bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid
Authors: Dumit Verónica I. , Cortez Néstor , Matthias Ullmann G. 
Published: March 2011

AbstractFlavin‐containing reductases are involved in a wide variety of physiological reactions such as photosynthesis, nitric oxide synthesis, and detoxification of foreign compounds, including therapeutic drugs. Ferredoxin‐NADP(H)‐reductase (FNR) is the prototypical enzyme of this family. The fold of this protein is highly conserved and occurs as one domain of several multidomain enzymes such as the members of the diflavin reductase family. The enzymes of this family have emerged as fusion of a FNR and a flavodoxin. Although the active sites of these enzymes are very similar, different enzymes function in opposite directions, that is, some reduce oxidized nicotinamide adenine dinucleotide phosphate (NADP+) and some oxidize reduced nicotinamide adenine dinucleotide phosphate (NADPH). In this work, we analyze the protonation behavior of titratable residues of these enzymes through electrostatic calculations. We find that a highly conserved carboxylic acid in the active site shows a different titration behavior in different flavin reductases. This residue is deprotonated in flavin reductases present in plastids, but protonated in bacterial counterparts and in diflavin reductases. The protonation state of the carboxylic acid may also influence substrate binding. The physiological substrate for plastidic enzymes is NADP+, but it is NADPH for the other mentioned reductases. In this article, we discuss the relevance of the environment of this residue for its protonation and its importance in catalysis. Our results allow to reinterpret and explain experimental data. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Analysis of protein function and its prediction from amino acid sequence
Authors: Clark Wyatt T. , Radivojac Predrag 
Published: March 2011

AbstractUnderstanding protein function is one of the keys to understanding life at the molecular level. It is also important in the context of human disease because many conditions arise as a consequence of alterations of protein function. The recent availability of relatively inexpensive sequencing technology has resulted in thousands of complete or partially sequenced genomes with millions of functionally uncharacterized proteins. Such a large volume of data, combined with the lack of high‐throughput experimental assays to functionally annotate proteins, attributes to the growing importance of automated function prediction. Here, we study proteins annotated by Gene Ontology (GO) terms and estimate the accuracy of functional transfer from protein sequence only. We find that the transfer of GO terms by pairwise sequence alignments is only moderately accurate, showing a surprisingly small influence of sequence identity (SID) in a broad range (30–100%). We developed and evaluated a new predictor of protein function, functional annotator (FANN), from amino acid sequence. The predictor exploits a multioutput neural network framework which is well suited to simultaneously modeling dependencies between functional terms. Experiments provide evidence that FANN‐GO (predictor of GO terms; available from http://www.informatics.indiana.edu/predrag) outperforms standard methods such as transfer by global or local SID as well as GOtcha, a method that incorporates the structure ofGO. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Conformational dynamics of L‐lysine, L‐arginine, L‐ornithine binding protein reveals ligand‐dependent plasticity
Authors: Silva Daniel‐Adriano , Domínguez‐Ramírez Lenin , Rojo‐Domínguez Arturo , Sosa‐Peinado Alejandro 
Published: March 2011

AbstractThe molecular basis of multiple ligand binding affinity for amino acids in periplasmic binding proteins (PBPs) and in the homologous domain for class C G‐protein coupled receptors is an unsolved question. Here, using unrestrained molecular dynamic simulations, we studied the ligand binding mechanism present in the L‐lysine, L‐arginine, L‐ornithine binding protein. We developed an analysis based on dihedral angles for the description of the conformational changes upon ligand binding. This analysis has an excellent correlation with each of the two main movements described by principal component analysis (PCA) and it's more convenient than RMSD measurements to describe the differences in the conformational ensembles observed. Furthermore, an analysis of hydrogen bonds showed specific interactions for each ligand studied as well as the ligand interaction with the aromatic residues Tyr‐14 and Phe‐52. Using uncharged histidine tautomers, these interactions are not observed. On the basis of these results, we propose a model in which hydrogen bond interactions place the ligand in the correct orientation to induce a cation–π interaction with Tyr‐14 and Phe‐52 thereby stabilizing the closed state. Our results also show that this protein adopts slightly different closed conformations to make available specific hydrogen bond interactions for each ligand thus, allowing a single mechanism to attain multiple ligand specificity. These results shed light on the experimental evidence for ligand‐dependent conformational plasticity not explained by the previous crystallographic data. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Bridging the gap between weather and seasonal forecasting: intraseasonal forecasting for Australia
Authors: Hudson Debra , Alves Oscar , Hendon Harry H. , Marshall Andrew G. 
Published: March 2011

