bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification, analysis, and prediction of protein ubiquitination sites
Authors: Radivojac Predrag , Vacic Vladimir , Haynes Chad , Cocklin Ross R. , Mohan Amrita , Heyen Joshua W. , Goebl Mark G. , Iakoucheva Lilia M. 
Published: July 2009

AbstractUbiquitination plays an important role in many cellular processes and is implicated in many diseases. Experimental identification of ubiquitination sites is challenging due to rapid turnover of ubiquitinated proteins and the large size of the ubiquitin modifier. We identified 141 new ubiquitination sites using a combination of liquid chromatography, mass spectrometry, and mutant yeast strains. Investigation of the sequence biases and structural preferences around known ubiquitination sites indicated that their properties were similar to those of intrinsically disordered protein regions. Using a combined set of new and previously known ubiquitination sites, we developed a random forest predictor of ubiquitination sites, UbPred. The class‐balanced accuracy of UbPred reached 72%, with the area under the ROC curve at 80%. The application of UbPred showed that high confidence Rsp5 ubiquitin ligase substrates and proteins with very short half‐lives were significantly enriched in the number of predicted ubiquitination sites. Proteome‐wide prediction of ubiquitination sites in Saccharomyces cerevisiae indicated that highly ubiquitinated substrates were prevalent among transcription/enzyme regulators and proteins involved in cell cycle control. In the human proteome, cytoskeletal, cell cycle, regulatory, and cancer‐associated proteins display higher extent of ubiquitination than proteins from other functional categories. We show that gain and loss of predicted ubiquitination sites may likely represent a molecular mechanism behind a number of disease‐associatedmutations. UbPred is available at http://www.ubpred.org. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Dissecting the molecular mechanism of drosophila odorant receptors through activity modeling and comparative analysis
Authors: Guo Sheng , Kim Junhyong 
Published: July 2009

AbstractTo gain insight into the molecular mechanism of odorant receptors (ORs) in Drosophila species, we developed a Quantitative Structure Activity Relationship (QSAR) model that predicts experimentally measured electrophysiological activities between 24 D. melanogaster ORs and 108 odorants. Although the model is limited by the tested odorants,analyzing the model allowed dissection of specific topological and chemical properties necessary for an odorant to elicit excitatory or inhibitory receptor response. Linear odorants with five to eight nonhydrogen atoms at the main chain and hydrogen‐bond acceptor and/or hydrogen‐bond donor at its ends were found to stimulate strong excitatory response. A comparative sequence analysis of 90 ORs in 15 orthologous groups identified 15 putative specificity‐determining residues (SDRs) and 15 globally conserved residues that we postulate as functionally key residues. Mapping to a model of secondary structure resulted in 14 out of 30 key residues locating to the transmembrane (TM) domains. Twelve residues, including six SDRs and six conserved residues, are located at the extracellular halves of the TM domains. Combining the evidence from the QSAR modeling and the comparative sequence analysis, we hypothesize that the Drosophila ORs accept odorants into a binding pocket located on the extracellular halves of its TM domains. The QSAR modeling suggests that the binding pocket is around 15 Å in depth and about 6 Å in width. Twelve mainly polar or charged key residues, both SDRs and conserved, are located inthis pocket and postulated to distinguish docked odorants via primarily geometry fitting and hydrogen‐bond interaction. Proteins 2010. © 2009 Wiley‐Liss, Inc.
The time course of drug effects
Authors: Al‐Sallami Hesham S. , Pavan Kumar Venkata V. , Landersdorfer Cornelia B. , Bulitta Jurgen B. , Duffull Stephen B. 
Published: July 2009

AbstractThis review aims to introduce the concepts and principles underpinning the time course of drug effects. Models describing the time course of drug concentrations (pharmacokinetic models) and the ensuing concentration‐effect (pharmacodynamics models) as well as the linked time‐effect (pharmacokinetic‐pharmacodynamic models) are introduced. Different types of drug time‐effects models are discussed with examples which aim to explain the time course of onset, duration, and maximal effect that occurs from any given dosing schedule. These drug effects are also described in relation to disease progression models. Copyright © 2009 John Wiley & Sons, Ltd.
Characterization for water vapour barrier and heat sealability properties of heat‐treated paperboard/polylactide structure
Authors: Lahtinen Kimmo , Kotkamo Sami , Koskinen Tapio , Auvinen Sanna , Kuusipalo Jurkka 
Published: July 2009

