bluuebunny/crossref_metadata_2025_split huggingface dataset:
Successful application of the DBLOC method to the hydroxylation of camphor by cytochrome p450
Authors: Jerome Steven V. , Hughes Thomas F. , Friesner Richard A. 
Published: October 2015

AbstractThe activation barrier for the hydroxylation of camphor by cytochrome P450 was computed using a mixed quantum mechanics/molecular mechanics (QM/MM) model of the full protein‐ligand system and a fully QM calculation using a cluster model of the active site at the B3LYP/LACVP*/LACV3P** level of theory, which consisted of B3LYP/LACV3P** single point energies computed at B3LYP/LACVP* optimized geometries. From the QM/MM calculation, a barrier height of 17.5 kcal/mol was obtained, while the experimental value was known to be less than or equal to 10 kcal/mol. This process was repeated using the D3 correction for hybrid DFT in order to investigate whether the inadequate treatment of dispersion interaction was responsible for the overestimation of the barrier. While the D3 correction does reduce the computed barrier to 13.3 kcal/mol, it was still in disagreement with experiment. After application of a series of transition metal optimized localized orbital corrections (DBLOC) and without any refitting of parameters, the barrier was further reduced to 10.0 kcal/mol, which was consistent with the experimental results. The DBLOC method to CH bond activation in methane monooxygenase (MMO) was also applied, as a second, independent test. The barrier in MMO was known, by experiment, to be 15.4 kcal/mol. After application of the DBLOC corrections to the MMO barrier compute by B3LYP, in a previous study, and accounting for dispersion with Grimme's D3 method, the unsigned deviation from experiment was improved from 3.2 to 2.3 kcal/mol. These results suggested that the combination of dispersion plus localized orbital corrections could yield significant quantitative improvements in modeling the catalytic chemistry of transition‐metal containing enzymes, within the limitations of the statistical errors of the model, which appear to be on the order of approximately 2 kcal/mole.
Protein structure refinement with adaptively restrained homologous replicas
Authors: Della Corte Dennis , Wildberg André , Schröder Gunnar F. 
Published: October 2015

ABSTRACTA novel protein refinement protocol is presented which utilizes molecular dynamics (MD) simulations of an ensemble of adaptively restrained homologous replicas. This approach adds evolutionary information to the force field and reduces random conformational fluctuations by coupling of several replicas. It is shown that this protocol refines the majority of models from the CASP11 refinement category and that larger conformational changes of the starting structure are possible than with current state of the art methods. The performance of this protocol in the CASP11 experiment is discussed. We found that the quality of the refined model is correlated with the structural variance of the coupled replicas, which therefore provides a good estimator of model quality. Furthermore, some remarkable refinement results are discussed in detail. Proteins 2016; 84(Suppl 1):302–313. © 2015 Wiley Periodicals, Inc.
‘I Would Really Like to Go Where You Go’: Rethinking Migration Decision‐Making Among Educated Tied Movers
Authors: Clerge Orly , Sanchez‐Soto Gabriela , Song Jing , Luke Nancy 
Published: October 2015

AbstractThis paper studies ‘tied mover’ men and women who are the partners of graduate students. We use qualitative data to explore the relocation decision‐making process of married and unmarried partners. We find that, while many partners have educational and career aspirations of their own, the maintenance of the relationship is a strong priority that dictates how and when a tied move occurs. Furthermore, the decision‐making process is varied and depends on the stage of the relationship. Tied movers at earlier points in their relationships often make independent decisions to join their graduate student partners after the student has already initiated the move. Some of those in more mature relationships follow a traditional mover–follower model, while others participate in joint decision‐making about their destination. Finally, we find that over one‐third of the tied movers are male, reflecting both increases in women's migration for graduate school and men's openness to ‘following’ career‐oriented partners. This paper contributes to the study of family migration by developing a model focusing on individual and collective non‐economic determinants of couples' decisions to migrate for skill development. Copyright © 2015 John Wiley & Sons, Ltd.
Advanced light trapping interface for a‐Si:H thin film
Authors: Nasser Hisham , Saleh1 Zaki M. , Özkol Engin , Bek Alpan , Turan Raşit 
Published: October 2015