AbstractThis study examines the potential use of the Predictive Ocean Atmosphere Model for Australia (POAMA), the Bureau of Meteorology's dynamical seasonal forecast system, as an intraseasonal prediction tool for Australia. This would fill the current prediction capability gap between weather forecasts and seasonal outlooks for Australia. The intraseasonal forecast skill of a 27‐year hindcast dataset is investigated, focusing on precipitation and minimum and maximum temperatures over Australia in the second fortnight (average days 15–28 of the forecast). Most of the skill for forecasting precipitation and maximum temperature in the second fortnight is focused over eastern Australia, during austral winter and spring for precipitation and during spring for maximum temperature. For this region and seasons the forecast of the second fortnight performs generally better than using climatology, persistence of observed, or persistence of the forecast for the first fortnight (average days 1–14). The model has generally poor skill in predicting minimum temperatures. The role of key drivers of Australian climate variability for providing predictability at intraseasonal time‐scales is investigated. This is done for the austral winter and spring seasons, when POAMA's skill for predicting precipitation is highest. Forecast skill is found to be increased during extremes of the El Niño Southern Oscillation, the Indian Ocean Dipole and the Southern Annular Mode. The regions of impact of these modes of climate variability on forecast skill are similar to those regions identified in observed studies as being influenced by the respective drivers. In contrast, there is no significant relationship between intraseasonal forecast skill for precipitation and the amplitude of the Madden Julian Oscillation (MJO) in winter and spring, although the analysis does not distinguish between the phases of the MJO. The results indicate that the use of POAMA for intraseasonal forecasting is promising. Copyright © 2011 Royal Meteorological Society
Definition of a moist entropy potential temperature: application to FIRE‐I data flights
Authors: Marquet Pascal 
Published: March 2011

AbstractA moist entropy potential temperature–denoted byθs–is defined analytically in terms of the specific entropy for moist air. The expression forθsis valid for a general mixing of dry air, water vapour and possible condensed water species. It displays the same conservative properties as the moist entropy, even for varying dry air or total water content. The moist formulation forθsis equal to the dry formulationθif dry air is considered, and it displays new properties valid for the moist air cases, both saturated or unsaturated ones. Exact and approximate versions ofθsare evaluated for several stratocumulus cases, in particular by using the aircraft observation datasets from the FIRE‐I experiment. It appears that there is no (or only a small) jump inθsat the top of the planetary boundary layer (PBL). The mixing in moist entropy is almost complete in the PBL, with the same values observed in the clear air and the cloudy regions, including the very top of the entrainment region. The Randall–Deardorff Cloud‐Top Entrainment Instability analysis may be interpreted as a mixing in moist entropy criterion. The iso‐θslines are plotted on skewT–logpand conserved variable diagrams. All these properties could suggest some hints on the use of moist entropy (orθs) in cloud modelling or in mixing processes, with the marine stratocumulus considered as a paradigm of moist turbulence. Copyright © 2011 Royal Meteorological Society
Laplace transform integration of the shallow‐water equations. Part I: Eulerian formulation and Kelvin waves
Authors: Clancy Colm , Lynch Peter 
Published: March 2011

AbstractA filtering integration scheme is developed, using a modification of the contour used to invert the Laplace transform (LT). It is shown to eliminate components with frequencies higher than a specified cut‐off value. Thus it is valuable for integrations of the equations governing atmospheric flow. The scheme is implemented in a shallow‐water model with an Eulerian treatment of advection. It is compared to a reference model using the semi‐implicit (SI) scheme. The LT scheme is shown to treat dynamically important Kelvin waves more accurately than the SI scheme. Copyright © 2011 Royal Meteorological Society
Laplace transform integration of the shallow‐water equations. Part II: Semi‐Lagrangian formulation and orographic resonance
Authors: Clancy Colm , Lynch Peter 
Published: March 2011

