bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Regio‐ and Stereospecificity of Arachidonic Acid Peroxidation Catalyzed by Mammalian 15‐Lypoxygenases: A Combined Molecular Dynamics and QM/MM Study
Authors: Suardíaz Reynier , Masgrau Laura , Lluch José M. , González‐Lafont Àngels 
Published: October 2013

Abstract15‐Lipoxygenases (15‐LOs) catalyse the peroxidation reaction of arachidonic acid (AA) in mammals with remarkable regio‐ and stereospecificity. This positional‐specific peroxidation is of paramount importance because it determines the nature and biological functions of the final metabolites generated by each LO as a result of the oxidative metabolism of AA. Although several hypotheses have been formulated concerning the regio‐ and stereospecificity of LOs, the molecular basis of such behaviour is still unclear. Herein, we combined quantum mechanics/molecular mechanics calculations with molecular dynamics simulations of the complete rabbit 15‐LO/AA solvated model to examine the most accepted hypotheses for the regio‐ and stereospecificity of LOs. We have found that the clue to explain this specificity is the oxygen‐targeting hypothesis through steric shielding of specific residues (mainly Leu597, Gln548 and Phe175, as well as the AA tail itself). Our deductions are based primarily on the analysis of the energy barrier heights from the oxygen addition reaction profiles.
Fluorescent Silver Nanoclusters in Condensed DNA
Authors: Volkov Ivan L. , Ramazanov Ruslan R. , Ubyivovk Evgeniy V. , Rolich Valerij I. , Kononov Alexei I. , Kasyanenko Nina A. 
Published: October 2013

AbstractWe study the formation and fluorescent properties of silver nanoclusters encapsulated in condensed DNA nanoparticles. Fluorescent globular DNA nanoparticles are formed using a dsDNA–cluster complex and polyallylamine as condensing agents. The fluorescence emission spectrum of single DNA nanoparticles is obtained using tip‐enhanced fluorescence microscopy. Fluorescent clusters in condensed DNA nanoparticles appear to be more protected against destructive damage in solution compared to clusters synthesized on a linear polymer chain. The fluorescent clusters on both dsDNA and ssDNA exhibit the same emission bands (at 590 and 680 nm) and the same formation efficiency, which suggests the same binding sites. By using density functional theory, we show that the clusters may bind to the Watson–Crick guanine–cytosine base pairs and to single DNA bases with about the same affinity.
Straightforward Oxidation of a Copper Substrate Produces an Underwater Superoleophobic Mesh for Oil/Water Separation
Authors: Liu Na , Chen Yuning , Lu Fei , Cao Yingze , Xue Zhongxin , Li Kan , Feng Lin , Wei Yen 
Published: October 2013

AbstractA superhydrophilic and underwater superoleophobic Cu(OH)2‐covered mesh with micro‐ and nanoscale hierarchical composite structures is successfully fabricated through a one‐step chemical oxidation of a smooth‐copper mesh. Such mesh, without any further modification, can selectively separate water from oil/water mixtures with high separation efficiency, and possess excellent stability even after 60 uses. This method provides a simple, low‐cost, and scalable strategy for the purification of oily wastewater.
Playing with Structures at the Nanoscale: Designing Catalysts by Manipulation of Clusters and Nanocrystals as Building Blocks
Authors: Cargnello Matteo , Fornasiero Paolo , Gorte Raymond J. 
Published: October 2013

AbstractThe purpose of this Concept is to highlight some of the most recent and promising methods for the preparation of tailored catalysts by designing and preparing the component building blocks and by assembling them in a controlled fashion. We want to emphasize how rational design and synthesis of catalysts must be coupled to precise catalytic and structural characterization of the systems in an ideal feedback loop. New catalyst design and preparation techniques, dictated by information about the active sites that the specific application requires, are frequently available. The building blocks for developing these novel catalysts include colloidal methods for the preparation of uniform nanostructures, physical methods for rational assembly of the building blocks (Langmuir–Blodgett, liquid–air self‐assembly), and development of rational interactions between the building blocks for enhanced activity of the assemblies. These methods, which apply techniques normally used in other fields of nanotechnology to catalysis, offer exciting opportunities to help improve currently available catalytic systems in terms of activity, stability and selectivity.
Flow‐Based, Cerium Oxide Enhanced, Low‐Level Palladium Sonogashira and Heck Coupling Reactions by Perovskite Catalysts
Authors: Battilocchio Claudio , Bhawal Benjamin N. , Chorghade Rajeev , Deadman Benjamin J. , Hawkins Joel M. , Ley Steven V. 
Published: October 2013

