bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Basis for Sequence‐Dependent Induced DNA Bending
Authors: Rettig Michael , Germann Markus W. , Wang Shuo , Wilson W. David 
Published: January 2013

AbstractWith a growing understanding of the microstructural variations of DNA, it has become apparent that subtle conformational features are essential for specific DNA molecular recognition and function. DNA containing an A‐tract has a narrow minor groove and a globally bent conformation but the structural features of alternating AT DNA are less well understood. Several studies indicate that alternating AT sequences are polymorphic with different global and local properties from A‐tracts. The mobility of alternating AT DNA in gel electrophoresis is extensively reduced upon binding with minor‐groove binding agents such as netropsin. Although this suggests that such complexes are bent, similarly to A‐tract DNA, direct evidence and structural information on AT DNA and the induced conformational change is lacking. We have used NMR spectroscopy and residual dipolar coupling together with restrained molecular‐dynamics simulations to determine the solution structures of an alternating AT DNA segment, with and without netropsin, in order to evaluate the molecular basis of the binding‐induced effects. Complex formation causes a significant narrowing of the minor groove and a pronounced change in bending, from a slight bend towards the major groove for the free DNA to a pronounced bend towards the minor groove in the complex. This observation demonstrates that conformational features and the inherent malleability of AT sequences are essential for specific molecular recognition and function. These results take the field of DNA structures into new areas while opening up avenues to target novel DNA sequences.
Control of the Helical Chirality of Enantiopure Sulfinyl (Z)‐Azobenzene‐Based Photoswitches
Authors: Núñez Irene , Merino Estíbaliz , Lecea Mercedes , Pieraccini Silvia , Spada Gian Piero , Rosini Carlo , Mazzeo Giuseppe , Ribagorda María , Carreño M. Carmen 
Published: January 2013

AbstractA new class of enantiopure ortho,ortho‐disubstituted azobenzene photoswitches has been synthesized from (S)‐2‐(p‐tolylsulfinyl)benzoquinone and arylhydrazines. The sulfoxide acts as a unidirectional controller of the helical chirality that arises in the Z isomer after photoisomerization. Highly congested E‐azobenzenes 5 c showed two atropisomeric diastereoconformers in the solid state that converged upon irradiation into a unique Z isomer with defined helicity (M), as evident in the X‐ray structure. The chiroptical properties of this three‐state enantiopure switch can be externally tuned both photochemically and/or thermally. Theoretical CD spectra calculated by using time‐dependent DFT methods support the existence of two atropoisomeric E isomers and only one Z isomer with (M) helicity. Complementary to the classical azobenzene‐based switches, the photoswiching event is promoted under green/blue light and do not occur under UV irradiation.
Efficient Stacking on Protein Amide Fragments
Authors: Harder Michael , Kuhn Bernd , Diederich François 
Published: January 2013

AbstractThe less polar π‐surface of protein amide groups is exposed in many receptor binding sites, either as part of the backbone or in Gln/Asn side chains. Using quantum chemical calculations and Protein Data Bank (PDB) searches on model systems, we investigate the energetics and geometric preferences for the stacking on amide groups of a large number of heteroarenes that are relevant to medicinal chemistry. From this study, we discern that the stacking energy of an aromatic ligand substituent can be improved by: 1) orienting the fragment dipole vector such that it is aligned in an antiparallel fashion with the dipole of the interacting protein amide group, 2) increasing its dipole moment, and 3) decreasing its π‐electron density. These guidelines should be helpful to more rationally exploit this interaction type in future structure‐based drug design.
Three‐Component (Domino) Reaction Affording Substituted Pyrroloquinazolines: Cyclization Regioselectivity and Stereoselectivity
Authors: Paleta Oldřich , Dolenský Bohumil , Paleček Jiří , Kvíčala Jaroslav 
Published: January 2013