AbstractIn this article we combine the Laplace transform (LT) scheme with a semi‐Lagrangian advection scheme, and implement it in a shallow‐water model. It is compared to a reference model using the semi‐implicit (SI) scheme, with both Eulerian and Lagrangian advection. We show that the LT scheme is accurate and computationally competitive with these reference schemes. We also show, both analytically and numerically, that the LT scheme is free from the problem of orographic resonance that is found with semi‐implicit schemes. Copyright © 2011 Royal Meteorological Society
THE FLORA OF URBAN RIVER WALLSCAPES
Authors: Francis R. A. , Hoggart S. P. G. 
Published: March 2011

ABSTRACTUrban river walls represent some of the most common habitat available to riparian species within heavily engineered urban river corridors, but research into the characteristics and diversity of river walls is very rare. In this study, the flora of urban river walls was surveyed at 16 sites (92 walls) along 32 km of the river Thames through central London to determine the characteristics and habitat origins of species found on these walls, whether these species indicated ‘an urban cliff effect’ occurring on wall habitats and whether plant species richness varied between different wall types. A total of 90 species were found on the walls, with the majority of species associated with disturbed areas and riparian habitats, supporting the idea of a ‘mass effect’ occurring, whereby the flora is maintained by propagule pressure from remnant or introduced habitats within urban or peri‐urban areas, rather than walls selecting for cliff/rock species. There was an increased incidence of plants from cliff/rock habitats found in the flora however, suggesting that an urban cliff effect does still occur. Species were organized along the river walls based on riparian/terrestrial gradients and stress tolerance, probably reflecting a gradient of wall height above river flows. Plant species richness was significantly higher on brick walls than that on sheet piling, indicating key differences between materials probably based on surface integrity. Large areas of connected river walls (‘wallscapes’) through heavily engineered urban rivers represent potential sites for the enactment of reconciliation ecology via habitat improvement in urban ecosystems. Copyright © 2011 John Wiley & Sons, Ltd.
Mindfulness‐based Coping with University Life: A Non‐randomized Wait‐list‐controlled Pilot Evaluation
Authors: Lynch Siobhan , Gander Marie‐Louise , Kohls Niko , Kudielka Brigitte , Walach Harald 
Published: March 2011

AbstractThe aim of this study was to explore the feasibility of implementing a new 8‐week mindfulness‐based programme, ‘Mindfulness‐Based Coping with University Life’ (MBCUL), specifically tailored to the needs and demand of students and to explore its impact in a pilot evaluation. Participants were drawn from the University of Northampton (MBCUL N = 10; control N = 6). A non‐randomized wait‐list‐controlled design was employed. Measures examined anxiety and depression, perceived stress, mindfulness and personally relevant change before and immediately after the programme. The diurnal profile of salivary cortisol and alpha‐amylase level was collected for two consecutive days. No significant intergroup differences were observed on any of the measures at either time point. However, significant change was observed for the MBCUL group in terms of perceived stress (d = 1.06; z = −2.25, p = 0.03), anxiety (d = 1.04; z = −2.14, p = 0.03), depression (d = 0.52; z = −0.69, p = 0.5) and personally relevant change (d = 2.63; z = −2.68, p = 0.01), along with an increase in mindfulness (d = 1.06; z = −1.89, p = 0.06). In contrast, no significant change was found in the daily profiles of cortisol and alpha‐amylase. The data from this pilot tentatively suggest that MBCUL appears to be a promising programme that warrants further evaluation using a randomized study with a larger sample size. Copyright © 2011 John Wiley & Sons, Ltd.
Convective Assembly of 2D Lattices of Virus‐like Particles Visualized by In‐Situ Grazing‐Incidence Small‐Angle X‐Ray Scattering
Authors: Ashley Carlee E. , Dunphy Darren R. , Jiang Zhang , Carnes Eric C. , Yuan Zhen , Petsev Dimiter N. , Atanassov Plamen B. , Velev Orlin D. , Sprung Michael , Wang Jin , Peabody David S. , Brinker C. Jeffrey 
Published: March 2011

