bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning generative models for protein fold families
Authors: Balakrishnan Sivaraman , Kamisetty Hetunandan , Carbonell Jaime G. , Lee Su‐In , Langmead Christopher James 
Published: November 2010

AbstractWe introduce a new approach to learning statistical models from multiple sequence alignments (MSA) of proteins. Our method, called GREMLIN(Generative REgularized ModeLs of proteINs), learns an undirected probabilistic graphical model of the amino acid composition within the MSA. The resulting model encodes both the position‐specific conservation statistics and the correlated mutation statistics between sequential and long‐range pairs of residues. Existing techniques for learning graphical models from MSA either make strong, and often inappropriate assumptions about the conditional independencies within the MSA (e.g., Hidden Markov Models), or else use suboptimal algorithms to learn the parameters of the model. In contrast, GREMLINmakes noa prioriassumptions about the conditional independencies within the MSA. We formulate and solve a convex optimization problem, thus guaranteeing that we find a globally optimal model at convergence. The resulting model is also generative, allowing for the design of new protein sequences that have the same statistical properties as those in the MSA. We perform a detailed analysis of covariation statistics on the extensively studied WW and PDZ domains and show that our method out‐performs an existing algorithm for learning undirected probabilistic graphical models from MSA. We then apply our approach to 71 additional families from thePFAMdatabase and demonstrate that the resulting models significantly out‐perform Hidden Markov Models in terms of predictive accuracy. Proteins 2011; © 2011 Wiley‐Liss, Inc.
The α‐sheet: A missing‐in‐action secondary structure?
Authors: Babin Volodymyr , Roland Christopher , Sagui Celeste 
Published: November 2010

AbstractThe α‐sheet has been speculated to play a role as a toxic conformer in amyloid diseases. However, except for relatively short fragments, its detection has remained elusive. Here, we present molecular dynamics simulations that support the existence of the α‐sheet as a stable, metastable, or long‐lived secondary structure in polyglutamine and, to a lesser extent, in polyasparagine aggregates. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Analysis of the peroxiredoxin family: Using active‐site structure and sequence information for global classification and residue analysis
Authors: Nelson Kimberly J. , Knutson Stacy T. , Soito Laura , Klomsiri Chananat , Poole Leslie B. , Fetrow Jacquelyn S. 
Published: November 2010

AbstractPeroxiredoxins (Prxs) are a widespread and highly expressed family of cysteine‐based peroxidases that react very rapidly with H2O2, organic peroxides, and peroxynitrite. Correct subfamily classification has been problematic because Prx subfamilies are frequently not correlated with phylogenetic distribution and diverge in their preferred reductant, oligomerization state, and tendency toward overoxidation. We have developed a method that uses the Deacon Active Site Profiler (DASP) tool to extract functional‐site profiles from structurally characterized proteins to computationally define subfamilies and to identify new Prx subfamily members from GenBank(nr). For the 58 literature‐defined Prx test proteins, 57 were correctly assigned, and none were assigned to the incorrect subfamily. The >3500 putative Prx sequences identified were then used to analyze residue conservation in the active site of each Prx subfamily. Our results indicate that the existence and location of the resolving cysteine vary in some subfamilies (e.g., Prx5) to a greater degree than previously appreciated and that interactions at the A interface (common to Prx5, Tpx, and higher order AhpC/Prx1 structures) are important for stabilization of the correct active‐site geometry. Interestingly, this method also allows us to further divide the AhpC/Prx1 into four groups that are correlated with functional characteristics. The DASP method provides more accurate subfamily classification than PSI‐BLAST for members of the Prx family and can now readily be applied to other large protein families. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate‐binding cleft conformations
Authors: Elmabrouk Zainab H. , Vincent Florence , Zhang Meng , Smith Nicola L. , Turkenburg Johan P. , Charnock Simon J. , Black Gary W. , Taylor Edward J. 
Published: November 2010