AbstractThe cyclization involving 2‐(aminomethyl)aniline, methyl 3,3,3‐trifluoropyruvate, and various oxo compound afforded linearly annulated pyrroloquinazolines, for example, (2R*,3aS*)‐2‐hydroxy‐3a‐phenyl‐2‐trifluoromethyl‐3,3a,4,9‐tetrahydropyrrolo[2,1‐b]quinazolin‐1(2H)‐one (cis‐8), as the major product, possessing the skeleton of the alkaloids of the vasicine group, along with angularly annulated products, for example, (2S*,3aR*)‐2‐hydroxy‐3a‐phenyl‐2‐trifluoromethyl‐3,3a,4,5‐tetrahydropyrrolo[1,2‐a]quinazolin‐1(2H)‐one(cis‐18). The effects of the nature of the oxo compound and the temperature on the ratio of the linear and angular cyclization products, as well as the diastereoselectivity of the product formation, were studied, with an increase in temperature leading to improved selectivity. Some of the linear pyrroloquinazolines were stereoselectively didehydrogenated at the quinazoline ring by the trifluoropyruvate.
The performance of grass filter strips in controlling high‐concentration suspended sediment from overland flow under rainfall/non‐rainfall conditions
Authors: Ma Lan , Pan Chengzhong , Teng Yanguo , Shangguan Zhouping 
Published: January 2013

ABSTRACTThere is little information on the performance of vegetative filter strips (VFS) in filtering high‐concentration sediment from subcritical overland flow. Flume experiments on simulated grass strips were conducted using combinations of three slope gradients (3°, 9° and 15°), five 1‐m‐wide slope positions (from upslope to downslope), two flow rates (60 and 20 L min‐1 m‐1) and sediment concentrations of 100–300 kg m‐3 under simulated rainfall and non‐rainfall conditions. The results showed that sediment deposition efficiency increased with VFS width as a power function. Rainfall significantly reduced sediment deposited within VFS. Higher sediment concentration corresponded to a larger sediment deposition load but reduced deposition efficiency. Flow rate had a negative effect on deposition efficiency but no effect on deposition load. Sediments were more easily deposited at the upper slope position than downslope, and the upper slope position had a higher percentage of coarse sediments. The deposited sediment had significantly greater median diameters (D50) than the inflow sediment. A greater proportion of coarse sediments larger than 25 µm in diameter were deposited, and particles smaller than 1 µm and of 10–25 µm had a better deposition performance than particles of 1–10 µm. Rainfall reduced the deposited sediment D50 at a slope gradient of 3° and had no significant influence on it at 9° or 15°. A higher sediment concentration led to a smaller D50 of the deposited sediment. Rainfall had no significant effect on overland flow velocity. Both the deposited sediment load and D50 decreased with increasing flow velocity, and flow velocity was the most sensitive factor impacting sediment deposition. The results from this study should be useful to control sediment flowing into rivers in areas with serious soil erosion. Copyright © 2013 John Wiley & Sons, Ltd.
Fire characteristics of steel members coated with nano‐enhanced polymers
Authors: Butler Kathryn M. , Cheng Alexander H.‐D. , Mullen Christopher , Al‐Ostaz Ahmed 
Published: January 2013

ABSTRACTPolymeric coatings applied to masonry infill walls have been demonstrated to provide protection against blast. Steel frames may be embedded in these walls to improve the structural characteristics of the building. During the process of retrofitting the walls with blast protection polymeric coatings, the steel frame may be fully or partially coated with these materials to provide adequate anchorage of the retrofit system to the frame and to avoid global failure of walls subjected to blast loading. The development of a blast‐resistant coating for masonry walls that safeguards all structural elements in a fire would provide buildings with protection against explosions and a fire following the blast, as well as against ordinary building fires. This paper uses a numerical tool based on the particle finite element method to evaluate the melting and dripping of nano‐enhanced polymeric coatings applied on steel members embedded within masonry walls. Viscosity measurements were performed to obtain needed parameters for the simulations. Polyurea nanocomposite residues showed a minimum in viscosity with temperature, possibly caused by cross‐linking and charring. Model results for the polyurea residue with the lowest value of minimum viscosity showed that the coating remained attached, although there was some flow that caused a chunk of material to break off from an overhang. Copyright © 2013 John Wiley & Sons, Ltd.
Implementation and analysis of a partial‐element wetting and drying framework for generalized wave continuity equation‐based hydrodynamic models
Authors: Dick C. G. , Tromble E. M. , Dresback K. M. , Kolar R. L. 
Published: January 2013

