the White Spirit.For a pigmented HDPE material, with the implemented combined exposures, no relevant damage was observed, within applied the exposure period. Copyright © 2011 John Wiley & Sons, Ltd.
Three‐unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides
Authors: Li Yushuang , Qin Yufang , Zheng Xiaoqi , Zhang Yu 
Published: July 2011

AbstractA new three‐dimensional graphical representation of DNA sequences, three‐unit semicircles (TUS)‐curve, which maps a given sequence into a dot sequences embedded in three‐unit semicircles, is proposed based on three biclassifications of nucleotides. TUS‐curve has the merit of compactness and could avoid the degeneracy and loss of information. The geometrical center of the curve, which indicates the distribution of base frequencies of the corresponding DNA sequence, is extracted and applied to analyze the similarity of various species. Phylogenetic tree of 11 species based on their first exons of β‐globin genes showed that the TUS‐curve is a powerful tool to get valuable biological information. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Modeling of properties of amino acids with random, semirandom, and molecular connectivity descriptors
Authors: Pogliani Lionello 
Published: July 2011

AbstractSets of random indices, sets of molecular connectivity indices (MCIs), and mixed sets of random and MCIs have been used to model nine properties of amino acids. The number of amino acids throughout the concerned properties is not constant, it ranges from 21 for the isoelectric point to eight for the unfrozen water content. The quality of the descriptors has been submitted to the leave‐one‐out (loo) and to the training/evaluation statistical tests. Molecular connectivity descriptors made of MCIs only show exceptionally good model characteristics for the volume side‐chain throughout both tests, while the model of the solubility holds only at the loo level. Random descriptors made of random indices, and semirandom descriptors, made of random and MCIs show good descriptive characteristics of all other properties at the loo level, while they fail at the training/evaluation level. Molecular connectivity descriptors achieve a good model at the training/evaluation level for the hydration potential and for the specific rotation. Practically, at the loo level all properties, excluding the unfrozen water content, can satisfactorily be modeled, while at the training/evaluation level, only side‐chain volume, hydration potential, and specific rotation can be modeled in a satisfactory way. To notice is the importance, at both statistical levels, of the hydrogen content of the amino acids, which is encoded with a perturbation parameter at the level of the valence delta number of the valence MCIs. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
State and output feedback control of time‐delay switched linear systems
Authors: Galbusera Luca , Bolzern Paolo , Deaecto Grace S. , Geromel José C. 
Published: July 2011

SUMMARYIn this paper, we propose contributions on the stabilization and control of switched linear systems subject to time‐delays through the assignment of the switching law. As a first step, based on previous results related to switched linear systems with no time‐delays and exploiting the concept of piecewise quadratic Lyapunov–Krasovskii functionals, we solve the problem of finding suitable state‐dependent switching laws ensuring the prescribed control objectives. Secondly, we extend such results and present a strategy to construct an output feedback switching law, based on the available measurements made on the system. In both cases, the design of the control strategy is done by computing a feasible solution to a set of matrix inequalities associated to the modes of the switched linear system. Copyright © 2011 John Wiley & Sons, Ltd.
Flocking of multi‐agent dynamical systems with intermittent nonlinear velocity measurements
Authors: Wen Guanghui , Duan Zhisheng , Li Zhongkui , Chen Guanrong 
Published: July 2011

SUMMARYIn this paper, the problem of flocking control in networks of multiple dynamical agents with intermittent nonlinear velocity measurements is studied. A new flocking algorithm is proposed to guarantee the states of the velocity variables of all the dynamical agents to converge to consensus while ensuring collision avoidance of the whole group, where each agent is assumed to obtain some nonlinear measurements of the relative velocity between itself and its neighbors only on a sequence of non‐overlapping time intervals. The results are then extended to the scenario of flocking with a nonlinearly dynamical virtual leader, where only a small fraction of agents are informed and each informed agent can obtain intermittent nonlinear measurements of the relative velocity between itself and the virtual leader. Theoretical analysis shows that the achieved flocking in systems with or without a virtual leader is robust against the time spans of the agent speed‐sensors. Finally, some numerical simulations are provided to illustrate the effectiveness of the new design. Copyright © 2011 John Wiley & Sons, Ltd.
BENCHMARKING RIVER HABITAT IMPROVEMENT
Authors: Boavida I. , Santos J. M. , Cortes R. , Pinheiro A. , Ferreira M. T. 
Published: July 2011