AbstractBacterial enzymatic degradation of glycosaminoglycans such as hyaluronan and chondroitin is facilitated by polysaccharide lyases. Family 8 polysaccharide lyase (PL8) enzymes contain at least two domains: one predominantly composed of α‐helices, the α‐domain, and another predominantly composed of β‐sheets, the β‐domain. Simulation flexibility analyses indicate that processive exolytic cleavage of hyaluronan, by PL8 hyaluronate lyases, is likely to involve an interdomain shift, resulting in the opening/closing of the substrate‐binding cleft between the α‐ and β‐domains, facilitating substrate translocation. Here, the Streptomyces coelicolor A3(2) PL8 enzyme was recombinantly expressed in and purified from Escherichia coli and biochemically characterized as a hyaluronate lyase. By using X‐ray crystallography its structure was solved in complex with hyaluronan and chondroitin disaccharides. These findings show key catalytic interactions made by the different substrates, and on comparison with all other PL8 structures reveals that the substrate‐binding cleft of the S. coelicolor enzyme is highly occluded. A third structure of the enzyme, harboring a mutation of the catalytic tyrosine, created via site‐directed mutagenesis, interestingly revealed an interdomain shift that resulted in the opening of the substrate‐binding cleft. These results add further support to the proposed processive mechanism of action of PL8 hyaluronate lyases and may indicate that the mechanism of action is likely to be universally used by PL8 hyaluronate lyases. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Molecular dynamics simulation of β2‐microglobulin in denaturing and stabilizing conditions
Authors: Fogolari Federico , Corazza Alessandra , Varini Nicola , Rotter Matteo , Gumral Devrim , Codutti Luca , Rennella Enrico , Viglino Paolo , Bellotti Vittorio , Esposito Gennaro 
Published: November 2010

Abstractβ2‐Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β2‐microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β2‐microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β2‐microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis‐trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native‐like trans‐conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis‐trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β2‐microglobulin provides details of the binding modes of the drug and a rationale for its effect. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Kinetics of sorption‐desorption of benfuracarb insecticide in mollisols
Authors: Srivastava Anjana , Chandra Raju , Srivastava Prakash Chandra 
Published: November 2010

AbstractBACKGROUND: Sorption‐desorption processes govern the movement of pesticides in soil. These processes determine the potential hazard of the pesticide in a given environment for groundwater contamination and need to be investigated.RESULTS: In the present study, sorption‐desorption processes of benfuracarb were investigated using a batch method in two mollisols. The kinetics of benfuracarb sorption in mollisols conformed to two‐compartment (1 + 1) first‐order kinetics. The fast sorption rate constant was about 3 times higher for silt loam than for loam soil. However, the slow sorption rate constants were statistically similar for both soils. The concentration‐dependent sorption‐desorption isotherms of benfuracarb could not closely conform to the Freundlich isotherm in mollisols of high organic C content. The computed values of both the sorption (log K) and desorption (log K′) capacities were higher for silt loam than for loam soil. The desorption index (n′/n) values in the range 30.0–41.3 indicated poor reversibility of sorbed benfuracarb in mollisols.CONCLUSION: In view of the strong sorption of benfuracarb in mollisols with only partial desorption, the possibility of the leaching of soil‐applied benfuracarb to contaminate groundwaters appears to be low. Copyright © 2010 Society of Chemical Industry
Gas‐phase synthesis of hydrodiphenylcyclopropenylium via nonclassical Favorskii rearrangement from alkali‐cationized α,α′‐dibromodibenzyl ketone
Authors: Zhao Zhi‐Xiong , Wang Hao‐Yang , Xu Chu , Guo Yin‐Long 
Published: November 2010

AbstractThe gas‐phase synthesis of hydrodiphenylcyclopropenylium from alkali‐cationized α,α′‐dibromodibenzyl ketone (1) via nonclassical Lewis‐acid‐induced Favorskii rearrangement has been studied by electrospray ionization/tandem mass spectrometry (ESI‐MS/MS) and theoretical methods, showing that cations [1–Br]+ by debromination from 1 and 1 · M+(M = Li or Na) by alkali‐metal cationization of 1 could convert into the protonated diphenylcyclopropenone 2 · H+ by collision‐induced dissociation in the gas phase. A concerted mechanism for the Lewis‐acid‐induced Favorskii rearrangement from alkali‐metal‐cationized α,α′‐dibromodibenzyl ketone was proposed and studied, based on mass spectrometric results and theoretical methods. Copyright © 2010 John Wiley & Sons, Ltd.
Encapsulation and Release of Molecular Cargos via Temperature‐Induced Vesicle‐To‐Micelle Transitions
Authors: Chen Qi , Schönherr Holger , Vancso G. Julius 
Published: November 2010