SUMMARYThe ADCIRC hydrodynamic model has been used extensively to predict the effects of storm surge in coastal regions. In an effort to create a more holistic representation of coastal inundation (i.e., the total water level), some recent applications of ADCIRC have focused on modeling coastal river systems. Initial attempts to model river systems with ADCIRC have encountered complications associated with mass balance (artificial increase in mass in the downstream direction) and model instabilities when flow leaves the main channel, which suggests that complications may be attributed to the current treatment of the wet/dry boundary in CG ADCIRC. A new wetting/drying framework has been developed for, and implemented in, the 1D continuous Galerkin ADCIRC code, which is based on the generalized wave continuity equation (GWCE) formulation of the shallow water equations. The new algorithm allows for the inclusion of partially wet elements within the computational domain of ADCIRC, and the focus of this manuscript is flooding‐type wetting/drying processes (e.g., tidal fluctuations and storm surge inundation). The new framework uses a scaling factor, η, placed on the time derivative term in the primitive continuity equation, prior to formulation of the GWCE. Benefits of the new approach include better mass balance and more accurate tracking of the location of the wet/dry interface, compared with the current wetting and drying algorithm.Copyright © 2013 John Wiley & Sons, Ltd.
Evaluating the SWAT's snow hydrology over a Northern Quebec watershed
Authors: Troin Magali , Caya Daniel 
Published: January 2013

AbstractThe snow treatment becomes an important component of Soil and Water Assessment Tool (SWAT)’s hydrology when spring flows are dominated by snow melting. However, little is known about SWAT's snow hydrology performance because most studies using SWAT were conducted in rainfall‐driven catchments. To fill this gap, the present study aims to evaluate the ability of SWAT in simulating snow‐melting‐dominated streamflow in the Outardes Basin in Northern Quebec. SWAT performance in simulating snowmelt is evaluated against observed streamflow data and compared to simulations from the operationally used Streamflow Synthesis and Reservoir Regulation (SSARR) model over that catchment. The SWAT 5‐year calibration showed a satisfactory performance at the daily and seasonal time scales with low volume biases. The SWAT validation was conducted over two (17‐year and 15‐year) periods. Performances were similar to the calibration period in simulating the daily and seasonal streamflows again with low model biases. The spring‐snowmelt‐generated peak flow was accurately simulated by SWAT both in magnitude and timing. When SWAT's results are compared to SSARR, similar performances in simulating the daily discharges were observed. SSARR simulates more accurately streamflow generated at the snowmelt onset whereas SWAT better predicts streamflow in summer, fall and winter. SWAT provided reasonable streamflow simulations for our snow‐covered catchment, but refinement of the process‐driven baseflow during the snowmelt onset could improve spring performances. Therefore, SWAT becomes an attractive tool for evaluating water resources management in Nordic environments when a distributed model is preferred or when water quality information (e.g. temperature) is required. Copyright © 2013 John Wiley & Sons, Ltd.
Maternal Role Confusion: Relations to Maternal Attachment and Mother–Child Interaction from Infancy to Adolescence
Authors: Vulliez‐Coady Lauriane , Obsuth Ingrid , Torreiro‐Casal Monica , Ellertsdottir Lydia , Lyons‐Ruth Karlen 
Published: January 2013

AbstractSelf‐reports of role confusion with the parent in childhood are associated with a variety of adverse outcomes. However, role‐confusion has been studied primarily from the point of view of the child. The current study evaluated an instrument for assessing role confusion from maternal interviews rather than from child observations or self‐reports in adulthood. Fifty‐one mothers participating in a longitudinal study since their own child's infancy were administered the Experiences of Caregiving Interview (C. George & J. Solomon, 1996) when the child was age 20. Interviews were coded using the newly developed Parental Assessment of Role Confusion (PARC; L. Vulliez‐Coady & K. Lyons‐Ruth, 2009). Maternal PARC scores were related to observational measures of role‐confusion in interaction with the child both in infancy and late adolescence. PARC scores also were related to mothers’ hostile‐helpless states of mind on the Adult Attachment Interview (C. George, N. Kaplan, & M. Main, 1984, 1985, 1986) and to the extent of Unresolved loss, but not Unresolved Trauma. PARC scores also were related to mothers’ self‐reports of helplessness experienced in the parenting role. Discriminant validity of the PARC was demonstrated in that role confusion on the PARC was not related to hostile or disoriented forms of parent–child interaction. Implications for clinical assessment of role confusion are discussed.
Identification of a Novel Metalloproteinase and Its Role in Juvenile Development of the Tobacco Hornworm, Manduca sexta (Linnaeus)
Authors: Vishnuvardhan Smitha , Ahsan Rubina , Jackson Kathryn , Iwanicki Rebecca , Boe Jordan , Haring Jodie , Greenlee Kendra J. 
Published: January 2013