AbstractA flow chemistry procedure for Sonogashira and Heck cross‐coupling reactions using a low‐level palladium perovskite catalyst (LaFe0.95Pd0.05O3) deposited on cerium oxide is reported. The catalyst was generated in situ at high temperature using a flow platform. The system could be applied to a wide range of functionalised substrates, allowing clean and fast delivery of the products within a few minutes (10–30 min), after scavenging with thiourea polymer (QP‐TU) and sulfonic acid resin (QP‐SA). The use of an in‐line evaporator/solvent switching device allowed us to recover the solvent and transport the material into the following stage. The catalyst could be continuously used for at least 24 h, without any noticeable decrease in the catalytic efficiency. In one example the system was scaled to deliver 10 mmol of product.
Engineering Biomaterials for Myocardial Regeneration and Repair
Authors: Ruvinov Emil , Cohen Smadar 
Published: October 2013

AbstractAugmentation of myocardial tissue regeneration processes in injured hearts represents a major challenge in cardiology as current therapeutic approaches do not regenerate the myocardial tissue. Herein, we describe three emerging biomaterial‐based strategies to treat heart injuries, as stand‐alone therapies or in combination with regeneration‐inducing signals and/or cells. One strategy relies on the injection of acellular biomaterials, at an early stage after myocardial infarction (MI); these materials replace the damaged extracellular matrix, maintain left ventricular (LV) thickness, and prevent the negative LV remodeling and progression to heart failure. This strategy is currently being investigated in advanced clinical trials using a novel alginate‐based biomaterial. The second strategy employs engineered biomaterials, spatially presenting multiple regeneration‐inducing factors, to promote myocardial tissue regeneration in chronic infarcted hearts. The recent attempts to understand the “natural capacity” of the myocardium to heal and the factors involved in these processes are promising to advance this therapy. The third strategy applies biomaterials to promote cardiac tissue engineering and create a pre‐vascularized cardiac patch to replace damaged or missing myocardial tissue. Collectively, this review emphasizes the increasing importance of biomaterials in cardiology, describes the engineering schemes used in their fabrication, and their implementation in various therapeutic strategies aimed at cardiac tissue regeneration and repair. It mainly highlights the contribution of our group in developing these strategies.
Gold‐Catalyzed Cascade Reactions of Alkynes for Construction of Polycyclic Compounds
Authors: Ohno Hiroaki 
Published: October 2013

AbstractThe development of cascade reactions is an area of considerable interest in modern organic chemistry. Efficient cascade reactions realize the economical synthesis of complex target molecules through multiple bond formations in a single operation. Elementary reactions that form fewer waste products are desirable in terms of atom economy and in order to suppress side product formation in sequential processes. Recent advances in homogeneous gold catalysis have opened up further possibilities for cascade reactions. In this review, recent advances in gold‐catalyzed cascade cyclizations of alkynes are summarized. In particular, cascade reactions based on nucleophilic/electrophilic addition, carbene cyclopropanation/insertion, ring expansion, and cycloaddition are highlighted. Notably, many of the cascade reactions shown in this mini‐review feature no theoretical waste products.
Gene Delivery by Liposomes
Authors: Nordling‐David Mirjam M. , Golomb Gershon 
Published: October 2013