AbstractThe moisture barrier and heat sealability properties of polylactide (PLA) extrusion‐coated paperboard were investigated. The first part of the study focused on the influences of coating weight and surroundings temperature and relative humidity on the water vapour transmission rate (WVTR) of the structure. The outcome arising from this part was a simple and practical equation that allows calculating the WVTR as a function of PLA coating weight under specific thermo‐hygrometric conditions. The second part of the study investigated the effect of heat treatments between 100 and 150°C on the WVTR and heat sealability of a 20 g/m2 PLA‐coated paperboard. According to the results, the lowest WVTR values achieved were about 2.5 times lower than the WVTR of the untreated structure. Presumably, the PLA coating experienced two types of reordering mechanisms: crystalline growth and packing of the amorphous structure. The greatest barrier improvement was achieved when both of these mechanisms were accumulated effectively. This was observed from the samples after a 40 min treatment at 130°C. Ultimately, the crystalline growth was experienced by PLA at 100–130°C temperatures. The packing of the amorphous section, which was also accumulated at higher temperatures, was suggested to be the decisive factor influencing WVTR. According to the heat sealing results, the heat treatments causing crystalline growth resulted in considerably increased sealing temperatures and reduced applicability of the material in high‐speed packaging applications. The treatments at 140–150°C caused only a slight increase in the sealing temperature and maintained the sealing performance of PLA. Copyright © 2009 John Wiley & Sons, Ltd.
Quantum chemical metabolism‐based simulation of carcinogenic potency of benzene derivatives
Authors: D'Yachkov Pavel N. , Kharchevnikova Nina V. , Zholdakova Zoya I. , Fjodorova Nathalia , Novich Mariana , Vrachko Marian 
Published: July 2009

AbstractUsing an oxenoid model, we investigated dependences of carcinogenic potency of the benzenes C6H5‐X on a nature of substituents X. According to the model, a P450 enzyme breaks a dioxygen molecule and generates the oxens, which readily react with substrates. We suggest that a stability of the intermediate OC6H6‐X with tetrahedrally coordinated C atom relative to the molecule C6H5‐X determines a rate of substrate biotransformation. Using MO LCAO MNDO approach, we calculated the total energies of molecules C6H6‐X and arene oxides OC6H6‐X. A difference ΔEminof these values determines activation energy of oxidation reaction. The compounds with the low ΔEminvalues are noncarcinogenic. Benzene derivatives with high ΔEminvalues belong to carcinogenic compounds series. The carcinogenicity of amino‐ and nitro‐substituted benzenes is also determined by N‐oxidation of amino and reduction of the nitro group. As the phenylhydroxylamines XC6H4NHOH and nitrenium ions XC6OH4NH+are the common metabolites of the nitro‐ and amino‐substituted benzenes and nitrenium ions XC6H4NH+are the ultimate carcinogens, we use the differences ΔEN=E(XC6H4NH+) −E(XC6H4NHOH) as the second parameter characterizing the carcinogenic activity of amino‐ and nitro‐substituted benzenes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Evaluation and reliability of the organic certification system: perceptions by farmers in Latin America
Authors: Albersmeier Friederike , Schulze Holger , Spiller Achim 
Published: July 2009

AbstractIn recent years, organic agriculture has developed rapidly, and organic certification systems are now used worldwide. However, if these standards are unable to meet their promises, their reliability will be called into question and trust in organic products will fade. As major suppliers of organic food to the European market, it is crucial for Latin American farmers to show their customers that the standards they have implemented are actually delivering what they promise. Considering the manifold resources that are being poured into these systems, it seems reasonable to critically review their reliability. A central indicator for the reliability of the system is the overall evaluation of organic certification. Therefore, it is the objective to analyse the relationship of both constructs. Findings show that most farmers are satisfied with the organic certification system and believe in its reliability; however, they fear the costs of bureaucracy and documentation. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment.
On the use of a similarity function for test case selection in the context of model‐based testing
Authors: Cartaxo Emanuela G. , Machado Patrícia D. L. , Neto Francisco G. Oliveira 
Published: July 2009