AbstractTemperature‐induced vesicle‐to‐micelle transitions of polystyrene‐block‐poly acrylic acid (PS139‐b‐PAA17) aggregates in tetrahydrofuran (THF)/H2O solvent mixtures are studied. For a typical system with an initial concentration of PS139‐b‐PAA17 of 2 wt% and 50 vol% of H2O, the morphology of the aggregates changes from vesicles to micelles upon heating from room temperature to 45 °C. The transition temperature is found to depend on the polymer concentration as well as solvent composition. A higher polymer concentration results in a higher transition temperature. The morphological change is attributed to a change in the solvent‐polymer interactions, which results in a reduction in interfacial energy. The corresponding temperature‐induced morphological change is employed as a strategy for the reversible release and encapsulation of small molecules. The release of Rhodamine 110 bisamide above the transition temperature is observed as a result of the trypsin‐catalyzed hydrolysis of the bisamide into Rhodamine 110. Likewise, the successful encapsulation of Rhodamine 110 below the transition temperature is proven using sodium nitrite as a chemical quencher.
A study of multi‐hop cellular networks
Authors: Tam Y. Hung , Hassanein Hossam S. , Akl Selim G. 
Published: November 2010

ABSTRACTThe number of cellular communication subscribers continues to grow, attesting to the great success of this technology. However, cellular networks have inherent limitations on cell capacity and coverage and shortcomings such as the dead spot and the hot spot problems. Multi‐hop cellular networks (MCNs) help enhance the cell capacity and coverage, while, at the same time, alleviating the dead spot and hot spot problems, increasing the utilization of radio resource, and reducing the power consumption of mobile terminals. In the past decade, more than a dozen of MCN architectures were proposed. In this paper, we study various types of MCN proposals. We identify and discuss the design decision factors and use these factors to classify most existing MCN proposals. Future research directions, including studies of capacity and energy consumption, and approaches addressing design issues such as cell size, routing, channel assignment, load balancing for MCNs are discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Isolation of Pichia pastoris PIR genes and their utilization for cell surface display and recombinant protein secretion
Authors: Pal Khasa Yogender , Conrad Sara , Sengul Mustafa , Plautz Sarah , Meagher Michael M. , Inan Mehmet 
Published: November 2010

AbstractProteins with internal repeats are highly conserved among budding yeasts. In this study, the isolation of two proteins with internal repeats (PIR) genes, i.e. PpPIR1 and PpPIR2, from the methylotrophic yeast Pichia pastoris has been reported. The PIR1 and PIR2 genes' open reading frames were found to contain 1068 and 972 bases, respectively. The sequence homology search showed a homologous conserved repeat of PIR yeast block (SQIGDGQIQATT) in both proteins. The PIR yeast block was present eight times in the PpPir1p and four times in the PpPir2p proteins. Both proteins showed conserved glutamine (Q) and aspartic acid (D) in the repeated sequences, indicating a possible alkali‐sensitive β1,3‐glucan ester linkage. The fusion constructs of PpPir1‐2p and enhanced green fluorescent protein (EGFP) were developed for yeast cell surface display. The immunofluorescence assay showed uniform localization of EGFP protein on the P. pastoris cell surface in all fusion constructs. Furthermore, new vectors were developed for recombinant protein secretion in P. pastoris, utilizing the pre‐pro signal of PpPir1p protein. Efficient processing of the signal sequence was observed from EGFP and human α1‐antitrypsin (AAT) fusion constructs and recombinant protein secretion was obtained in the culture supernatant. The DNA sequences of the P. pastoris PpPIR1 and PpPIR2 genes have been submitted to GenBank under Accession Nos HM446634 and HM446635, respectively. Copyright © 2010 John Wiley & Sons, Ltd.
Local and Permeating Disorder of Copper(I) Cations in Cu3BiS2Br2 and Cu4Bi3S5Br3–xClx (x = 1.19)
Authors: Heerwig Andreas , Nitsche Fabian , Ruck Michael 
Published: November 2010