AbstractIn gene therapy, genetic materials, such as plasmid DNA, antisense oligonucleotides (asODNs), and small interfering RNA (siRNA), can be used to treat or prevent disease. This includes replacing a mutated gene, inactivating a mutated gene, or introducing a new gene. Although gene therapy is a promising treatment option for a number of diseases (including inherited disorders, some types of cancer, and certain viral infections), successful gene therapy is hampered by the lack of effective delivery systems (viral and nonviral). There are several nonviral gene carriers, such as lipids, polymers, and peptides, that can be used for this purpose. Liposomal delivery of nucleic acids, such as plasmid DNA, asODNs, and siRNAs, represents a very promising nanocarrier system that is relatively safe and effective in delivering genes to targeted locations in the body. Lipoid‐based delivery systems have also been shown to be stable in serum and plasma, have improved biodistribution, prolonged circulation half‐life, and enhanced target tissue selectivity. The most common lipids used in liposomes are cationic lipids, which facilitate binding between their positively charged head group(s) to negatively charged nucleic acids. This review is focused on the most common methods of lipoid‐based nanocarriers of nucleic acids for gene therapy in vivo.
When NHC Ligands Make a Difference in Gold Catalysis
Authors: Gatineau David , Goddard Jean‐Philippe , Mouriès‐Mansuy Virginie , Fensterbank Louis 
Published: October 2013

AbstractThanks to their unique electronic and steric properties, carbene ligands offer highly valuable features for catalysis, including homogenous gold catalysis. The use of carbene‐gold complexes has improved existing reactions, either by modifying reactivity modes or by leading to highly asymmetric processes. These topics will be discussed on the basis of selected examples.
Engineering Cardiac Tissues from Pluripotent Stem Cells for Drug Screening and Studies of Cell Maturation
Authors: Miklas Jason W. , Nunes Sara S. , Radisic Milica 
Published: October 2013

AbstractUsing cardiomyocytes derived from human pluripotent stem cells (hPSC‐CMs), it is now possible to develop models of human cardiac diseases and to screen novel pharmaceutical agents on human cardiac cells and tissues. However, since hPSC‐CMs display an immature phenotype, significant focus has turned to cardiac tissue engineering to deliver a means to mature these cells. In this review we discuss the maturation state of currently available hPSC‐CMs and provide an overview of the processes involved in cardiomyocyte maturation. We then explore the differences between pathological and physiological hypertrophy and discuss how tissue engineering techniques that rely on the combined use of biomaterials and bioreactors can be utilized to enhance and study the hypertrophic response.
Induction of Angiogenesis and Vasculogenesis in Cell‐Embedded Biomaterials
Authors: Dado‐Rosenfeld Dekel , Levenberg Shulamit 
Published: October 2013

AbstractThe central role of prevascularization of engineered tissue grafts in postimplantational survival and integration is becoming increasingly appreciated. An in‐depth understanding of the regulating factors and intricacies of generation of three‐dimensional vascular networks in vitro will facilitate effective fabrication of clinically relevant vascularized tissues. In this review we aim to examine the influence of different biomaterials on vasculogenesis and angiogenesis, with particular focus on the impact of various matrix properties, such as composition, stiffness and geometry, on the resulting vasculature. Additionally, the contribution of externally applied mechanical forces, mimicking blood flow patterns, to tissue vascularization efforts is reviewed. We present here pivotal studies focusing on the influence of mechanical forces, such as shear stress and stretching tension, on vascular network formation in biomaterial‐based scaffolds. Comprehensive understanding of the key factors dictating the patterns and functionality of engineered vasculature will facilitate more efficient fabrication of viable tissue grafts, with a broad range of medical applications.
Multifunctional SilkTropoelastin Biomaterial Systems
Authors: Ghezzi Chiara E. , Rnjak‐Kovacina Jelena , Weiss Anthony S. , Kaplan David L. 
Published: October 2013

AbstractNew multifunctional, degradable, polymeric biomaterial systems would provide versatile platforms to address cell and tissue needs in both in vitro and in vivo environments. While protein‐based composites or alloys are the building blocks of biological organisms, similar systems have not been largely exploited, to date, to generate ad hoc biomaterials able to control and direct biological functions by recapitulating their inherent structural and mechanical complexities. Therefore, we have recently proposed silktropoelastin material platforms that are able to conjugate a mechanically robust and durable protein, silk, to a highly flexible and biologically active protein, tropoelastin. This review focuses on the elucidation of the interactions between silk and tropoelastin to control the structure of the material its properties, and ultimately functions. In addition, an approach is provided for novel material designs to provide tools to control biological outcomes through surface roughness, elasticity, and net charge for neuronal and mesenchymal stem‐cell‐based tissue engineering.
Core and Corona Modifications for the Design of Polymeric Micelle Drug‐Delivery Systems
Authors: McLaughlin Christopher K. , Logie Jennifer , Shoichet Molly S. 
Published: October 2013