AbstractTest case selection in model‐based testing is discussed focusing on the use of a similarity function. Automatically generated test suites usually have redundant test cases. The reason is that test generation algorithms are usually based on structural coverage criteria that are applied exhaustively. These criteria may not be helpful to detect redundant test cases as well as the suites are usually impractical due to the huge number of test cases that can be generated. Both problems are addressed by applying a similarity function. The idea is to keep in the suite the less similar test cases according to a goal that is defined in terms of the intended size of the test suite. The strategy presented is compared with random selection by considering transition‐based and fault‐based coverage. The results show that, in most of the cases, similarity‐based selection can be more effective than random selection when applied to automatically generated test suites. Copyright © 2009 John Wiley & Sons, Ltd.
Physical properties of MnCl2 fillers incorporated into a PVDF/PVC blend and their complexes
Authors: Abdelrazek E.M. , Elashmawi I.S. , Soliman M.A. , Aly A. 
Published: July 2009

AbstractFilms of a PVDF/PVC blend filled with different concentrations of MnCl2 were prepared by using a casting technique. The prepared films were investigated by different methods. X‐ray diffraction scans revealed the amorphous nature of the blend for low concentrations and a crystalline nature for higher ones. Results obtained by FTIR led to conclusions about the specific interactions in the polymer matrices and hence about the complexation. The morphological structure of the prepared samples was studied by SEM, which confirmed the results of XRD and DC electrical conductivity measurements. The ESR spectra of the samples exhibited resonance signals only after the introduction of Mn2+ ions into the blend. The DC conductivity was measured in the temperature range of 300–435 K in order to analyze the mechanism of the conduction. The conductivity–temperature plots were found to follow an Arrhenius relationship. J. VINYL ADDIT. TECHNOL., 2009. © 2009 Society of Plastics Engineers
Fabrication and characterization of in situ synthesized nano‐CaCo3‐reinforced polypropylene composite materials
Authors: Cui Yi‐Hua , Jin Xin , Shen Feng , Han Chen , Wang Jiabao 
Published: July 2009

AbstractTo improve the impact toughness of polypropylene (PP), nano‐CaCO3 was prepared by an in situ synthesis. The surface of the nano‐CaCO3 was modified by KH‐550 silane coupling agent and NDZ‐401 titanium acid ester coupling agent. Nano‐CaCO3/PP composite materials were fabricated through a melt‐blending method and characterized, and their mechanical properties were analyzed. The impact toughness and the tensile strength of the PP were improved significantly by the incorporation of nano‐CaCO3. When the weight fraction of nano‐CaCO3 was 2%, the maximum impact toughness and tensile strength of the PP nanocomposites were 293% and 259%, respectively, of the values for neat PP. Observation of the impact fracture surface of the nanocomposites indicated that the dispersion of nano‐CaCO3 modified by NDZ‐401 coupling agent was more homogeneous than that of nano‐CaCO3 modified by the KH‐550 silane coupling agent. J. VINYL ADDIT. TECHNOL., 2009. © 2009 Society of Plastics Engineers
Modeling of the migration of glycerol monoester plasticizers in highly plasticized poly(vinyl chloride)
Authors: Lundsgaard Rasmus , Kontogeorgis Georgios M. , Kristiansen Jørgen K. , Jensen Torkil F. 
Published: July 2009

