bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes
Authors: Knight Jennifer L. , Yesselman Joseph D. , Brooks Charles L. 
Published: January 2013

AbstractMultipurpose atom‐typer for CHARMM (MATCH), an atom‐typing toolset for molecular mechanics force fields, was recently developed in our laboratory. Here, we assess the ability of MATCH‐generated parameters and partial atomic charges to reproduce experimental absolute hydration free energies for a series of 457 small neutral molecules in GBMV2, Generalized Born with a smooth SWitching (GBSW), and fast analytical continuum treatment of solvation (FACTS) implicit solvent models. The quality of hydration free energies associated with small molecule parameters obtained from ParamChem, SwissParam, and Antechamber are compared. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, these automated parameterization schemes with GBMV2 and GBSW demonstrate reasonable agreement with experimental hydration free energies (average unsigned errors of 0.9–1.5 kcal/mol and R2 of 0.63–0.87). GBMV2 and GBSW consistently provide slightly more accurate estimates than FACTS, whereas Antechamber parameters yield marginally more accurate estimates than the current generation of MATCH, ParamChem, and SwissParam parameterization strategies. Modeling with MATCH libraries that are derived from different CHARMM topology and parameter files highlights the importance of having sufficient coverage of chemical space within the underlying databases of these automated schemes and the benefit of targeting specific functional groups for parameterization efforts to maximize both the breadth and the depth of the parameterized space. © 2013 Wiley Periodicals, Inc.
A simple “hands‐off” apparatus to inflate concealed soft parts of the genitalia of small insect specimens
Authors: Hünefeld Frank , Brehm Gunnar , Pohl Hans 
Published: January 2013

ABSTRACTWe describe a simple, effective and relatively cheap instrument for the inflation of soft parts of insect genitalia, particularly the vesica (endophallus) of small male lepidopteran specimens. It can also be applied in female genitalia and for the hyperextension of postabdominal segments of the telescoping type. A fine glass capillary is mounted on a self‐constructed micromanipulator system with capillary holder, moveably placed aside a microscope. The micromanipulator is constructed from the x‐ and y‐pinions of a discarded microscope table and the z‐pinion of a discarded microscope. Preparation is carried out as usual on a microscopic slide. The inflatable soft parts are pushed out mechanically and then fully inflated and subsequently hardened by pumping absolute alcohol with a medical syringe via a flexible PVC tube, the capillary holder and the glass capillary into the phallus. With affordable effort, our “hands‐off”apparatus might considerably ease preparation. Microsc. Res. Tech. 76:258–262, 2013. © 2013 Wiley Periodicals, Inc.
A practical implementation of multifrequency widefield frequency‐domain fluorescence lifetime imaging microscopy
Authors: Chen Hongtao , Gratton Enrico 
Published: January 2013

ABSTRACTWidefield frequency‐domain fluorescence lifetime imaging microscopy (FD‐FLIM) is a fast and accurate method to measure the fluorescence lifetime, especially in kinetic studies in biomedical researches. However, the small range of modulation frequencies available in commercial instruments makes this technique limited in its applications. Herein, we describe a practical implementation of multifrequency widefield FD‐FLIM using a pulsed supercontinuum laser and a direct digital synthesizer. In this instrument we use a pulse to modulate the image intensifier rather than the more conventional sine‐wave modulation. This allows parallel multifrequency FLIM measurement using the Fast Fourier Transform and the cross‐correlation technique, which permits precise and simultaneous isolation of individual frequencies. In addition, the pulse modulation at the cathode of image intensifier restores the loss of optical resolution caused by the defocusing effect when the cathode is sinusoidally modulated. Furthermore, in our implementation of this technique, data can be graphically analyzed by the phasor method while data are acquired, which allows easy fit‐free lifetime analysis of FLIM images. Here, our measurements of standard fluorescent samples and a Föster resonance energy transfer pair demonstrate that the widefield multifrequency FLIM system is a valuable and simple tool in fluorescence imaging studies. Microsc. Res. Tech. 76:282–289, 2013. © 2013 Wiley Periodicals, Inc.
Application of microscopy for discrimination of eight Swertia species utilized in the traditional Chinese medicine “Qingyedan”
Authors: Li Yao‐Li , Shang Ming‐Ying , Chen Ji‐Jun , Cai Shao‐Qing 
Published: January 2013