AbstractSurface texturing of transparent conducting oxides and plasmonic interfaces are two important techniques used separately in thin film solar cells to reduce reflection and enhance light‐trapping. In this study, we merge the effects of Al:ZnO surface texturing and Ag nanoparticles (AgNPs) plasmonics in a single light‐trapping interface to investigate their combined light trapping efficiency on a‐Si:H thin film. Light scattered by this interface is optimized by placing a thin SiO2 spacer layer between AgNPs and a‐Si:H absorber layer. Our results indicate that the AgNPs embedded in SiO2 significantly enhance absorption at energies close to the band gap of a‐Si:H. Surface texturing by wet etching of Al:ZnO combined with AgNP produces the highest optical extinction of a‐Si:H thin film at the band edge. Furthermore, the measured photocurrent in a‐Si:H shows a clear increase not only at AgNPs resonance wavelength but over the entire wavelength range. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
High‐perfomance Ce‐doped multicomponent garnet single crystalline film scintillators
Authors: Zorenko Yu. , Gorbenko V. , Zorenko T. , Sidletskiy O. , Fedorov A. , Bilski P. , Twardak A. 
Published: October 2015

In our article, we had mentioned a wrong affiliation for the third author O. Sidletskiy.The correct affiliation is now given.
Clear‐sky stable boundary layers with low winds over snow‐covered surfaces. Part 2: Process sensitivity
Authors: Sterk H. A. M. , Steeneveld G. J. , Bosveld F. C. , Vihma T. , Anderson P. S. , Holtslag A. A. M. 
Published: October 2015

This study evaluates the relative impact of snow‐surface coupling, long‐wave radiation, and turbulent mixing on the development of the stable boundary layer over snow. Observations at three sites are compared to WRF single‐column model (SCM) simulations. All three sites have snow‐covered surfaces but are otherwise contrasting: Cabauw (Netherlands, grass), Sodankylä (Finland, needle‐leaf forest) and Halley (Antarctica, ice shelf). All cases are characterized by stable, clear‐sky, and calm conditions. Part 1 of this study determined the optimal SCM forcing strategy. In this study, the process intensities from that reference are perturbed to study their relative significance and to assess which process could be responsible for the most optimal agreement between model and observation.The analysis reveals a large variability in the modelled atmospheric state and surface parameters. Overall, the modelled gradients of temperature and moisture are underestimated but decreasing the process intensities improves this. The impact is strongest with reduced mixing, though this then causes the model to overestimate the near‐surface wind speed.To study the surface energy balance terms, we use so‐called ‘process diagrams’. The achieved variation between the sensitivity runs indicates the model sensitivity to each process. The overall sensitivity is similar for the three sites but the relative offsets in the position of the sensitivity runs with respect to the observations differ, hampering general recommendations for model improvement. Furthermore, sometimes a meaningful interpretation of observations is troublesome, which hampers the comparison with model results. Radiation is relatively more important at Cabauw and Sodankylä, whilst coupling plays a more important role at Halley.The sensitivity analysis is performed with two boundary‐layer schemes (MYJ, YSU). YSU generates larger, more accurate gradients of atmospheric temperature and humidity, while wind speeds are predicted better with MYJ. The behaviour of an increase in 2 m temperature with decreased mixing is most obvious with YSU.
Comparison of initial perturbation methods for ensemble prediction at convective scale
Authors: Raynaud Laure , Bouttier F. 
Published: October 2015

Convective‐scale ensemble prediction systems (EPSs) are often initialized with downscaled initial condition perturbations (ICPs) from a global coarser EPS. Although downscaled ICPs have been shown to have a positive impact at short ranges, they cannot represent the uncertainty at small scales. Hence, there is a spin‐up of around 9–12 h until the forecast perturbations develop realistic small‐scale structures. On the other hand, ensemble data assimilation (EDA) is a common approach to obtain initial perturbations at all scales resolved by the numerical model. However, the high computational cost of EDA systems severely limits their size and their resolution. An alternative cheaper method to derive small‐scale ICPs is considered here, based on a random sampling of the model background‐error covariances. This article provides an evaluation of random and EDA‐based IC perturbation methods against the baseline downscaling approach, in the framework of the pre‐operational convective‐scale EPS developed at Météo‐France with the AROME‐France model at a 2.5 km horizontal resolution.Small‐scale IC perturbation methods are shown to significantly improve the short‐range EPS performance for surface weather variables. For 2 m temperature and 10 m wind speed, random ICPs give as good results as the EDA, owing to the very short spin‐up of random perturbations. Precipitation forecasts are also strongly improved during the first six forecast hours, especially when initial humidity perturbations are included. The sensitivity of the EPS performance to the EDA size, horizontal resolution and representation of model errors is discussed. It is found that a large fraction of the initial uncertainty can be properly described with an EDA of reasonable size and at a slightly coarser resolution than the EPS.
Hyphenating size‐exclusion chromatography with electrospray mass spectrometry; using on‐line liquid‐liquid extraction to study the lipid composition of lipoprotein particles
Authors: Osei Michael , Griffin Julian L. , Koulman Albert 
Published: October 2015