ABSTRACTRiver ecosystems have witnessed a long history of human pressure, particularly the disruption of freshwater fish populations. The awareness of this situation has led to many habitat improvement projects, with a variable degree of success. In natural situations, fish populations co‐inhabit throughout the hydrological cycle with different degrees of adequacy, and the sequence of favourable and unfavourable conditions dictates abiotic constraints and biotic interactions that shape the final biological assemblages. We postulate that a part of unsuccessful restoration results is related to insufficient closeness to the natural habitat conditions of the river type that is to be restored, including the naturally adverse periods. We used the river2d model to predict habitat availability as weighted usable area (WUA) at a degraded site that is to be restored, for two native Mediterranean species and their life stages—the Southwestern nase Iberochondrostoma almacai and the Arade chub Squalius aradensis. We then analysed the yearly evolution of the natural WUA at a nearby reference site. Overall, the reference site exhibited the longest periods during which the WUA was continuously lower than the chosen WUA thresholds for each of the four bioperiods. Considerable divergences from natural habitat availability values can be seen for the spawning, rearing and growth bioperiods. Restoration outcomes can result in appreciable deviations—favourable or unfavourable to fish populations—from the WUA occurring under natural conditions over the course of the year. Restoration should therefore take account of local hydraulic and habitat patterns that govern population dynamics and result in the final fish assemblage. Copyright © 2011 John Wiley & Sons, Ltd.
Dynamics of the evolution of the strategy concept 1962–2008: a co‐word analysis
Authors: Ronda‐Pupo Guillermo Armando , Guerras‐Martin Luis Ángel 
Published: July 2011

AbstractThe aim of this paper is to extend recent reflection on the evolution of strategic management by analyzing the field's object of study: strategy. We show how the concept of strategy has formed the backbone of the development of strategic management as an academic field and how consensus regarding it has evolved in the academic community during the stages of its historical development. We also address changes in the structure of the definition as it evolved through the growth of internal consistency, the centrality degree of the key terms that have shaped it, and how this evolution fostered the emergence of new research topics during the development of the discipline. Copyright © 2011 John Wiley & Sons, Ltd.
The role for ‘community’ in carbon governance
Authors: Walker Gordon 
Published: July 2011

AbstractThe notion of community‐based activity has increasingly been enrolled within carbon governance discourses and programs of recognized and supported activity. Community is a term used in various ways, to distinguish an actor, a scale of activity, a spatial setting, a form of network, and a type of process through which carbon reduction objectives can be implemented. In this review the various expectations linked to community‐based initiatives are identified and discussed in relation to the range of meanings of community in carbon governance. Working through and with communities is typically expected to better embed individual behavior change, as well as generate social innovations and facilitate the consensual deployment of sustainable energy technologies. Research into the experience of implementing community renewable energy projects is discussed to explore the challenges involved in realizing such outcomes. WIREs Clim Change 2011 2 777–782 DOI: 10.1002/wcc.137This article is categorized under:

Perceptions, Behavior, and Communication of Climate Change > Behavior Change and Responses
Policy and Governance > Governing Climate Change in Communities, Cities, and Regions
Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant
Authors: Smith Sarah B. , Kiss Daniel L. , Turk Edward , Tartakoff Alan M. , Andrulis Erik D. 
Published: July 2011

AbstractSubunits of the RNA processing exosome assemble into structurally distinct protein complexes that function in disparate cellular compartments and RNA metabolic pathways. Here, in a genetic, cell biological and transcriptomic analysis, we examined the role of Dis3, an essential polypeptide with endo‐ and 3′ → 5′ exo‐ribonuclease activity, in cell cycle progression. We present several lines of evidence that perturbation of DIS3 affects microtubule (MT) localization and structure in Saccharomyces cerevisiae. Cells with a DIS3 mutant: (a) accumulate anaphase and pre‐anaphase mitotic spindles; (b) exhibit spindles that are misorientated and displaced from the bud neck; (c) harbour elongated spindle‐associated astral MTs; (d) have an increased G1 astral MT length and number; and (e) are hypersensitive to MT poisons. Mutations in the core exosome genes RRP4 and MTR3 and the exosome cofactor gene MTR4, but not other exosome subunit gene mutants, also elicit MT phenotypes. RNA deep sequencing analysis (RNA‐seq) shows broad changes in the levels of cell cycle‐ and MT‐related transcripts in mutant strains. Collectively, the data presented in this study suggest an evolutionarily conserved role for Dis3 in linking RNA metabolism, MTs and cell cycle progression. Copyright © 2011 John Wiley & Sons, Ltd.
Use of stepwise versus straightforward clamping of biliary drainage tubes after living‐donor liver transplantation: a prospective, randomized trial
Authors: Eguchi Susumu , Takatsuki Mitsuhisa , Soyama Akihiko , Hidaka Masaaki , Muraoka Izumi , Kanematsu Takashi 
Published: July 2011