ABSTRACTMany Swertia species are utilized as a traditional medicine under the name “Qingyedan” in China, but are easily confused with one another. To distinguish eight Swertia species (S. mileensis, S. cincta, S. patens, S. punicea, S. delavayi, S. nervosa, S. macrosperma, and S. yunnanensis) and to ensure their safety and efficacy, the microscopic and macroscopic characteristics of the roots, stems, leaves, and flowers of them were examined. The results showed that microscopic and macroscopic features helpful for authentication of the eight species were the sinuosity of the anticlinal walls of epidermal cells and presence or absence of hairs on the leaf lamina; presence or absence of V‐shaped fibers and fibers with sinuous abaxial wall in the sepals; shape of epidermal cells and pattern of papillae on hairs on the margin of corolla nectary; distribution of stomata in leaf and sepal epidermises, stone cells in cortex and phloem of roots and in cortex and pith of stems, crystals in parenchymatous cells of mesophyll and stem, stomata size, stem diameter, and 4‐ or 5‐merous flowers, and so on. Two keys to the eight Swertia species based on macroscopic and microscopic characteristics are presented. The study indicates that microscopy and related techniques are convenient, practicable, and can be unambiguously applied for authentication of Swertia species. Microsc. Res. Tech. 76:296–310, 2013. © 2013 Wiley Periodicals, Inc.
Hot and steady: Elevated temperatures do not enhance muscle disuse atrophy during prolonged aestivation in the ectotherm Cyclorana alboguttata
Authors: Young K.M. , Cramp R.L. , Franklin C.E. 
Published: January 2013

AbstractCover illustration. The cover image shows a Australian Green‐striped burrowing frog, Cyclorana albogutatta, emerging from its burrow after aestivation. In this issue of the Journal of Morphology, Young et al. study the effect of temperature on the extent of muscle disuse atrophy in the gastrocnemius and iliofibularis muscles during aestivation in the burrowing frog C. alboguttata. (pp. 165‐174). They show that despite being inactive and immobile for many months during aestivation this frogs protects it skeletal muscles from extensive disuse atrophy even at elevated temperatures. Photo: Karen Young.
Re‐analysis of key evidence in the case for a hemispherically synchronous response to the Younger Dryas climatic event
Authors: Green Helen , Woodhead Jon , Hellstrom John , Pickering Robyn , Drysdale Russell 
Published: January 2013

AbstractA south‐east Australian speleothem stable isotope record displaying an apparent cooling synchronous with the northern hemisphere Younger Dryas climate event (12.9–11.7 ka) has significantly influenced scientific thinking on the climatic response of the southern hemisphere following the Last Glacial Maximum. This is one of very few records displaying such a response, and yet the cooling was inferred from substantial extrapolation between just three uranium‐series ages. Technological advances since then have produced major improvements in both the spatial resolution and the accuracy of uranium‐series geochronologies. Re‐analysis of this sample has yielded ages of 7.96 ± 0.36 to 7.69 ± 0.33 ka for the interval previously inferred to span the Younger Dryas, and reveals a substantial hiatus in deposition from 6.93 ± 0.64 to 1.83 ± 0.16 ka. These data not only refute the original evidence for an inter‐hemispheric synchroneity of the Younger Dryas but also reject any evidence for neoglacial conditions at 3 ka. Copyright © 2013 John Wiley & Sons, Ltd.
Surface initiated polymerization of a cationic monomer on inner surfaces of silica capillaries: Analyte separation by capillary electrophoresis versus polyelectrolyte behavior
Authors: Witos Joanna , Karesoja Mikko , Karjalainen Erno , Tenhu Heikki , Riekkola Marja‐Liisa 
Published: January 2013