RationaleLipoproteins belong to the most commonly measured clinical biochemical parameters. Lipidomics is an orthogonal approach and aims to profile the individual lipid molecules that jointly form the lipoprotein particles. However, in the first step of the extraction of lipid molecules from serum, an organic solvent is used leading to dissociation of the lipoproteins. Thus far it has been impossible to combine lipidomics and lipoprotein analysis in one analytical system.MethodsHuman plasma was diluted in phosphate‐buffered saline (PBS) and injected onto a Superose 6 PC 3.2 column with PBS as a mobile phase to separate lipoproteins. The eluent was led to a Syrris FLLEX module, which also received CHCl3/MeOH (3:1). The two phases were mixed and subsequently separated using a Teflon membrane in an especially designed pressurized flow chamber. The organic phase was led to a standard electrospray source of an Orbitrap mass spectrometer.ResultsSize‐exclusion chromatography (SEC) has been commonly applied to separate lipoproteins and is considered a practical alternative to ultracentrifugation. Through the on‐line liquid‐liquid extraction method it becomes possible to obtained detailed mass spectra of lipids across different lipoprotein fractions. The extracted ion chromatograms of specific lipid signals showed their distribution against the size of lipoprotein particles.ConclusionsThe application of on‐line liquid‐liquid extraction allows for the continuous electrospray‐based mass spectral analysis of SEC eluent, providing the detailed lipid composition of lipoprotein particles separated by size. This approach provides new possibilities for the study of the biochemistry of lipoproteins. © 2015 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.
Skin secretion peptides: the molecular facet of the deimatic behavior of the four‐eyed frog, Physalaemus nattereri (Anura, Leptodactylidae)
Authors: Barbosa Eder Alves , Iembo Tatiane , Martins Graciella Ribeiro , Silva Luciano Paulino , Prates Maura Vianna , Andrade Alan Carvalho , Bloch Carlos 
Published: October 2015

RationaleAmphibians can produce a large amount of bioactive peptides over the skin. In order to map the precise tissue localization of these compounds and evaluate their functions, mass spectrometry imaging (MSI) and gene expression studies were used to investigate a possible correlation between molecules involved in the antimicrobial defense mechanisms and anti‐predatory behavior by Physalaemus nattereri.MethodsTotal skin secretion of P. nattereri was analyzed by classical Protein Chemistry and proteomic techniques. Intact inguinal macroglands were dissected from the rest of the skin and both tissues were analyzed by MSI and real‐time polymerase chain reaction (RT‐PCR) experiments. Peptides were primarily identified by de novo sequencing, automatic Edman degradation and cDNA data.ResultsFifteen bradykinin (BK)‐related peptides and two antimicrobial peptides were sequenced and mapped by MSI on the inguinal macrogland and the rest of P. nattereri skin. RT‐PCR results revealed that BK‐related peptide levels of expression were about 30,000 times higher on the inguinal macroglands than on the any other region of the skin, whilst antimicrobial peptide ions appear to be evenly distributed in both investigated regions.ConclusionsThe presence of antimicrobial peptides in all investigated tissue regions is in accordance with the defensive role against microorganisms thoroughly demonstrated in the literature, whereas BK‐related molecules are largely found on the inguinal macroglands suggesting an intriguing link between their noxious activities against potential predators of P. nattereri and the frog's deimatic behavior. Copyright © 2015 John Wiley & Sons, Ltd.
Bemessung von Trägern mit Anschlüssen in Form des hängenden Profils
Authors: Liu Dasu , Lange Jörg 
Published: October 2015