AbstractMatrix metalloproteinases (MMPs) are a class of zinc‐dependent endopeptidases that are highly conserved across numerous taxa, from bacteria to humans. Recently, MMPs have been identified in several insect species and are hypothesized to function in immunity and development. In this study, we identify a putative MMP and correlate its proteolytic activity and gene and protein expression in the tracheae with developmental stage. Ms‐MMP gene expression increases 10‐fold during molting, which is accompanied by an increase in both protein expression and gelatinolytic activity. To directly test the hypothesis that Ms‐MMP plays a critical role in juvenile development of Manduca sexta, we injected a broad‐spectrum MMP inhibitor and recorded its effects on growth and development. Inhibition of MMPs caused a delay in juvenile development and decreased growth rates. Understanding the function of MMPs will help us better understand molting and control of body size in insects. Furthermore, elucidating functions for MMPs in lower taxa may yield critical information about the evolution of the numerous MMPs found in vertebrates. J. Exp. Zool. (Mol. Dev. Evol.) 320B:105–117, 2013. © 2013 Wiley Periodicals, Inc.
Quadratic Upper Bounds on the Erdős–Pósa Property for a Generalization of Packing and Covering Cycles
Authors: Fomin Fedor V. , Lokshtanov Daniel , Misra Neeldhara , Philip Geevarghese , Saurabh Saket 
Published: January 2013

AbstractAccording to the classical Erdős–Pósa theorem, given a positive integer k, every graph G either contains k vertex disjoint cycles or a set of at most vertices that hits all its cycles. Robertson and Seymour (J Comb Theory Ser B 41 (1986), 92–114) generalized this result in the best possible way. More specifically, they showed that if is the class of all graphs that can be contracted to a fixed planar graph H, then every graph G either contains a set of k vertex‐disjoint subgraphs of G, such that each of these subgraphs is isomorphic to some graph in or there exists a set S of at most vertices such that contains no subgraph isomorphic to any graph in . However, the function f is exponential. In this note, we prove that this function becomes quadratic when consists all graphs that can be contracted to a fixed planar graph . For a fixed c, is the graph with two vertices and parallel edges. Observe that for this corresponds to the classical Erdős–Pósa theorem.
American and Chinese Similarities and Differences in Defining and Valuing Creative Products
Authors: Lan Lan , Kaufman James C. 
Published: January 2013

AbstractThis review of the literature explores how Americans and Chinese view creativity and what they expect from creative products. American and Chinese explicit beliefs about creativity (i.e., expert opinions) share many similarities. Implicit beliefs, however, show more divergence: Americans tend to value novelty and more “groundbreaking” types of creativity, whereas Chinese tend to appreciate creativity within constraints, such as reworking a traditional concept. The context of how people respond to creativity obviously varies by culture, although there are also some communal and universal creative ideals.
Selection and characterization of wheat genotypes for saline soils prone to water‐logging
Authors: Saqib Muhammad , Akhtar Javaid , Qureshi Riaz Hussain , Nasim Muhammad 
Published: January 2013

AbstractWheat (Tritcum aestivum L.) genotypes were screened and characterized for performance under salt stress and/or water‐logging. In a solution‐culture study, ten wheat genotypes were tested under control, 200 mM–NaCl salt stress and 4‐week water‐logging (nonaerated solution stagnated with 0.1% agar), alone or in combination. Shoot and root growth of the wheat genotypes was reduced by salinity and salinity × water‐logging, which was associated with increased leaf Na+ and Cl– concentrations as well as decreased leaf K+ concentration and K+ : Na+ ratio. The genotypes differed significantly for their growth and leaf ionic composition. The genotypes Aqaab and MH‐97 were selected as salinity×water‐logging‐resistant and sensitive wheat genotypes, respectively, on the basis of their shoot fresh weights in the salinity × water‐logging treatment relative to control. In a soil experiment, the effect of water‐logging was tested for these two genotypes under nonsaline (EC = 2.6 dS m–1) and saline (EC = 15 dS m–1) soil conditions. The water‐logging was imposed for a period of 21 d at various growth stages, i.e., tillering, stem elongation, booting, and grain filling alone or in combinations. The maximum reduction in grain yield was observed after water‐logging at stem‐elongation + grain‐filling stages followed by water‐logging at grain‐filling stage, booting stage, and stem‐elongation stage, respectively. Salinity intensified the effect of water‐logging at all the growth stages. It is concluded that the existing genetic variation in wheat for salinity × water‐logging resistance can be successfully explored using relative shoot fresh weight as a selection criterion in nonaerated 0.1% agar–containing nutrient solution and that irrigation in the field should be scheduled to avoid temporary water‐logging at the sensitive stages of wheat growth.
Recent advances in monoclinic crystal optics
Authors: Petit Yannick , Joly Simon , Segonds Patricia , Boulanger Benoît 
Published: January 2013