AbstractThe rapid assembly of icosohedral virus‐like particles (VLPs) into highly ordered (domain size > 600 nm), oriented 2D superlattices directly onto a solid substrate using convective coating is demonstrated. In‐situ grazing‐incidence small‐angle X‐ray scattering (GISAXS) is used to follow the self‐assembly process in real time to characterize the mechanism of superlattice formation, with the ultimate goal of tailoring film deposition conditions to optimize long‐range order. From water, GISAXS data are consistent with a transport‐limited assembly process where convective flow directs assembly of VLPs into a lattice oriented with respect to the water drying line. Addition of a nonvolatile solvent (glycerol) modified this assembly pathway, resulting in non‐oriented superlattices with improved long‐range order. Modification of electrostatic conditions (solution ionic strength, substrate charge) also alters assembly behavior; however, a comparison of in‐situ assembly data between VLPs derived from the bacteriophages MS2 and Qβ show that this assembly process is not fully described by a simple Derjaguin–Landau–Verwey–Overbeek model alone.
Superiority of Branched Side Chains in Spontaneous Nanowire Formation: Exemplified by Poly(3‐2‐methylbutylthiophene) for High‐Performance Solar Cells
Authors: Chen Hsieh‐Chih , Wu I‐Che , Hung Jui‐Hsiang , Chen Fu‐Je , Chen I‐Wen P. , Peng Yung‐Kang , Lin Chao‐Sung , Chen Chun‐Hsien , Sheng Yu‐Jane , Tsao Heng‐Kwong , Chou Pi‐Tai 
Published: March 2011

AbstractOne‐dimensional nanostructures containing heterojunctions by conjugated polymers, such as nanowires, are expected to greatly facilitate efficient charge transfer in bulk‐heterojunction (BHJ) solar cells. Thus, a combined theoretical and experimental approach is pursued to explore spontaneous nanowire formation. A dissipative particle dynamics simulation is first performed to study the morphologies formed by rodlike polymers with various side‐chain structures. The results surprisingly predict that conjugated polymers with branched side chains are well suited to form thermodynamically stable nanowires. Proof of this concept is provided via the design and synthesis of a branched polymer of regioregular poly(3‐2‐methylbutylthiophene) (P3MBT), which successfully demonstrates highly dense nanowire formation free from any stringent conditions and stratagies. In BHJ solar cells fabricated using a blend of P3MBT and [6,6]‐phenyl‐C71‐butyric acid methyl ester (PC71BM), P3MBT polymers are self‐organized into highly crystalline nanowires with a d100 spacing of 13.30 Å. The hole mobility of the P3MBT:PC71BM (1:0.5 by weight) blend film reaches 3.83 × 10−4 cm2 V−1 s−1, and the maximum incident photon‐to‐current efficiency reaches 68%. The results unambiguously prove the spontaneous formation of nanowires using solution‐processable conjugated polymers with branched alkyl side chains in BHJ solar cells.
Assembly and Degradation of Low‐Fouling Click‐Functionalized Poly(ethylene glycol)‐Based Multilayer Films and Capsules
Authors: Leung Melissa K. M. , Such Georgina K. , Johnston Angus P. R. , Biswas Dhee P. , Zhu Zhiyuan , Yan Yan , Lutz Jean‐François , Caruso Frank 
Published: March 2011

AbstractNano‐/micrometer‐scaled films and capsules made of low‐fouling materials such as poly(ethylene glycol) (PEG) are of interest for drug delivery and tissue engineering applications. Herein, the assembly and degradation of low‐fouling, alkyne‐functionalized PEG (PEGAlk) multilayer films and capsules, which are prepared by combining layer‐by‐layer (LbL) assembly and click chemistry, are reported. A nonlinear, temperature‐responsive PEGAlk is synthesized, and is then used to form hydrogen‐bonded multilayers with poly(methacrylic acid) (PMA) at pH 5. The thermoresponsive behavior of PEGAlk is exploited to tailor film buildup by adjusting the assembly conditions. Using alkyne–azide click chemistry, PEGAlk/PMA multilayers are crosslinked with a bisazide linker that contains a disulfide bond, rendering these films and capsules redox‐responsive. At pH 7, by disrupting the hydrogen bonding between the polymers, PEGAlk LbL films and PEGAlk‐based capsules are obtained. These films exhibit specific deconstruction properties under simulated intracellular reducing conditions, but remain stable at physiological pH, suggesting potential applications in controlled drug release. The low‐fouling properties of the PEG films are confirmed by incubation with human serum and a blood clot. Additionally, these capsules showed negligible toxicity to human cells.
Graphene Devices: Structured Graphene Devices for Mass Transport (Small 6/2011)
Authors: Barreiro Amelia , Rurali Riccardo , Hernández Eduardo R. , Bachtold Adrian 
Published: March 2011