AbstractDas so genannte hängende Profil ist ein in der Praxis gängiger Anschlusstyp für horizontale Verbände. Das besondere Merkmal dieses Anschlusses ist, dass der Träger nur über einen Gurt an die Knotenbleche angeschlossen wird. Bisher wurden Träger mit diesen Anschlusstypen stets vereinfacht als gabelgelagerte Einfeldträger nachgewiesen. Da die Nachgiebigkeit im Anschlussbereich dabei nicht erfasst wird, ist die Annahme der Gabellager nicht ohne weitere Untersuchungen gerechtfertigt.Basierend auf einer Reihe von Bauteilversuchen sowie der darauf folgenden umfangreichen Parameterstudie anhand nichtlinearer FE‐Rechnungen wurde ein auf dem gegenwärtigen Nachweisformat nach EC 3 aufgebautes Bemessungsmodell entwickelt, welches das Tragverhalten von Bauteilen mit Anschlüssen dieser Art sicher, genau und wirtschaftlich erfassen kann. Dieses Bemessungsmodell wurde nach Anhang D der EN 1990 gemäß dem semi‐probabilistischen Konzept kalibriert, sodass das normativ geforderte Sicherheitsniveau erfüllt wird.Analysis and design of members with hanging‐profile connections. The so called hanging‐profile is a commonly used type of joint in steel structures for horizontal bracing systems, where large compression forces are transferred. This kind of joint is characterized by the connection of a bracing beam to gusset plates only at the top flange. This type of structure is usually simplified as a single‐span beam with fork bearings. Due to the overestimation of the system stiffness in the connection areas under this assumption, basic engineering with this conventional approach has been considered generally not safe.Based on an extensive parametric study using finite‐element‐models calibrated on a serial of 1:1 scale tests, a new design approach was developed for the lateral torsional buckling check of members with this kind of connection. To meet the standards safety level, the new design formulae were further analyzed with the semi‐probabilistic method according to EN 1990 Annex D.
Vorschläge für eine anwenderfreundliche und praxistaugliche Novellierung der allgemeinen Bemessungsregeln und Regeln für den Hochbau (EN 1993 Teil 1‐1)
Authors: Egner Ralf , Heyde Stefan , Laumann Jörg , Prokop Ines 
Published: October 2015

AbstractDie Eurocodes werden bis zum Jahr 2020 im Europäischen Komitee für Normung (CEN), Technisches Komitee TC 250 überarbeitet. In Vorbereitung auf die Eurocode‐Novellierung haben engagierte Ingenieure im Rahmen der Initiative PraxisRegeln Bau (PRB) die bei der praktischen Anwendung am häufigsten genutzten Teile des Eurocodes 3 untersucht. Dazu gehört als Grundlagenteil für den Stahlbau die EN 1993‐1‐1. Mit dem Ziel, die Anwenderfreundlichkeit und Praxistauglichkeit der EN 1993‐1‐1 zu verbessern, wurden die bestehende Norm analysiert und Vorschläge für die europäische Novellierung erarbeitet. Die Analysen zeigen, dass vielfach eine Straffung der Texte ohne Inhaltsverlust möglich ist und dass durch Umstrukturierungen die Verständlichkeit und Anwenderfreundlichkeit der Bemessungsregeln und Regeln für den Hochbau bedeutend erhöht werden können.Proposals for a user‐friendly amendment suited for practice of the general rules and rules for buildings of steel structures (EN 1993 Part 1‐1). The Eurocodes will be revised in the European Committee for Standardization (CEN), Technical Committee (TC) 250, up to 2020. In preparation on the eurocode amendment engaged engineers have examined the most frequently used parts of the Eurocode 3 within the Initiative Practice‐oriented Rules in Building Construction (PRB). The EN 1993‐1‐1 belongs to the examined parts as a basis part for the steel construction. With the aim to improve the user‐friendliness and ease of use of EN 1993‐1‐1 the existing norm was analysed and proposals were compiled for the European amendment. The analyses show that lots of the texts can be shortened without loss of information. Restructuring can enhance comprehensiveness and ease of use of the general rules and rules for buildings of steel structures considerably.
Stream restoration and the surprisingly social dynamics of science
Authors: Lave Rebecca 
Published: October 2015

Stream restoration is deeply shaped by social influences. A substantial body of literature has demonstrated the ways in which social dynamics shape myriad aspects of restoration practice. After illustrating these findings via brief reviews of existing research on public participation and environmental justice, I turn to the less commonly addressed influence of social dynamics on the practice and content of river science. I first review the approach and some of the key findings of Science and Technology Studies, a body of research that takes the practice of science as its empirical object of study. I then use the Rosgen Wars, a conflict that has strongly influenced the development of stream restoration science and practice in the United States, as a case study for examining the impacts of social dynamics on the practice of river scientists, the redistribution of scientific authority, and on fluvial landscapes more broadly. Given that is impossible to avoid social influences, I argue that it is crucial that we examine them, and that we choose research and implementation practices that reflect our ecological, scientific, and political commitments rather than passively accepting the existing commitments embedded in our work. WIREs Water 2016, 3:75–81. doi: 10.1002/wat2.1115This article is categorized under:

Human Water > Value of Water
Robust spectrum sensing algorithm based on free probability theory
Authors: Wang Lei , Chen Jianxin , Jiang Guoping , Zheng Baoyu 
Published: October 2015

AbstractIn low signal‐to‐noise ratio (SNR) cases, the performance of spectrum sensing algorithms cannot meet the practical needs, which is a major problem faced by spectrum sensing technology in current cognitive radio field. Now, existing algorithms based on random matrix theory (RMT) have high sensing performance, but they require a large number of samples, which are very difficult to satisfy in practice. Free probability theory (FPT) is a main branch of RMT. It describes the asymptotic behavior of large random matrices and portrays a strong link between two matrices and their sum or product matrices. FPT can also be utilized to the digital communication system that can be modeled by random matrices and has been applied to spectrum sensing in simplified ideal channels, for example, additive white Gaussian noise channel. The most pivotal issue and difficulty of the FPT‐based methods is to set up and solve the asymptotic freeness equation corresponding to a specific communication model. In this paper, FPT‐based spectrum sensing schemes are proposed for some typical wireless communication systems, such as multiple‐input multiple‐output system, Rayleigh multipath fading system, and orthogonal frequency division multiplexing system. It is shown that the asymptotic freeness behavior of random matrices and the property of Wishart distribution can be used to assist spectrum sensing for these typical systems with low SNR and very limited samples. Simulation results demonstrate that compared with the existing RMT‐based spectrum detection methods, for example, the maximum and minimum eigenvalue detectors, the proposed FPT‐based schemes offer superior detection performance and are more robust to low SNR cases, especially for a small sample of observations. Copyright © 2015 John Wiley & Sons, Ltd.
Substituent and Temperature Effect on the Assemblies of Three Lead(II) Coordination Polymers based on Asymmetrical Biphenyl Tritopic Ligands
Authors: Li Zhi‐Sen , Li Xiu‐Yuan , Liu Jing‐Wei , He Tian , Yue Ke‐Fen 
Published: October 2015

AbstractThree Pb‐based metal‐organic frameworks, [Pb6(L1)4]·H2O (1), [Pb2(L2)2(H2O)]·H2O (2), and [Pb(L2)(H2O)]·H2O (3) were constructed based on two asymmetrical tritopic ligands, 3‐(2′,5′‐dicarboxylphenyl)benzoic acid (H3L1) and 3‐(2′,5′‐dicarboxylphenyl)pyridine acid (H2L2), under hydrothermal conditions. The substituents on the two ligands and the induced temperature had effects on the resulting structures. All of the complexes were structurally characterized by X‐ray diffraction analyses and further identified by infrared spectra, elemental analyses, powder X‐ray diffraction, and thermogravimetric analyses. Complexes 1 and 3 are 3D frameworks, which construct from 1D inorganic Pb–O–Pb rod‐shaped secondary building units (SBUs) and H3L1/H2L2 ligands as pillars. Complex 2 is a 3D framework based on discrete tetranuclear Pb4(COO)8 clusters SBUs and H2L2 ligands. The effects of both the substituent groups on the aromatic rings and the reaction temperature are discussed in details. The fluorescence properties and thermal stabilities of complexes 1–3 were also measured.
RbBrF4 Revisited
Authors: Ivlev Sergei I. , Karttunen Antti J. , Ostvald Roman , Kraus Florian 
Published: October 2015

AbstractRubidium tetrafluoridobromate(III) was synthesized and structurally characterized. The compound is isotypic to sodium and potassium tetrafluoridobromate(III), and crystallizes in the tetragonal space group I4/mcm (tI24, KBrF4 structure type) with a = 6.3718(2), c = 11.4934(3) Å, V = 466.63(2) Å3, Z = 4, at T = 293 K. Additionally we investigated the compound by means of IR and Raman spectroscopy as well as theoretical studies. The data obtained by quantum chemical calculations confirm the crystal structure, and also the atomic distances and angles with an average deviation of 2.2 to 2.7 %.