[2‐(Methacryloyl)oxyethyl]trimethylammonium chloride was successfully polymerized by surface‐initiated atom transfer radical polymerization method on the inner surface of fused‐silica capillaries resulting in a covalently bound poly([2‐(methacryloyl)oxyethyl]trimethylammonium chloride) coating. The coated capillaries provided in capillary electrophoresis an excellent run‐to‐run repeatability, capillary‐to‐capillary and day‐to‐day reproducibility. The capillaries worked reliably over 1 month with EOF repeatability below 0.5%. The positively charged coated capillaries were successfully applied to the capillary electrophoretic separation of three standard proteins and five β‐blockers with the separation efficiencies ranging from 132 000 to 303 000 plates/m, and from 82 000 to 189 000 plates/m, respectively. In addition, challenging high‐ and low‐density lipoprotein particles could be separated. The hydrodynamic sizes of free polymer chains in buffers used in the capillary electrophoretic experiments were measured for the characterization of the coatings.
Addressing the Measurement of Tourism in Terms of Poverty Reduction: Tourism Value Chain Analysis in Lao PDR and Mali
Authors: Thomas Frederic 
Published: January 2013

ABSTRACTAlthough tourism obviously contributes to the economic growth of developing countries, the idea that it can be an efficient tool to alleviate poverty does not always receive unanimous support. The absence of a consensual methodology to measure the employee pro‐poor income impact of tourism has had a negative impact on two major levels: on research, to begin with, and on the acknowledgement of tourism as a tool to alleviate poverty. This paper discusses two recent tourism value chains, which allow the use and then the comparison of different poverty measures and then show that tourism impact strongly depends on the chosen poverty threshold. Copyright © 2013 John Wiley & Sons, Ltd.
Efficiency droop in light‐emitting diodes: Challenges and countermeasures
Authors: Cho Jaehee , Schubert E. Fred , Kim Jong Kyu 
Published: January 2013

AbstractEfficiency droop, i.e. the loss of efficiency at high operating current, afflicts nitride‐based light‐emitting diodes (LEDs). The droop phenomenon is currently the subject of intense research, as it retards the advancement of solid‐state lighting which is just starting to supplant fluorescent as well as incandescent lighting. Although the technical community does not yet have consented to a single cause of droop, this article provides a summary of the present state of droop research, reviews currently discussed droop mechanisms, and presents a recently developed theoretical model for the efficiency droop. In the theoretical model, carrier leakage out of the active region caused by the asymmetry of the pn junction, specifically the disparity between electron and hole concentrations and mobilities, is discussed in detail. The model is in agreement with the droop's key behaviors not only for GaInN LEDs but also for AlGaInP LEDs.
Advanced optical trapping by complex beam shaping
Authors: Woerdemann Mike , Alpmann Christina , Esseling Michael , Denz Cornelia 
Published: January 2013

AbstractOptical tweezers, a simple and robust implementation of optical micromanipulation technologies, have become a standard tool in biological, medical and physics research laboratories. Recently, with the utilization of holographic beam shaping techniques, more sophisticated trapping configurations have been realized to overcome current challenges in applications. Holographically generated higher‐order light modes, for example, can induce highly structured and ordered three‐dimensional optical potential landscapes with promising applications in optically guided assembly, transfer of orbital angular momentum, or acceleration of particles along defined trajectories. The non‐diffracting property of particular light modes enables the optical manipulation in multiple planes or the creation of axially extended particle structures. Alongside with these concepts which rely on direct interaction of the light field with particles, two promising adjacent approaches tackle fundamental limitations by utilizing non‐optical forces which are, however, induced by optical light fields. Optoelectronic tweezers take advantage of dielectrophoretic forces for adaptive and flexible, massively parallel trapping. Photophoretic trapping makes use of thermal forces and by this means is perfectly suited for trapping absorbing particles. Hence the possibility to tailor light fields holographically, combined with the complementary dielectrophoretic and photophoretic trapping provides a holistic approach to the majority of optical micromanipulation scenarios.
Graphene supports the propagation of subwavelength optical solitons
Authors: Nesterov Maxim L. , Bravo‐Abad Jorge , Nikitin Alexey Yu. , García‐Vidal Francisco J. , Martin‐Moreno Luis 
Published: January 2013

AbstractNonlinear propagation of light in a graphene monolayer is studied theoretically. It is shown how the large intrinsic nonlinearity of graphene at optical frequencies enables the formation of quasi one‐dimensional self‐guided beams (spatial solitons) featuring subwavelength widths at moderate electric‐field peak intensities. A novel class of nonlinear self‐confined modes resulting from the hybridization of surface plasmon polaritons with graphene optical solitons is also demonstrated.
Phase‐controlled directional switching of surface plasmon polaritons via beam interference
Authors: Lee Seung‐Yeol , Lee Wooyoung , Lee Yohan , Won Jun‐Yeon , Kim Joonsoo , Lee Il‐Min , Lee Byoungho 
Published: January 2013