AbstractPolymeric nanoparticle micelles are formed from amphiphilic polymers with a hydrophobic core and a hydrophilic corona. Often comprised of a biodegradable, biocompatible polymer core and a poly(ethylene glycol) corona, these nanoparticle micelles encapsulate a hydrophobic drug and enable surface modification with targeting ligands. Strategies to enhance hydrophobic drug encapsulation are described as chemistries that facilitate covalent modification with antibodies using water‐based click chemistry.
The anomalous ionosphere between solar cycles 23 and 24
Authors: Solomon Stanley C. , Qian Liying , Burns Alan G. 
Published: October 2013

AbstractThe solar minimum period during 2008–2009 was characterized by lower thermospheric density than the previous solar minimum and lower than any previously measured. Recent work used the NCAR Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model to show that the primary cause of density changes from 1996 to 2008 was a small reduction in solar extreme ultraviolet (EUV) irradiance, causing a decrease in thermospheric temperature and hence a contracted thermosphere. There are similar effects in the ionosphere, with most measurements showing an F region ionosphere that is unusually low in density, and in peak altitude. This paper addresses the question of whether model simulations previously conducted, and their solar, geomagnetic, and anthropogenic inputs, produce ionospheric changes commensurate with observations. We conducted a 15 year model run and obtained good agreement with observations of the global mean thermospheric density at 400 km throughout the solar cycle, with a reduction of ~30% from the 1996 solar minimum to 2008–2009. We then compared ionosonde measurements of the midday peak density of the ionospheric F region (NmF2) to the model simulations at various locations. Reasonable agreement was obtained between measurements and the model, supporting the validity of the neutral density comparisons. The global average NmF2 was estimated to have declined between the two solar minima by ~15%. In these simulations, a 10% reduction of solar EUV plays the largest role in causing the ionospheric change, with a minor contribution from lower geomagnetic activity and a very small additional effect from anthropogenic increase in CO2.
Variations in middle atmospheric water vapor from 2004 to 2013
Authors: Nedoluha Gerald E. , Michael Gomez R. , Allen Doug R. , Lambert Alyn , Boone Chris , Stiller Gabriele 
Published: October 2013

AbstractWe show measurements of middle atmospheric water vapor as measured by two ground‐based Water Vapor Millimeter‐wave Spectrometer instruments and three satellite‐based instruments: the Aura Microwave Limb Sounder, the Atmospheric Chemistry Experiment (ACE), and the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS). We also show CH4 measurements from the MIPAS and ACE instruments and use these to help interpret the H2O variations. We find that interannual changes in stratospheric H2O of ~0.5 ppmv, observed from Table Mountain, California, at 26 km and 40 km from 2010 to 2012, are caused primarily by dynamically driven changes in CH4 during this period. The interannual variations in H2O observed over Mauna Loa, Hawaii, are shown to be quite similar to the average variations observed over 50°S–50°N in the lower mesosphere; thus, we conclude that a single ground‐based microwave instrument can provide a useful estimate of interannual globally averaged lower mesospheric H2O variations, even when such changes are as small as ~0.2–0.3 ppmv. We find that the increase of ~0.2–0.3 ppmv in H2O in the lower mesosphere since 2006 is qualitatively consistent with an increase in tropical tropopause temperature since around 2001.
N‐alkylpyridinium quaternization for assisting electrospray ionization of sterols in oil by quadrupole‐time of flight mass spectrometry
Authors: Wang Hang , Wang Haoyang , Zhang Li , Zhang Jing , Leng Jiapeng , Cai Tingting , Guo Yinlong 
Published: October 2013