AbstractThis article is mainly devoted to the modeling and measurement of the absorption and fluorescence angular distributions in polarized light of monoclinic crystals. Up to now theoretical crystal optics were mostly devoted to crystals having a high crystallographic symmetry. In these crystals belonging to the cubic, hexagonal, tetragonal, trigonal or orthorhombic lattice classes, the tensor properties related to the real part of the dielectric permittivity and to its imaginary part can be described in the same frame which orientation does not vary as a function of wavelength. The situation is much more complicated in the case of monoclinic crystals because it is necessary to define a specific frame for each property and each wavelength that are considered. The main features of monoclinic crystal optics are described in detail, followed by a review of monoclinic materials and the consequence of these features on their related optical properties.
An ultra‐compact multimode interference coupler with a subwavelength grating slot
Authors: Ortega‐Moñux Alejandro , Alonso‐Ramos Carlos , Maese‐Novo Alejandro , Halir Robert , Zavargo‐Peche Luis , Pérez‐Galacho Diego , Molina‐Fernández Iñigo , Wangüemert‐Pérez J. Gonzalo , Cheben Pavel , Schmid Jens H. , Lapointe Jean , Xu Danxia , Janz Siegfried 
Published: January 2013

AbstractMultimode interference couplers (MMIs) are fundamental building blocks in photonic integrated circuits. Here it is experimentally demonstrated, for the first time, a two‐fold length reduction in an MMI coupler without any penalty on device performance. The design is based on a slotted 2 × 2 MMI fabricated on a commercial silicon‐on‐insulator (SOI) substrate. The slot is implemented with a subwavelength grating (SWG) comprising holes fully etched down to the oxide cladding, thereby allowing single etch step fabrication. The device has been designed using an in‐house tool based on the Fourier Eigenmode Expansion Method. It has a footprint of only 3.5 μm x 23 μm and it exhibits a measured extinction ratio better than 15 dB within the full C‐band (1530 nm‒1570 nm). SWG engineered slots thus offer excellent perspectives for the practical realization of MMIs couplers with substantially reduced footprint yet with outstanding performance.
Biodegradable Microparticles with Surface Dimples as a Bi‐Modal Imaging Contrast Agent
Authors: Kim Mi Ri , Lim Yong Taik , Cho Kuk Young 
Published: January 2013

AbstractFabrication of physically engineered colloids and their application to the biological fields is emerging importance because of their potential to provide an enhanced performance without altering the chemical properties of biomaterials used. A facile approach is reported to fabricate sub‐10‐μm‐sized PLGA microparticle with small dimples covering the surface by droplet imprinting. Optical and magnetic resonance bioimaging agents are easily co‐encapsulated inside the microparticles to obtain a bi‐modal imaging agent. Cell internalization efficacy of dimpled particles in DC 2.4 cell is enhanced compared with conventional smooth round‐shaped colloids. Our result indicates that morphology‐controlled microparticles show promise as a cell labeling with improved cell interaction.
The interaction of epoxy adhesives with steel surfaces
Authors: Munkert H. , Voigts F. , Wegewitz L. , Palkowski H. , Maus‐Friedrichs W. 
Published: January 2013

AbstractDeformable sandwich sheet materials have the advantage to be produced as raw materials and to be formed afterwards to even complex geometries. Moreover they are cost effective and predestinated for mass production. For such systems the necessity is given for a good bonding to guarantee a good shear transfer between the single layers. Because of deformation, failures by delamination often occur at the interface between the metal and the epoxy layer. Therefore investigations at this interface were performed using Atomic Force Microscopy (AFM) and X‐ray Photoelectron Spectroscopy (XPS), to understand the basic effect of the surfaces’ bonding behavior in selected preparation steps of the system. Basic information about the adhesion mechanisms between the stainless steel 316L and the epoxy is given. The chemical interaction between the epoxy and the steel results in a significant reduction of Fe3+ to Fe2+.