AbstractA novel method for switching the direction of surface plasmon polarition (SPP) launching is proposed. The principle behind the switching mechanism is based on the relative phase difference between the reference beam and the control beam. Selective guidance of the direction of SPP can be explained by the composition of the charge parity that is induced near the slit edge, which is caused by interference created by two incident beams. The switching of SPP launching direction could be implemented by simple phase modulation of the control beam when the slit parameters satisfy the specific conditions at the designed specific wavelength. An experimental demonstration, in good agreement with numerical results, shows that our configuration of SPP switching can be operated by a quite simple interaction.
A note on quarkonial systems and multilevel partition of unity methods
Authors: Dahlke Stephan , Oswald Peter , Raasch Thorsten 
Published: January 2013

AbstractWe discuss the connection between the theory of quarkonial decompositions for function spaces developed by Hans Triebel, and the multilevel partition of unity method. The central result is an alternative approach to the stability of quarkonial decompositions in Besov spaces\documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}$B_{pp}^s({\mathbb {R}}^n)$\end{document},s>n(1/p− 1)+, which leads to relaxed decay assumptions on the elements of a quarkonial system as the monomial degree grows.
Affiliated subspaces and infiniteness of von Neumann algebras
Authors: Hamhalter Jan , Turilova Ekaterina 
Published: January 2013

AbstractWe show that the structural properties of von Neumann algebra s are connected with the metric and order theoretic properties of various classes of affiliated subspaces. Among others we show that properly infinite von Neumann algebra s always admit an affiliated subspace for which (1) closed and orthogonally closed affiliated subspaces are different; (2) splitting and quasi‐splitting affiliated subspaces do not coincide. We provide an involved construction showing that concepts of splitting and quasi‐splitting subspaces are non‐equivalent in any GNS representation space arising from a faithful normal state on a Type I factor. We are putting together the theory of quasi‐splitting subspaces developed for inner product spaces on one side and the modular theory of von Neumann algebra s on the other side.
Garcinol sensitizes human pancreatic adenocarcinoma cells to gemcitabine in association with microRNA signatures
Authors: Parasramka Mansi A. , Ali Shadan , Banerjee Sanjeev , Deryavoush Tara , Sarkar Fazlul H , Gupta SmitiV. 
Published: January 2013

BackgroundAlterations in microRNA (miRNA/miR) genes are of biological importance in the pathophysiology of cancers, including pancreatic cancer (PaCa). Although growing evidence supports the role of miRNA in cancer, their response to dietary phytochemicals is less known. Previously, we showed that garcinol induces PaCa cell growth arrest and apoptosis in vitro. The present study, discusses chemo‐sensitization by garcinol in synergism with first‐line PaCa drug, gemcitabine. The miRNA expression profile of gemcitabine‐resistant Panc‐1 cells treated with garcinol and/or gemcitabine was also evaluated.Methods and resultsGarcinol synergizes with gemcitabine to inhibit cell proliferation and induce apoptosis in PaCa cells with significant modulation of key cancer regulators including PARP, VEGF, MMPs, ILs, caspases, and NF‐κB. In addition, biostatistical analyses, quantitative reverse transcription PCR data, and in silico modeling using TargetScan5, PicTar, and DNA intelligent analysis, microT‐V.B4 database showed that these two agents modulated a number of microRNAs (miR‐21, miR‐196a, miR‐495, miR‐605, miR‐638, and miR‐453) linked to various canonical oncogenic signaling pathways.ConclusionWe identified garcinol‐specific miRNA biomarkers that sensitize PaCa cells to gemcitabine treatment, thus attenuating the drug‐resistance phenotype. These results prompt further interest in garcinol and gemcitabine combination strategy as a drug modality to improve treatment outcome in patients diagnosed with PaCa.
Gel Formation in Aqueous Suspension Nitroxide‐Mediated Radical Co‐Polymerization of Styrene/Divinylbenzene
Authors: Gonçalves Miguel A. D. , Pinto Virgínia D. , Dias Rolando C. S. , Costa Mário Rui P. F. N. , Aguiar Leandro G. , Giudici Reinaldo 
Published: January 2013