AbstractMelting reactions of Bi2S3, CuX (X = Cl, Br), copper, and sulfur resulted in black needles of qua‐ and quinternary copper bismuth sulfide halogenides. Cu3BiS2Br2 (I) has a melting point of 638(5) K and crystallizes in the orthorhombic space group Pnma with a = 804.50(6) pm, b = 393.27(3) pm, and c = 2253.2(2) pm at T = 293(2) K. Cu4Bi3S5Br3–xClx (x = 1.19(2)) (II) crystallizes in the monoclinic space group I2/m with lattice parameters a = 1573.7(2) pm, b = 397.52(3) pm, c = 2164.9(3) pm, and β = 95.66(1) °. Both compounds exhibit networks of thio‐halogenido‐bismuthate(III) polyhedra that join corners, edges, and faces. The copper(I) cations are spread over numerous contiguous trigonal or tetrahedral voids. In case of (II) a continuous pathway for copper ion transport along [010] is formed. The pseudo‐potential barrier for hopping of copper ions was calculated as 30 meV only.
Synthesis, Structural Characterization and Physical Properties of a New Member of Ternary Lithium Layered Compounds – Li2RhO3
Authors: Todorova Vanya , Jansen Martin 
Published: November 2010

AbstractLi2RhO3was synthesized by solid state reaction and its crystal structure was refined from X‐ray powder data by the Rietveld‐method. The compound was obtained as a black powder and crystallizes in the monoclinic space groupC2/m, with unit cell parametersa= 5.1198(1),b= 8.8497(1),c= 5.1030(1) Å,β= 109.61(2) °,V= 217.80(1), andZ= 4. The structure determination shows that the oxygen atoms in Li2RhO3form an approximate cubic close packing, where all octahedral voids are occupied by Rh4+and Li+cations. The structure is closely related to the α‐NaFeO2and Li2MnO3layered structure types (layered variants of the NaCl‐type), but in Li2RhO3the lithium and rhodium atoms are partially disordered. Li2RhO3behaves as a semiconductor with rather small activation energy of 7.68 kJ·mol–1and is thermally stable up to 1273 K in argon atmosphere. According to measurements of the magnetic susceptibility in the temperature range from 2 to 330 K, Li2RhO3is paramagnetic, obeys the Curie–Weiss law at temperatures above 150 K, and has an effective magnetic moment of 1.97 μBat 300 K.
A Lua-based AOP infrastructure
Authors: Cacho Nélio , Batista Thaís , Fernandes Fabrício 
Published: November 2010

AbstractIn this paper we describe an aspect-oriented infrastructure to handle dynamic AOP based on the Lua language. This infrastructure is composed of AspectLua, a Lua extension that allows the declaration of aspects, and a meta-object protocol, LuaMOP, that unifies the introspective and reflective mechanisms provided by Lua. Aspects are defined in isolation using AspectLua and then they are weaved through LuaMOP. An important feature of AspectLua is to allow the association of aspects with undeclared elements of the application code (anticipated join points). Furthermore, it combines a range of features to make AOP easier and powerful.
A new approach for regularized image interpolation
Authors: El-Khamy S. E. , Hadhoud M. M. , Dessouky M. I. , Salam B. M. , Abd El-Samie F. E. 
Published: November 2010