AbstractBackground/purposeThere has been no report describing the optimal clamping method for biliary drainage tubes in living‐donor liver transplantation (LDLT), although biliary splinting and drainage plays an important role in this procedure.MethodsWhen performing LDLT, we generally use a 2‐mm drainage tube for the splint at the biliary anastomosis, and externalize it through the lower common bile duct. In the present study, when the serum levels of total bilirubin were lower than 5 mg/dl, and negativity for biliary complications and good passage of contrast media to the duodenum were confirmed, the drainage tubes were clamped. To determine the optimal clamping method, patients were randomly divided into two groups; those whose drainage tubes were subjected to stepwise clamping for 3, 6, 12, and 24 h per day (n = 20), and those whose drainage tubes were subjected to straightforward clamping (n = 20).ResultsThe results of liver function tests and rates of clamping failure were not different between the two groups after the different clamping methods were used.ConclusionsStraightforward clamping could be a simple and reasonable method to close a biliary drainage tube after LDLT.
Conflict Transformation, Stigma, and HIV‐Preventive Structural Change
Authors: Miller Robin Lin , Reed Sarah J. , Francisco Vincent T. , Ellen Jonathan M. 
Published: July 2011

AbstractOver the prior decade, structural change efforts have become an important component of community‐based HIV prevention initiatives. However, these efforts may not succeed when structural change initiatives encounter political resistance or invoke conflicting values, which may be likely when changes are intended to benefit a stigmatized population. The current study sought to examine the impact of target population stigma on the ability of 13 community coalitions to achieve structural change objectives. Results indicated that coalitions working on behalf of highly stigmatized populations had to abandon objectives more often than did coalitions working for less stigmatized populations because of external opposition to coalition objectives and resultant internal conflict over goals. Those coalitions that were most successful in meeting external challenges used opposition and conflict as transformative occasions by targeting conflicts directly and attempting to neutralize oppositional groups or turn them into strategic allies; less successful coalitions working on behalf of stigmatized groups struggled to determine an appropriate response to opposition. The role of conflict transformation as a success strategy for working on behalf of stigmatized groups is discussed.
Synthesis and Biocidal Activity of Some Naphthalene‐Based Cationic Surfactants
Authors: Aiad Ismail A. , Badawi Abdelfatah M. , El‐Sukkary Mohammed M. , El‐Sawy Abdallah A. , Adawy Ahmed I. 
Published: July 2011

AbstractIn this study, different cationic surfactants were prepared by reacting dodecyl bromide with tertiary amines to produce a series of quaternary ammonium salts that were converted subsequently to stannous and cobalt cationic complexes via complexing them with stannous (II) or cobalt (II) ions. Surface properties such as surface‐ and interfacial‐tension, and the emulsifying power of these surfactants were investigated. The surface parameters including critical micelle concentration, maximum surface excess, minimum surface area, tension lowering efficiency and effectiveness were studied. The free energy of micellization and adsorption were calculated. Antimicrobial activity was determined via the inhibition zone diameter of the prepared compounds, which was measured against six strains of a representative group of microorganisms. The antimicrobial activity of some of the prepared surfactants against sulfate reducing bacteria was determined by the dilution method. FTIR spectra, elemental analysis and a H1 NMR spectrum were examined to confirm compound structure and purity. The results obtained indicate that these compounds have good surface properties and good biocidal effect on broad spectrum of micro organisms.
Depression among women with obstetric fistula in Kenya
Authors: Weston Khisa , Mutiso Stephen , Mwangi Judy W. , Qureshi Zahida , Beard Jessica , Venkat Pavithra 
Published: July 2011

AbstractObjectiveTo establish the prevalence of depression and describe associated factors among fistula patients attending an obstetric fistula surgical camp in Kenya.MethodsA cross‐sectional study was conducted focusing on obstetric fistula patients attending a national fistula camp held in August 2008 at Kenyatta National Hospital, Nairobi, Kenya. A structured questionnaire was used to obtain sociodemographic data and medical histories for all consenting patients before surgery. Depression measures were obtained using the Patient Health Questionnaire‐9.ResultsOf the 70 women interviewed, 2 (2.9%) and 12 (17.1%) reported a history of psychiatric illness and suicidal ideations, respectively. Depression was present in 51 (72.9%) patients, with 18 (25.7%) meeting criteria for severe depression. Depression was significantly associated with women older than 20 years of age (P = 0.01), unemployment (P = 0.03), lack of social support following fistula (P = 0.04), and living with fistula for over 3 months (P = 0.01).ConclusionWomen with obstetric fistula are predisposed to high levels of depression. A holistic management approach, including mental health care and family support, is recommended.