AbstractDifferent migration models were evaluated on the basis of data from migration experiments carried out by Danisco in 2005. The migration experiments were set up to investigate the behavior of the three plasticizers GRINDSTED®SOFT‐N‐SAFE (SNS), GRINDSTED®ACETEM 95 CO (Acetem), and epoxidized soybean oil (ESBO) with regard to their migration from three different types of poly(vinyl chloride) into isooctane at 20, 40, and 60°C. Diffusion coefficients derived from the experimental migration data were evaluated against diffusion coefficients estimated from a model based solely on the migration data for ESBO. The diffusion coefficient estimation model proved to be very good in estimating the diffusion coefficients at 20°C but overestimated them at 40°C and 60°C. By using a migration model originally derived by Kontominas [Kondyli et al., Polymer, 34, 2592 (1993)] and the estimated diffusion coefficients, it was possible to obtain a more satisfactory representation of the experimental migration data at 40°C than that obtained with the commonly used migration model of Crank [Crank, Mathematics of diffusion, (1956)] based on the experimental diffusion coefficients. J. VINYL ADDIT. TECHNOL., 2009. © 2009 Society of Plastics Engineers
A panel method free‐wake code for aeroelastic rotor predictions
Authors: Roura M. , Cuerva A. , Sanz‐Andrés A. , Barrero‐Gil A. 
Published: July 2009

AbstractA panel method free‐wake model to analyse the rotor flapping is presented. The aerodynamic model consists of a panel method, which takes into account the three‐dimensional rotor geometry, and a free‐wake model, to determine the wake shape. The main features of the model are the wake division into a near‐wake sheet and a far wake represented by a single tip vortex, and the modification of the panel method formulation to take into account this particular wake description. The blades are considered rigid with a flap degree of freedom. The problem solution is approached using a relaxation method, which enforces periodic boundary conditions. Finally, several code validations against helicopter and wind turbine experimental data are performed, showing good agreement. Copyright © 2009 John Wiley & Sons, Ltd.
Hydrothermal Synthesis, Crystal Structures, and Thermal Stabilities of Two New Zinc Phosphonates with a Layered and a 3D Framework Structures
Authors: Lu Xin , Li Jing , Sun Zhen‐Gang , Dong Da‐Peng , Hua Rui‐Nian , Zhang Na , Liu Lei , Tong Fei , Wang Wei‐Nan 
Published: July 2009

AbstractBy using ethylenediamine as a structure‐directing agent, two new zinc phosphonates [enH2]0.5Zn[(L)(H2O)]·H2O (1) and [enH2]0.5Zn5[(HL)(L)3(H2O)2]·3H2O (2) (H3L = H2O3PCH(OH)CO2H, en = ethylenediamine), have been synthesised by hydrothermal reaction and structurally characterised by single crystal X‐ray diffraction as well as with infrared spectroscopy, elemental analysis and thermogravimetric analysis. The structure of compound 1 comprises ZnO6 octahedra and CPO3 tetrahedra connected by [O3PCH(OH)CO2]3– to form a 2D layered structure with one‐dimensional channel system along the a axis, and the protonated ethylenediamine cations are being located between two adjacent layers. In compound 2, the connections of alternately arranged ZnO6, ZnO5 polyhedra, and CPO3 tetrahedra result in a 3D framework structure with channels containing the [NH3(CH2)2NH3]2+ cations.
On the distinction between creation and conservation: a partial defence of continuous creation
Authors: MILLER TIMOTHY D. 
Published: July 2009

AbstractThe traditional view of divine conservation holds that it is simply a continuation of the initial act of creation. In this essay, I defend the continuous-creation tradition against William Lane Craig's criticism that continuous creation fundamentally misconstrues the intuitive distinction between creation and conservation. According to Craig, creation is the unique causal activity of bringing new patient entities into existence, while conservation involves acting upon already existing patient entities to cause their continued existence. I defend continuous creation by challenging Craig's intuitive distinction and by showing that the alternative account of creation and conservation he bases upon it is fraught with serious internal difficulties.
A Communitarian Utility Function and its Social and Economic Implications
Authors: Kapur Basant K. 
Published: July 2009