AbstractThis paper presents a non-iterative regularized inverse solution to the image interpolation problem. This solution is based on the segmentation of the image to be interpolated into overlapping blocks and the interpolation of each block, separately. The purpose of the overlapping blocks is to avoid edge effects. A global regularization parameter is used in interpolating each block. In this solution, a single matrix inversion process of moderate dimensions is required in the whole interpolation process. Thus, it avoids the large computational cost due to the matrices of large dimensions involved in the interpolation process. The performance of this approach is compared to the standard iterative regularized interpolation scheme and to polynomial based interpolation schemes such as the bicubic and cubic spline techniques. A comparison of the suggested approach with some algorithms implemented in the commercial ACDSee software has been performend in the paper. The obtained results reveal that the suggested solution has a better performance as compared to other algorithms from the MSE and the edges preservation points of view. Its computation time is relatively large as compared to traditional algorithms but this is acceptable when image quality is the main concern.
Specular highlights detection and reduction with multi-flash photography
Authors: Feris Rogerio , Raskar Ramesh , Tan Kar-Han , Turk Matthew 
Published: November 2010

AbstractWe present a novel method to reduce the effect of specularities in digital images. Our approach relies on a simple modification of the capture setup: a multi-flash camera is used to take multiple pictures of the scene, each one with a differently positioned light source. We then formulate the problem of specular highlights reduction as solving a Poisson equation on a gradient field obtained from the input images. The obtained specular reduced image is further refined in a matting process with the maximum composite of the input images. Experimental results are demonstrated on real and synthetic images. The entire setup can be conceivably packaged into a self-contained device, no larger than existing digital cameras.
Crosscutting interfaces for aspect-oriented modeling
Authors: Chavez Christina , Garcia Alessandro , Kulesza Uirá , Sant’Anna Cláudio , Lucena Carlos 
Published: November 2010

AbstractAspect-oriented software development promotes improved separation of concerns by introducing a new modular unit, called aspect, for the modularization of crosscutting concerns. As a new kind of modular unit, aspects should have explicit interfaces that describe the way they interact with the rest of the system and how they affect other modules. This interaction can be homogeneous or heterogeneous. In this paper, we present crosscutting interfaces as a conceptual tool for dealing with the complexity of heterogeneous aspects at the design level. Crosscutting interfaces have been incorporated by the aSideML modeling language in order to enhance aspect description at the design level. Moreover, we present a modeling notation for the description of architecture-level aspects that also supports the explicit representation of crosscutting interfaces. Finally, we present two large-scale case studies we have performed using this modeling language that support our arguments in favor of crosscutting interfaces.
Infeasible paths in the context of data flow based testing criteria: Identification, classification and prediction
Authors: Vergilio Silvia Regina , Maldonado José Carlos , Jino Mario 
Published: November 2010

AbstractInfeasible paths constitute a bottleneck for the complete automation of software testing, one of the most expensive activities of software quality assurance. Research efforts have been spent on infeasible paths, basically on three main approaches: prediction, classification and identification of infeasibility. This work reports the results of experiments on data flow based criteria and of studies aimed at the three approaches above. Identification, classification, and prediction of infeasible paths are revisited in the context of data flow based criteria (Potential Uses Criteria-PU). Additionally, these aspects are also addressed in the scope of integration and object-oriented testing. Implementation aspects of mechanisms and facilities to deal with infeasibility are presented taking into consideration Poketool — a tool that supports the application of the Potential Uses Criteria Family. The results and ideas presented contribute to reduce the efforts spent during the testing activity concerning infeasible paths.
Concurrent blind channel equalization with phase transmittance RBF neural networks
Authors: Loss Diego Vier , De Castro Maria Cristina Felippetto , Franco Paulo Roberto Girardello , de Castro Fernando César Comparsi 
Published: November 2010

AbstractThis paper presents a new complex valued radial basis function (RBF) neural network (NN) with phase transmittance between the input nodes and output, which makes it suitable for channel equalization on quadrature digital modulation systems. The new Phase Transmittance RBFNN (PTRBFNN) differs from the classical complex valued RBFNN in that it does not strictly rely on the Euclidean distance between the input vector and the center vectors, thus enabling the transference of phase information from input to output. In the context of blind channel equalization, results have shown that the PTRBFNN not only solves the phase uncertainty of the classical complex valued RBFNN but also presents a faster convergence rate.comes the abstract of the paper.