AbstractResults from an experimental study concerning gel formation with nitroxide‐mediated radical polymerization (NMRP) of styrene (S) and divinylbenzene (DVB) in aqueous suspension are reported. Influence of certain polymerization parameters on the dynamics of network formation was measured, namely the polymerization temperature and initial composition. Soluble polymer formed at different polymerization times was analyzed by size exclusion chromatography (SEC) with refractive index (RI) and multi angle laser light scattering (MALLS) detection. Concentration of pendant double bonds (PDB) was quantified by means of ICl titration and the morphology of the S/DVB particles was inspected by SEM. Incidence of cyclizations was assessed and the improvement of network homogeneity when using NMRP/FRP is discussed. magnified image
Kinetic Investigation of Poly(ethylene glycol) Hydrogel Formation via Perfusion‐Based Frontal Photopolymerization: Influence of Free‐Radical Polymerization Conditions on Frontal Velocity and Swelling Gradients
Authors: Turturro Michael V. , Rendón Daniela María Vélez , Teymour Fouad , Papavasiliou Georgia 
Published: January 2013

AbstractPoly(ethylene glycol) diacrylate (PEGDA) hydrogels are extensively used as scaffolds in tissue engineering. The ability to spatially control hydrogel properties is critical for designing scaffolds that direct cell behavior and tissue regeneration. To this end, we have recently developed a polymerization technique, perfusion‐based frontal photopolymerization, to generate tunable gradients in PEG hydrogels. This study explores the effects of polymerization conditions on the velocity of the propagating front and its influence on gradients in hydrogel swelling. Alterations in photoinitiator perfusion rate result in the largest variations in frontal velocity and in the magnitude of the swelling gradient among all polymerization conditions investigated. magnified image
Generalized poroelastic wellbore problem
Authors: Mehrabian Amin , Abousleiman Younane N. 
Published: January 2013

SUMMARYThis paper presents a novel analytical solution to the transient, z‐dependent, and asymmetric problem of an infinite wellbore drilled into a fluid‐saturated porous medium. The formulations are based on Biot's linear theory of poroelasticity, in which the dependency of poroelastic field variables to spatial coordinates as well as time domain is considered in the most general form. This gives flexibility to the solution in cases that cannot be analyzed using the conventional plane strain or symmetric models. One such case is when calculating the stress variations around an inclined wellbore where the far‐field stresses are acting over a finite vertical section. The results of our solution to this case with a three‐dimensional state of far‐field stress are used to analyze the stability of inclined wellbores passing through abnormally stressed formations.The presented solution is capable of finding expressions for fundamental solutions with stress or flow boundary conditions at the wellbore. These solutions are here adopted to analyze the pressure disturbances generated by multiprobe formation tester, a standard wireline device that is designed for downhole fluid sampling as well as estimating the directional permeabilities of subsurface earth formations. A comparison with the conventional solution for the relevant pressure diffusion equation indicates that the poroelastic effect is relatively significant in relation to the transient response of the pore pressure. Further, it is shown that the finite dimensions of sink probe would, to a great extent, contribute to the formation's pore pressure variations at its immediate proximity. Copyright © 2013 John Wiley & Sons, Ltd.
A stabilized assumed deformation gradient finite element formulation for strongly coupled poromechanical simulations at finite strain
Authors: Sun WaiChing , Ostien Jakob T. , Salinger Andrew G. 
Published: January 2013

SUMMARYAn adaptively stabilized finite element scheme is proposed for a strongly coupled hydro‐mechanical problem in fluid‐infiltrating porous solids at finite strain. We first present the derivation of the poromechanics model via mixture theory in large deformation. By exploiting assumed deformation gradient techniques, we develop a numerical procedure capable of simultaneously curing the multiple‐locking phenomena related to shear failure, incompressibility imposed by pore fluid, and/or incompressible solid skeleton and produce solutions that satisfy the inf‐sup condition. The template‐based generic programming and automatic differentiation (AD) techniques used to implement the stabilized model are also highlighted. Finally, numerical examples are given to show the versatility and efficiency of this model. Copyright © 2013 John Wiley & Sons, Ltd.