The term ‘communitarianism’ is often identified with ‘altruism’: an individual is taken to be communitarian-minded if he or she is concerned with the well-being of others, and not only with his or her own well-being. While communitarianism may embrace altruism, it is most appositely viewed as having a broader connotation. Consider, for example, the puzzle of voting behaviour, discussed by Amitai Etzioni (1988) and many others (including, very recently, Aldrich (1997)). Casting one's vote entails a cost, albeit usually a small one: however, if there are large numbers voting, then one's own vote has a negligible effect on the outcome. An altruist might therefore rationally refrain from voting (just as an entirely self-interested individual would), since he incurs a cost, and neither he nor anybody else receives a benefit. And yet, millions of people the world over regularly vote in elections. Other examples could also be given.‘Group-oriented’ behaviour has been the focus of a number of recent studies. C. Clague (1993), for example, examines the roles of guilt and shame in discouraging tax evasion, and informally discusses how social influences may affect the strength of these sentiments. R. Naylor and M. Cripps (1993) examine the influence of social custom on individuals' propensity to join trade unions, while P. Nelson (1994) argues that in choosing which party to vote for people assign some weight to the preferences of persons they associate with.
Distributive Considerations in Smith's Conception of Economic Justice
Authors: Witztum Amos 
Published: July 2009

In spite of the numerous occasions on which Adam Smith expresses his reservations regarding the morality of commercial societies, there seems to be an agreement that he believed such systems to be fundamentally just. To some, this is so because they attribute to Smith a concept of justice which is narrowly confined to the ‘right to have [one's] body free from injury, and [one's] liberty free from infringement’ (Lectures on Jurisprudence, p. 401). In a world where people have an interest in the fortune of others regardless of how selfish their motives for action might be, injuring someone else's body or restricting someone else's liberty is unlikely to be the behavioural norm.To others, natural liberty in the sphere of economic activity is just not only because individuals behind the system naturally comply with justice in its commutative sense, but also because the system itself generates justice in the distributive sense. Such arguments are based on either the working of the invisible hand — which produces the ‘same distribution of the necessities of life, which would have been made, had the earth been divided into equal portions among all its inhabitants …’ (TMS, p. 185) — or on the approval of the ‘impartial spectator’ of the distribution which is associated with the natural price (Young, 1986).
Measures to Prevent Collisions with Offshore Installations on the Dutch Continental Shelf
Authors: Der Meer Mohr Pauline F.M.Van 
Published: July 2009

1. INTRODUCTIONOn February 1988, the M.S. Cape, a 2,000 ton coaster sailing under the Honduran flag, passed the K14 FA 1 production platform belonging to the Nederlandsche Aardolie Maatschappij (NAM) at a distance of 25 meters. The ship had been drifting because of an engine failure but did not communicate this fact until it had reached an adjacent production platform, by which time it had successfully solved its engine problem. As a result of this incident, the production of gas was halted for some time and the operator of the platform suffered considerable losses. On 28 February 1988, the Swedish ferry M.S. “Vinca Gorthon” entered a field with severe weather conditions, ran into trouble, sent a MAY-DAY call, listed and sunk right on top of a Unocal pipeline, which was damaged. Oil transport through this pipeline had to be stopped immediately. The daily loss suffered by the operator was approximately Dfl.1,5 million.
A Hard Look at the Effects Doctrine of Jurisdiction in Public International Law
Authors: Coppel Jason 
Published: July 2009

The extraterritorial application of competition law on the basis of the effects doctrine of jurisdiction has long been controversial. An analysis of the assumptions which underlie the discourse of jurisdictional assertion leads, however, to the conclusion that the effects doctrine is the only principle on which competition law jurisdiction can reasonably be based.Moreover, a form of qualified effects principle, founded upon the consent of the undertakings involved, would be supported by most, if not all, of the leading players in the competition law arena.
The Kalshoven Commission
Authors: de Zayas Alfred 
Published: July 2009

By Resolution 780 of October 6, 1992 the United Nations Security Council requested the Secretary-Generalto establish, as a matter of urgency, an impartial Commission of Experts to examine and analyse the information submitted […] together with such further information as the Commission of Experts may obtain through its own investigations or efforts […] with a view to providing the Secretary-General with its conclusions on the evidence of grave breaches of the Geneva Conventions and other violations of international law committed in the territory of the former Yugoslavia.