Rationale: The illegal cooking oil has become a serious social problem and raised widespread alarm recently. However, an efficient and sensitive technique for identifying the potential illegal cooking oil is still unavailable, especially when mixed with the ordinary ones; there is an urgent need to develop an efficient method for identifying the illegal cooking oil. Sterols in the cooking oil could be used as an indicator to identify the source and quality of oil by detecting the kinds of phytosterols and zoosterols. However, those sterols are difficult to be ionized by electrospray ionization, which resulted in the low sensitivity in electrospray ionization (ESI)‐mass spectrometric (MS) analysis.Methods: N‐alkylpyridinium isotope quaternization was extended to charge label sterols in different cooking oil and attached N‐cationic pyridinium tag onto the sterols in the presence of trifluoromethanesulfonic anhydride (Tf2O); the kinds of sterols were identified and quantified by comparing d0/d5 pairs and product scan from ESI‐quadrupole‐time of flight (Q‐TOF) MS analysis.Results: The derivatized sterols were attached with permanent charge, resulting in the significant enhancement of ionization in ESI‐Q‐TOF MS analysis. The detection limits of analytes were improved to 0.02–0.05 ng/mL; different kinds of phytosterol, zoosterol and oxides were identified and quantified by comparing d0/d5 pairs from full scan and product scan. The method was applied in the detection of zoosterol for identifying the potential recycled cooking oil, even when the illegal oil has been blended into the ordinary one. More zoosterol was detected in the recycled oil compared with other cooking oil.Conclusions: The use of N‐alkylpyridinium isotope quaternization method provided an alternative method for identifying the potential illegal cooking oil. Copyright © 2013 John Wiley & Sons, Ltd.
Universal Approach for Structural Interpretation of QSAR/QSPR Models
Authors: Polishchuk Pavel G. , Kuz'min Victor E. , Artemenko Anatoly G. , Muratov Eugene N. 
Published: October 2013

AbstractIn this paper we offer a novel approach for the structural interpretation of QSAR models. The major advantage of our developed methodology is its universality, i.e., it can be applied to any QSAR/QSPR model irrespective of chemical descriptors and machine learning methods applied. This universality was achieved by using only the information obtained from substructures of the compounds of interest to interpret model outcomes. Reliability of the offered approach was confirmed by the results of three case studies, including end‐points of different types (continuous and binary classification) and nature (solubility, mutagenicity, and inhibition of Transglutaminase 2), various fragment and whole‐molecule descriptors (Simplex and Dragon), and multiple modeling techniques (partial least squares, random forest, and support vector machines). We compared the global contributions of molecular fragments obtained using our methodology with known SAR rules derived experimentally. In all cases high concordance between our interpretation and results published by others was observed. Although the proposed interpretation approach could be easily extended to any type of descriptors, we would recommend using Simplex descriptors to achieve a larger variety of investigated molecular fragments. The developed approach is a good tool for interpretation of such “black box” models like random forest, neural networks, etc. Analysis of fragment global contributions and their deviation across a dataset could be useful for the identification of key fragments and structural alerts. This information could be helpful to maximize the positive influence of structural surroundings on the given fragment and to decrease the negative effects.
The MSSM Higgs sector at a high MSUSY: reopening the low tan β regime and heavy Higgs searches
Authors: Djouadi Abdelhak , Quevillon Jérémie 
Published: October 2013

AbstractOne of the main implications of the LHC discovery of a Higgs boson with a massMh ≈ 126 GeV is that the scale of supersymmetry-breaking in the Minimal Supersymmetric Standard Model (MSSM) might be rather high,MS ≫ MZ. In this paper, we consider the highMSregime and study the spectrum of the extended Higgs sector of the MSSM, including the LHC constraints on the mass and the rates of the observed lighthstate. In particular, we show that in a simplified model that approximates the important radiative corrections, the unknown scaleMS(and some other leading SUSY parameters) can be traded against the measured value ofMh. One would be then essentially left with only two free parameters to describe the Higgs sector, tanβand the pseudoscalar Higgs massMA, even at higher orders. The main phenomenological consequence of these highMSvalues is to reopen the low tanβregion, tanβ ≲ 3–5, which was for a long time buried under the LEP constraint on the lightesthmass when a low SUSY scale was assumed. We show that, in this case, the heavier MSSM neutralH/Aand chargedH±states can be searched for in a variety of interesting final states such as decays into gauge and lighter Higgs bosons (in pairs on in mixed states) and decays into heavy top quarks. Examples of sensitivity on the [tanβ, MA] parameter space at the LHC in these channels are given.