AbstractThe reversible atomic‐mass transport along graphene devices has been achieved. The motion of Al and Au in the form of atoms or clusters is driven by applying an electric field between the metal electrodes that contact the graphene sheet. It is shown that Al moves in the direction of the applied electric field whereas Au tends to diffuse in all directions. The control of the motion of Al is further demonstrated by achieving a 90° turn, using a graphene device patterned in a crossroads configuration. The controlled motion of Al is attributed to the charge transfer from Al onto the graphene so that the Al is effectively charged and can be accelerated by the applied electric field. To get further insight into the actuation mechanism, theoretical simulations of individual Al and Au impurities on a perfect graphene sheet were performed. The direct (electrostatic) force was found to be ∼1 pN and dominant over the wind force. These findings hold promise for practical use in future mass transport in complex circuits.
Micropatterning: Ultrafast Large‐Area Micropattern Generation in Nonabsorbing Polymer Thin Films by Pulsed Laser Diffraction (Small 6/2011)
Authors: Verma Ankur , Sharma Ashutosh , Kulkarni Giridhar U. 
Published: March 2011

AbstractAn ultrafast, parallel, and beyond‐the‐master micropatterning technique for ultrathin (30−400 nm) nonabsorbing polymer films by diffraction of laser light through a 2D periodic aperture is reported. The redistribution of laser energy absorbed by the substrate causes self‐organization of polymer thin films in the form of wrinklelike surface relief structures caused by localized melting and freezing of the thin film. Unlike conventional laser ablation and laser writing processes, low laser fluence is employed to only passively swell the polymer as a pre‐ablative process without loss of material, and without absorption/reaction with incident radiation. Self‐organization in the thin polymer film, aided by the diffraction pattern, produces microstructures made up of thin raised lines. These regular microstructures have far more complex morphologies than the mask geometry and very narrow line widths that can be an order of magnitude smaller than the openings in the mask. The microstructure morphology is easily modulated by changing the film thickness, aperture size, and geometry, and by changing the diffraction pattern.
Fundamental Study on Carbon Composite Iron Ore Hot Briquette Used as Blast Furnace Burden
Authors: Man‐sheng Chu , Zheng‐gen Liu , Zhao‐cai Wang , Jun‐ichiro Yagi 
Published: March 2011

AbstractCarbon composite iron ore hot briquette (CCB) is the product of fine iron ore and fine coal by hot briquetting process, which attracts more and more attention as a new type of ironmaking raw materials aiming to improve the operation efficiency and reduce the coke consumption of blast furnace. This paper is devoted to experimental study on metallurgical properties of CCB and numerical simulation of the BF operation with CCB charging. At first, the metallurgical properties of CCB, including cold crushing strength, RDI, RSI, reducibility, high temperature strength, and softening and dripping are experimentally tested and compared with the common burdens, which revealed that the CCB possesses the required metallurgical properties and is suitable to use as the blast furnace burden. Then, the effects of charging CCB on the dripping properties of comprehensive burdens are elucidated based on the experiments under simulated blast furnace conditions. The results showed that the maximum charging ratio of CCB in the iron burdens is 40%–50% for achieving appropriate dripping properties of the mixed burdens. Finally, a multi‐fluid blast furnace model is used to simulate BF operation with CCB charging. According to model simulations, charging CCB will cause the temperature level to decreases in the furnace and the location of the cohesive zone shifts downward. On the other hand, the productivity tends to increase while coke rate and total reducing agent rate decrease, the heat efficiency improves remarkably and the operation performance of BF is effectively enhanced.